CURAGEN CORP
S-1/A, 1998-03-17
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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<PAGE>
 
    AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MARCH 17, 1998
 
                                                     REGISTRATION NO. 333-38051
- -------------------------------------------------------------------------------
- -------------------------------------------------------------------------------
 
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C. 20549
 
                               ---------------
 
                                AMENDMENT NO. 8
 
                                      TO
 
                                   FORM S-1
                            REGISTRATION STATEMENT
                                     UNDER
                          THE SECURITIES ACT OF 1933
 
                               ---------------
 
                              CURAGEN CORPORATION
            (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)
 
        DELAWARE                     8731                  06-1331400
     (STATE OR OTHER     (PRIMARY STANDARD INDUSTRIAL   (I.R.S. EMPLOYER
     JURISDICTION OF      CLASSIFICATION CODE NUMBER)  IDENTIFICATION NO.)
    INCORPORATION OR
      ORGANIZATION)
 
                       555 LONG WHARF DRIVE, 11TH FLOOR
                         NEW HAVEN, CONNECTICUT 06511
                                (203) 401-3330
                           (203) 401-3333 FACSIMILE
  (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE, OF
                   REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)
 
                               ---------------
 
                          JONATHAN M. ROTHBERG, PH.D.
                    CHIEF EXECUTIVE OFFICER, PRESIDENT AND
                             CHAIRMAN OF THE BOARD
                              CURAGEN CORPORATION
                       555 LONG WHARF DRIVE, 11TH FLOOR
                         NEW HAVEN, CONNECTICUT 06511
                                (203) 401-3330
                           (203) 401-3333 FACSIMILE
(NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA CODE,
                             OF AGENT FOR SERVICE)
 
                               ---------------
 
                                  COPIES TO:
 
     JONATHAN L. KRAVETZ, ESQ.                 KEITH F. HIGGINS, ESQ.
  STANFORD N. GOLDMAN, JR., ESQ.                    ROPES & GRAY
    MINTZ, LEVIN, COHN, FERRIS,                ONE INTERNATIONAL PLACE
      GLOVSKY AND POPEO, P.C.                BOSTON, MASSACHUSETTS 02110
       ONE FINANCIAL CENTER                        (617) 951-7000
    BOSTON, MASSACHUSETTS 02111               (617) 951-7050 FACSIMILE
          (617) 542-6000
     (617) 542-2241 FACSIMILE
 
                               ---------------
 
  APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC: As soon as
practicable after this Registration Statement becomes effective.
 
  If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, as amended (the "Securities Act"), check the following box. [_]
 
  If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, check the following box and
list the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [_]
 
  If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [_]
 
  If this Form is a post-effective amendment filed pursuant to Rule 462(d)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective registration statement
for the same offering. [_]
 
  If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [_]
 
                               ---------------
 
  THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT
SHALL FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS
REGISTRATION STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH
SECTION 8(A) OF THE SECURITIES ACT OF 1933 OR UNTIL THIS REGISTRATION
STATEMENT SHALL BECOME EFFECTIVE ON SUCH DATE AS THE SECURITIES AND EXCHANGE
COMMISSION, ACTING PURSUANT TO SAID SECTION 8(A), MAY DETERMINE.
 
- -------------------------------------------------------------------------------
- -------------------------------------------------------------------------------
<PAGE>
 
                                    PART II
 
                    INFORMATION NOT REQUIRED IN PROSPECTUS
 
ITEM 13. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION
 
  The following table sets forth all expenses, other than underwriting
discounts and commissions, payable by the Company in connection with the sale
of the Common Stock being registered. All amounts are estimated except the
registration fee.
 
<TABLE>
      <S>                                                            <C>
      Commission Registration Fee................................... $   12,121
      NASD filing fee...............................................      5,000
      Nasdaq National Market listing fee............................     83,500
      Printing and engraving expenses...............................    200,000
      Legal fees and expenses.......................................    565,000
      Accounting fees and expenses..................................    225,000
      Blue sky fees and expenses (including legal fees).............      5,000
      Transfer agent and registrar fees and expenses................      2,000
      Miscellaneous.................................................      2,379
                                                                     ----------
        TOTAL....................................................... $1,100,000
                                                                     ==========
</TABLE>
 
ITEM 14. INDEMNIFICATION OF DIRECTORS AND OFFICERS.
 
  The amendment and restatement of the Company's Certificate of Incorporation
(the "Restated Certificate") provides that the Company shall indemnify to the
fullest extent authorized by the Delaware General Corporation Law ("DGCL"),
each person who is involved in any litigation or other proceeding because such
person is or was a director or officer of the Company or is or was serving as
an officer or director of another entity at the request of the Company,
against all expense, loss or liability reasonably incurred or suffered in
connection therewith. The Restated Certificate provides that the right to
indemnification includes the right to be paid expenses incurred in defending
any proceeding in advance of its final disposition; provided, however, that
such advance payment will only be made upon delivery to the Company of an
undertaking, by or on behalf of the director or officer, to repay all amounts
so advanced if it is ultimately determined that such director is not entitled
to indemnification. If the Company does not pay a proper claim for
indemnification in full within 60 days after a written claim for such
indemnification is received by the Company, the Restated Bylaws authorize the
claimant to bring an action against the Company and prescribe what constitutes
a defense to such action.
 
  Section 145 of the DGCL permits a corporation to indemnify any director or
officer of the corporation against expenses (including attorney's fees),
judgments, fines and amounts paid in settlement actually and reasonably
incurred in connection with any action, suit or proceeding brought by reason
of the fact that such person is or was a director or officer of the
corporation, if such person acted in good faith and in a manner that he or she
reasonably believed to be in, or not opposed to, the best interests of the
corporation, and, with respect to any criminal action or proceeding, if he or
she had no reason to believe his or her conduct was unlawful. In a derivative
action, (i.e., one brought by or on behalf of the corporation),
indemnification may be made only for expenses, actually and reasonably
incurred by any director or officer in connection with the defense or
settlement of such an action or suit, if such person acted in good faith and
in a manner that he reasonably believed to be in, or not opposed to, the best
interests of the corporation, except that no indemnification shall be made if
such person shall have been adjudged to be liable to the corporation, unless
and only to the extent that the court in which the action or suit was brought
shall determine that the defendant is fairly and reasonably entitled to
indemnity for such expenses despite such adjudication of liability.
 
  Pursuant to Section 102(b)(7) of the DGCL, Article Tenth of the Restated
Certificate eliminates the liability of a director or the corporation or its
stockholders for monetary damages for such breach of fiduciary duty as a
director, except for liabilities arising (i) from any breach of the director's
duty of loyalty to the corporation or its stockholders, (ii) from acts or
omissions not in good faith or which involve intentional misconduct or a
knowing
 
                                     II-1
<PAGE>
 
violation of law, (iii) under Section 174 of the DGCL, or (iv) from any
transaction from which the director derived an improper personal benefit.
 
  The Company has obtained primary and excess insurance policies insuring the
directors and officers of the Company against certain liabilities that they
may incur in their capacity as directors and officers. Under such policies,
the insurers, on behalf of the Company, may also pay amounts for which the
Company has granted indemnification to the directors or officers.
 
  Additionally, reference is made to the Underwriting Agreement filed as
Exhibit 1.1 hereto, which provides for indemnification by the Underwriters of
the Company, its directors and officers who sign the Registration Statement
and persons who control the Company, under certain circumstances.
 
ITEM 15. RECENT SALES OF UNREGISTERED SECURITIES.
 
  In the three years preceding the filing of this Registration Statement, the
Company has sold the following securities that were not registered under the
Securities Act.
 
 (a) Issuances of Capital Stock.
 
  On May 9, 1995, the Company issued an aggregate of 19,575 shares of its
Common Stock to two investors in exchange for financial advisory services
rendered by such investors to the Company having a value of $45,218.75.
 
  On December 29, 1995, the Company sold an aggregate of 100,000 shares of its
Common Stock to two investors at $1.00 per share in exchange for payments of
an aggregate of $100,000 by such investors upon the exercise of warrants to
purchase Common Stock.
 
  On March 30, 1996, the Company sold 100,000 shares of its Common Stock to
one investor at $1.52 per share in exchange for payment of $152,000 by such
investor upon the exercise of a warrant to purchase Common Stock.
 
  On December 27, 1996, the Company sold 307,167 shares of its Series A
Convertible Preferred Stock at a purchase price of $5.86 per share to
Genentech, Inc. in a private placement for $1,800,000.
 
  In March 1997, the Company issued 17,073 and 22,673 shares of its Common
Stock to Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. and Pennie &
Edmonds LLP, respectively, at $4.10 per share in exchange for legal services
rendered on behalf of the Company and having an aggregate value of
$162,958.60.
 
  On March 27, 1997, the Company sold an aggregate of 175,000 shares of its
Series B Redeemable Preferred Stock at a purchase price of $10.00 per share to
five investors in a private placement for $1,750,000 in cash. In connection
with this private placement, the Company issued five-year warrants to purchase
358,361 shares of Common Stock at an exercise price of $5.86 per share.
 
  On March 27, 1997, the Company sold an aggregate of 2,011,468 shares of its
Series C Convertible Preferred Stock at a purchase price of $5.86 per share to
eleven investors in a private placement for $11,787,202.48. In connection with
this private placement, the Company also issued three-year warrants to
purchase 366,894 shares of Common Stock at an exercise price of $9.00 per
share to two investors who each purchased 1,706,485 and 127,986 shares of
Series C Convertible Preferred Stock, respectively.
 
  On April 10, 1997, the Company sold 291,875 shares of its Common Stock to
Connecticut Innovations Incorporated in exchange for the cancellation of a
$600,000 principal amount promissory note (plus accrued interest thereon) upon
the exercise of a warrant to purchase Common Stock.
 
                                     II-2
<PAGE>
 
  On May 16, 1997, the Company sold 1,000,000 shares of its Series D
Convertible Preferred Stock at a purchase price of $7.50 per share to Pioneer
Hi-Bred International, Inc. in a private placement for $7,500,000.
 
  On June 25, 1997, the Company sold 100,000 shares of its Series E
Convertible Preferred Stock at a purchase price of $10.00 per share to Biogen,
Inc. in a private placement for $1,000,000.
 
  In October 1997, the Company agreed to sell $5,000,000 of its Common Stock
to Biogen, Inc. in a private placement concurrent with this offering at a
price per share equal to the price per share at which the Common Stock is sold
in this Offering.
 
  In November 1997, the Company agreed to sell $5,000,000 of its Common Stock
to Genentech, Inc. in a private placement concurrent with this offering at a
price per share equal to the price per share at which the Common Stock is sold
in this Offering.
 
  In November 1997, the Company agreed to sell $1,000,000 of its Common Stock
to the University of Florida Research Foundation, Inc. in a private placement
concurrent with this offering at a price per share equal to the price per
share at which the Common Stock is sold in this Offering.
 
  (b) Certain Grants and Exercises of Stock Options.
 
  Pursuant to the 1993 Stock Option and Incentive Award Plan (the "1993 Stock
Plan"), as of December 31, 1997, the Company has granted options to purchase
an aggregate of 1,028,884 shares of Common Stock, of which options to purchase
an aggregate of 347,611 shares of Common Stock are exercisable at a weighted
average exercise price of $3.32 per share. As of December 31, 1997, no options
pursuant to the foregoing have been exercised.
 
  Pursuant to the 1997 Employee, Director and Consultant Stock Plan (the "1997
Stock Plan"), as of December 31, 1997, the Company has granted options to
purchase an aggregate of 65,000 shares of Common Stock at a price per share
equal to the initial public offering price, of which options to purchase an
aggregate of 21,668 shares of Common Stock are exercisable. As of December 31,
1997, no options pursuant to the foregoing have been exercised.
 
  In addition to the options granted under the 1993 Stock Plan and the 1997
Stock Plan, as of December 31, 1997, the Company has issued options to
purchase an aggregate of 570,000 shares of Common Stock pursuant to individual
agreements with Company employees and consultants, of which options to
purchase an aggregate of 349,500 shares of Common Stock are exercisable at a
weighted average exercise price of $1.40 per share. As of December 31, 1997,
no options pursuant to the foregoing have been exercised.
 
  No underwriters were involved in the foregoing offers and sales of
securities. Such offers and sales were made in reliance upon an exemption from
the registration provisions of the Securities Act set forth in Section 4(2)
thereof relative to sales by an issuer not involving any public offering or
the rules and regulations thereunder, or, in the case of options to purchase
Common Stock, Rule 701 under the Securities Act. All of the foregoing
securities are deemed restricted securities for purposes of the Securities
Act.
 
ITEM 16. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES.
 
 (a) Exhibits
 
<TABLE>
<CAPTION>
 EXHIBIT
 NUMBER                               DESCRIPTION
 -------                              -----------
 <C>     <S>
  @1.1   Form of Underwriting Agreement
  @3.1   Amended and Restated Certificate of Incorporation of the Registrant
  @3.2   Certificate of Amendment of Restated Certificate of Incorporation of
         the Registrant and Certificate of Amendment of Certificate of
         Designation, Preferences, and Rights of Series E Preferred Stock of
         the Registrant.
</TABLE>
 
                                     II-3
<PAGE>
 
<TABLE>
<CAPTION>
 EXHIBIT
 NUMBER                                DESCRIPTION
 -------                               -----------
 <C>     <S>
   @3.3  Amended and Restated Certificate of Incorporation of the Registrant
   @3.4  Bylaws of the Registrant
   @3.5  Amended and Restated Bylaws of the Registrant
   @4.1  Article Fourth of the Amended and Restated Certificate of
         Incorporation of the Registrant (see Exhibit 3.3)
   @4.2  Form of Common Stock Certificate
   @5.1  Opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. with
         respect to the legality of the securities being registered
  @10.1  Lease Agreement (New Haven), dated December 23, 1996, between the
         Registrant and Fusco Harbour Associates, LLC
  @10.2  Standard Form of Office Lease, as amended (Branford), dated February
         11, 1993 and April 26, 1996, between the Registrant and Branford
         Office Venture
  @10.3  Sid Martin Biotechnology Development Institute Incubator License
         Agreement, dated July 15, 1997, between the Registrant and the
         University of Florida Research Foundation, Inc.
  @10.4  1997 Employee, Director and Consultant Stock Plan
  @10.5  1993 Stock Option and Incentive Award Plan
  @10.6  Amendment to 1993 Stock Option and Incentive Plan, dated May 12, 1997
  @10.7  Employment Letter, dated February 20, 1997, between the Registrant and
         Gregory T. Went, Ph.D.
  @10.8  Employment Letter, dated July 18, 1997, between the Registrant and
         David M. Wurzer
  @10.9  Employment Letter, dated August 21, 1997, between the Registrant and
         Peter A. Fuller, Ph.D.
  @10.10 Employment Letter, dated August 22, 1997, between the Registrant and
         Stephen F. Kingsmore, M.B., Ch.B.
 @+10.11 Option and Exclusive License Agreement, dated October 4, 1996, between
         the Registrant and Wisconsin Alumni Research Foundation
 @+10.12 Standard Non-Exclusive License Agreement--Brumley, dated July 1, 1996,
         between the Registrant and Wisconsin Alumni Research Foundation
 @+10.13 Collaborative Research and License Agreement, dated May 16, 1997,
         between the Registrant and Pioneer Hi-Bred International, Inc.
  +10.14 Research and Option Agreement, dated October 1, 1997, between the
         Registrant and Biogen, Inc.
  +10.15 Research and Option Agreement, dated November 20, 1997, between the
         Registrant and Genentech, Inc.
 @+10.16 Notice of Grant Award and Grant Application to Department of Health
         and Human Services for Automated Sequencing System for Human Genome
         Project, dated March 25, 1995
  @10.17 ATP Agreement for Integrated Microfabricated DNA Analysis Device for
         Diagnosis of Complex Genetic Disorders, dated February 1995
  @10.18 ATP Agreement for Molecular Recognition Technology for Precise Design
         of Protein-Specific Drugs, dated March 2, 1995
  @10.19 ATP Agreement for Programmable Nanoscale Engines for Molecular
         Separation, dated May 6, 1997
  @10.20 Material Transfer and Screening Agreement, dated January 15, 1998,
         between the Registrant and ArQule, Inc.
  @11.1  Schedule of Computation of Net Loss Per Share
  @21.1  Subsidiaries of the Registrant
  @23.1  Consent of Deloitte & Touche LLP
  @23.2  Consent of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
         (included in Exhibit 5.1)
  @23.3  Consent of Pennie & Edmonds LLP
  @24.1  Power of Attorney of Messrs. Went, Wurzer and DeVita
  @24.2  Power of Attorney of Messrs. Booth, Patricelli and Vincent
   27.1  Financial Data Schedule
</TABLE>
- --------
@  Previously filed.
+  Confidential treatment requested as to certain portions, which portions are
   omitted and filed separately with the Commission.
 
                                      II-4
<PAGE>
 
 (b) Financial Statement Schedules
 
  All schedules are omitted because they are not required, are not applicable
or the information is included in the financial statements or notes thereto.
 
ITEM 17. UNDERTAKINGS.
 
  The undersigned registrant hereby undertakes to provide to the Underwriters
at the closing specified in the Underwriting Agreement, certificates in such
denominations and registered in such names as required by the Underwriters to
permit prompt delivery to each purchaser.
 
  Insofar as indemnification for liabilities arising under the Securities Act
may be permitted to directors, officers and controlling persons of the
Registrant pursuant to the foregoing provisions, or otherwise, the Registrant
has been advised that in the opinion of the Securities and Exchange Commission
such indemnification is against public policy as expressed in the Securities
Act and is, therefore, unenforceable. In the event that a claim for
indemnification against such liabilities (other than the payment by the
Registrant of expenses incurred or paid by a director, officer or controlling
person of the Registrant in the successful defense of any action, suit or
proceeding), is asserted by such director, officer or controlling person in
connection with the securities being registered, the Registrant will, unless
in the opinion of its counsel the matter has been settled by controlling
precedent, submit to a court of appropriate jurisdiction the question whether
such indemnification by it is against public policy as expressed in the
Securities Act and will be governed by the final adjudication of such issue.
 
  The undersigned registrant hereby undertakes that:
 
    (1) For purposes of determining any liability under the Securities Act,
  the information omitted from the form of prospectus filed as part of this
  registration statement in reliance upon Rule 430A and contained in a form
  of prospectus filed by the registrant pursuant to Rule 424(b)(1) or (4) or
  497(h) under the Securities Act shall be deemed to be part of this
  registration statement as of the time it was declared effective.
 
    (2) For the purposes of determining any liability under the Securities
  Act, each post-effective amendment that contains a form of prospectus shall
  be deemed to be a new registration statement relating to the securities
  offered therein, and the offering of such securities at that time shall be
  deemed to be the initial bona fide offering thereof.
 
  The undersigned registrant hereby undertakes to provide to the Underwriters
at the Closing specified in the Underwriting Agreement, certificates in such
denominations and registered in such names as required by the Underwriters to
permit prompt delivery to each purchaser.
 
                                     II-5
<PAGE>
 
                                   SIGNATURES
 
  PURSUANT TO THE REQUIREMENTS OF THE SECURITIES ACT OF 1933, AS AMENDED, THE
REGISTRANT HAS DULY CAUSED THIS AMENDMENT NO. 8 TO THE REGISTRATION STATEMENT
TO BE SIGNED ON ITS BEHALF BY THE UNDERSIGNED, THEREUNTO DULY AUTHORIZED, IN
THE CITY OF BOSTON, MASSACHUSETTS ON THIS 17TH DAY OF MARCH, 1998.
 
                                         CuraGen Corporation (Registrant)
 
                                                 /s/ Jonathan M. Rothberg
                                         By: __________________________________
                                               JONATHAN M. ROTHBERGCHIEF
                                              EXECUTIVE OFFICER, PRESIDENT
                                                ANDCHAIRMAN OF THE BOARD
 
  PURSUANT TO THE REQUIREMENTS OF THE SECURITIES ACT OF 1933, AS AMENDED, THIS
AMENDMENT NO. 8 TO THE REGISTRATION STATEMENT HAS BEEN SIGNED BELOW BY THE
FOLLOWING PERSONS IN THE CAPACITIES AND ON THE DATES INDICATED.
 
<TABLE>
<S>  <C>
             SIGNATURE                       TITLE
                                                                   DATE
 
      /s/ Jonathan M. Rothberg        Chief Executive         March 17, 1998
- ------------------------------------   Officer, President
        JONATHAN M. ROTHBERG           and Chairman of
                                       the Board
                                       (principal
                                       executive officer)
 
                 *                    Executive Vice          March 17, 1998
- ------------------------------------   President and a
          GREGORY T. WENT              Director
 
                 *                    Executive Vice          March 17, 1998
- ------------------------------------   President,
          DAVID M. WURZER              Treasurer and
                                       Chief Financial
                                       Officer (principal
                                       financial and
                                       accounting
                                       officer)
 
                 *                    Director                March 17, 1998
- ------------------------------------
      VINCENT T. DEVITA, M.D.
 
                 *                    Director                March 17, 1998
- ------------------------------------
          RICHARD H. BOOTH
 
                 *                    Director                March 17, 1998
- ------------------------------------
        ROBERT E. PATRICELLI
 
                 *                    Director                March 17, 1998
- ------------------------------------
          JAMES L. VINCENT
</TABLE>
 
                                      II-6
<PAGE>
 
  *By executing his name hereto, Jonathan M. Rothberg is signing this document
on behalf of the persons indicated above pursuant to powers of attorney duly
executed by such persons and filed with the Securities and Exchange
Commission.
 
By:   /s/ Jonathan M. Rothberg
  ----------------------------------
        JONATHAN M. ROTHBERG
         (ATTORNEY-IN-FACT)
 
                                     II-7

<PAGE>
 
                                 EXHIBIT INDEX
 
<TABLE>
<CAPTION>
 EXHIBIT NO. DESCRIPTION
 ----------- -----------
 <C>         <S>
     @1.1    Form of Underwriting Agreement
     @3.1    Amended and Restated Certificate of Incorporation of the
             Registrant
     @3.2    Certificate of Amendment of Restated Certificate of Incorporation
             of the Registrant and Certificate of Amendment of Certificate of
             Designation, Preferences, and Rights of Series E Preferred Stock
             of the Registrant.
     @3.3    Amended and Restated Certificate of Incorporation of the
             Registrant
     @3.4    Bylaws of the Registrant
     @3.5    Amended and Restated Bylaws of the Registrant
     @4.1    Article Fourth of the Amended and Restated Certificate of
             Incorporation of the Registrant (see Exhibit 3.3)
     @4.2    Form of Common Stock Certificate
     @5.1    Opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
             with respect to the legality of the securities being registered
    @10.1    Lease Agreement (New Haven), dated December 23, 1996, between the
             Registrant and Fusco Harbour Associates, LLC
    @10.2    Standard Form of Office Lease, as amended (Branford), dated
             February 11, 1993 and April 26, 1996, between the Registrant and
             Branford Office Venture
    @10.3    Sid Martin Biotechnology Development Institute Incubator License
             Agreement, dated July 15, 1997, between the Registrant and the
             University of Florida Research Foundation, Inc.
    @10.4    1997 Employee, Director and Consultant Stock Plan
    @10.5    1993 Stock Option and Incentive Award Plan
    @10.6    Amendment to 1993 Stock Option and Incentive Plan, dated May 12,
             1997
    @10.7    Employment Letter, dated February 20, 1997, between the Registrant
             and Gregory T. Went, Ph.D.
    @10.8    Employment Letter, dated July 18, 1997, between the Registrant and
             David M. Wurzer
    @10.9    Employment Letter, dated August 21, 1997, between the Registrant
             and Peter A. Fuller, Ph.D.
    @10.10   Employment Letter, dated August 22, 1997, between the Registrant
             and Stephen F. Kingsmore, M.B., Ch.B.
   @+10.11   Option and Exclusive License Agreement, dated October 4, 1996,
             between the Registrant and Wisconsin Alumni Research Foundation
   @+10.12   Standard Non-Exclusive License Agreement--Brumley, dated July 1,
             1996, between the Registrant and Wisconsin Alumni Research
             Foundation
   @+10.13   Collaborative Research and License Agreement, dated May 16, 1997,
             between the Registrant and Pioneer Hi-Bred International, Inc.
    +10.14   Research and Option Agreement, dated October 1, 1997, between the
             Registrant and Biogen, Inc.
    +10.15   Research and Option Agreement, dated November 20, 1997, between
             the Registrant and Genentech, Inc.
   @+10.16   Notice of Grant Award and Grant Application to Department of
             Health and Human Services for Automated Sequencing System for
             Human Genome Project, dated March 25, 1995
    @10.17   ATP Agreement for Integrated Microfabricated DNA Analysis Device
             for Diagnosis of Complex Genetic Disorders, dated February 1995
    @10.18   ATP Agreement for Molecular Recognition Technology for Precise
             Design of Protein-Specific Drugs, dated March 2, 1995
    @10.19   ATP Agreement for Programmable Nanoscale Engines for Molecular
             Separation, dated May 6, 1997
    @10.20   Material Transfer and Screening Agreement, dated January 15, 1998,
             between the Registrant and ArQule, Inc.
    @11.1    Schedule of Computation of Net Loss Per Share
    @21.1    Subsidiaries of the Registrant
    @23.1    Consent of Deloitte & Touche LLP
    @23.2    Consent of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
             (included in Exhibit 5.1)
    @23.3    Consent of Pennie & Edmonds LLP
    @24.1    Power of Attorney of Messrs. Went, Wurzer and DeVita
    @24.2    Power of Attorney of Messrs. Booth, Patricelli and Vincent
     27.1    Financial Data Schedule
</TABLE>
- --------
@  Previously filed.
+  Confidential treatment requested as to certain portions, which portions are
   omitted and filed separately with the Commission.

<PAGE>
 
                                                                   Exhibit 10.14

CuraGen Corporation has omitted from this Exhibit 10.14 portions of the 
Agreement for which CuraGen Corporation has requested confidential treatment 
from the Securities and Exchange commission.  The portions of the Agreement for 
which confidential treatment has been requested are marked with X's in brackets 
and such confidential portions have been filed separately with the Securities 
and Exchange Commission.
 
                         RESEARCH AND OPTION AGREEMENT

     This Research and Option Agreement ("Agreement") is made effective as of
October 1, 1997 (the "Effective Date") by and between BIOGEN, INC., a
Massachusetts corporation having its principal business office at 14 Cambridge
Center, Cambridge, MA 02142 ("BIOGEN"), and CURAGEN CORPORATION, a Delaware
corporation with its principal place of business at 555 Long Wharf Drive, 11th
Floor, New Haven, Connecticut 06511 ("CURAGEN"). BIOGEN and CURAGEN are each
hereafter referred to individually as a "Party" and together as the "Parties".

     WHEREAS, BIOGEN desires to have access to CURAGEN's functional genomics
technologies (including GeneScape(R), QEA/GeneCalling, MIM/PathCalling and all
additional services provided by CURAGEN) and to have CURAGEN apply such
technologies to certain BIOGEN Proprietary Material in order to expedite the
discovery of information which may lead to the development of novel
pharmaceutical products;

     WHEREAS, BIOGEN and CURAGEN wish to initiate the performance of certain
research by CURAGEN;

     WHEREAS, BIOGEN wishes to obtain an option to evaluate and license the
inventions obtained or made by CURAGEN in the performance of the research
pursuant to this Agreement, as well as an option to evaluate and license certain
other inventions of CURAGEN;

     WHEREAS, BIOGEN will agree to make an equity investment in CURAGEN Common
Stock itself, or through one of its Affiliates, in the amount of Five Million
Dollars ($5,000,000), such investment to be made contemporaneously with the
initial public offering of CURAGEN Common Stock;


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     WHEREAS, BIOGEN will itself, or through one of its Affiliates, also agree
to loan CURAGEN up to Ten Million Dollars ($10,000,000) on the terms and
conditions as set forth herein; and

     WHEREAS, BIOGEN and CURAGEN therefore agree to undertake the foregoing, all
under the terms and conditions set forth in this Agreement.

     NOW, THEREFORE, in consideration of the mutual covenants contained
herein, and for other good and valuable consideration, the receipt and adequacy
of which are hereby acknowledged, the Parties hereby agree as follows:

                                1. DEFINITIONS

     Whenever used in the Agreement with an initial capital letter, the terms
defined in this Section 1 shall have the meanings specified.

     1.1  "Affiliate" shall mean any corporation, firm, limited liability
company, partnership or other entity which directly or indirectly controls or is
controlled by or is under common control with a Party to this Agreement.
"Control" means ownership, directly or through one or more Affiliates, of fifty
percent (50%) or more of the shares of stock entitled to vote for the election
of directors, in the case of a corporation, or fifty percent (50%) or more of
the equity interests in the case of any other type of legal entity, status as a
general partner in any partnership, or any other arrangement whereby a Party
controls or has the right to control the Board of Directors or equivalent
governing body of a corporation or other entity.

     1.2  [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]

     1.3  [XXXXXXXXXXXXXXXXX] shall have the meaning set forth in Section 2.6.

     1.4  "BIOGEN Proprietary Material" shall mean samples provided by BIOGEN to
CURAGEN for the purposes of performing the Research Program and shall also be
deemed to include the nucleic acids and other substances actually contained in
such samples.

     1.5  "Clone" shall mean a segment of DNA representing a whole or partial
gene whose sequence or utility is determined from the use of one or more Data
Sets.

                                       2
 
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     1.6  "CURAGEN Background Inventions" shall mean all patent rights and
know-how of CURAGEN, other than those relating primarily to Inventions, which
CURAGEN has the right to license as of the Effective Date or at any time during
the Term hereof, and which would be infringed by the activities of BIOGEN
permitted by this Agreement or by the development, manufacture, use, sale or
importation of a Licensed Product; provided, however, that CURAGEN Background
Inventions shall expressly exclude (i) any patent rights or know-how
specifically relating to Clones or genes not licensed by BIOGEN pursuant to an
executed License Agreement and (ii) any patent rights or know-how arising from
any CURAGEN collaboration with a third party, except to the extent permitted
thereby.

     1.7  "CURAGEN Data" shall mean all information obtained by CURAGEN from the
processing of specified CURAGEN samples, including QC data, expression data,
sequence data and any other information obtained or generated by CURAGEN in the
performance of a discrete CURAGEN Project outside the performance of the
Research Program.
 
     1.8  "CURAGEN Data Set" shall mean all CURAGEN Data resulting from a
discrete CURAGEN Project.
 
     1.9  "CURAGEN Project" shall mean a particular project undertaken by
CURAGEN outside the Research Program to process and analyze a specified set of
samples which do not contain BIOGEN Proprietary Material, and as to which
CURAGEN is free to grant rights to BIOGEN hereunder.

     1.10 "CURAGEN Project Invention" shall mean any discovery, invention,
know-how or trade secret conceived or made by employees of CURAGEN in the
performance of a CURAGEN Project that results in CURAGEN Data that becomes part
of an Exclusive Data Set, that is based on, incorporates or makes material use
of the corresponding CURAGEN Data.

     1.11 "CURAGEN Proprietary Material" shall mean all substances made by
CURAGEN in the performance of the Research Program other than mRNA pools
extracted from BIOGEN Proprietary Material . CURAGEN Proprietary Material shall
also mean all substances made by CURAGEN in the performance of CURAGEN Projects,
including mRNA pools. CURAGEN Proprietary Materials shall include, without
limitation, QEA fragments and materials derived or constructed from QEA
fragments, including, without limitation, fragment and full length cDNA clones.

                                       3
<PAGE>
 
     1.12 "Data Set," which may be either a Project Data Set or a CURAGEN Data
Set, shall mean all Project Data resulting from a discrete Research Project or
all CURAGEN Data resulting from a discrete CURAGEN Project, respectively.

     1.13 "Discovery Project" shall have the meaning set forth in Section 1.29.

     1.14 [XXXXXXXXXXXXXXX] shall have the meaning set forth in Section 7.5.

     1.15 "Exclusive Data Set" shall mean any Project Data Set during the
corresponding Exclusive Evaluation Period as provided in Section 2.4 or any
CURAGEN Data Set during the corresponding Exclusive Evaluation Period as
provided in Section 2.5.2.

     1.16 "Exclusive Evaluation Period" shall have the meaning set forth in
Section 2.4 or 2.5.2.

     1.17 "FTE" shall mean the equivalent of a full year of effort on a full
time basis of a researcher possessing skills and experience necessary to carry
out applicable tasks under the Research Program.

     1.18 "Invention" shall mean either a CURAGEN Project Invention or a
Research Project Invention.

     1.19 [XXXXXXXXXXXXXX] shall have the meaning set forth in Section 2.1.3.

     1.20 "License Agreement" shall mean a license agreement in the form of
Appendix C hereto executed by the Parties upon exercise of any Option pursuant
to Section 7.

     1.21 "Optioned Clone" shall have the meaning set forth in Section 7.1.

     1.22 "Option Period" shall have the meaning set forth in Section 7.3.

     1.23 "Patent Rights" means the rights and interests in and to issued
patents and pending patent applications in any country, including, but not
limited to, all provisional applications, substitutions, continuations,
continuations-in-part, divisions, and renewals, all letters patent granted
thereon, and all reissues, reexaminations and extensions thereof, whether owned
solely or jointly by a Party or licensed in by a Party, with the right to
sublicense, now or in the future, wherein at least one claim of such patent
right is to an Invention.

     1.24 "Previously Committed Clone" shall mean any Clone (a) which is subject
to a license or an option previously granted by CURAGEN to any third party, (b)
which a third party has requested CURAGEN to full-length clone, or (c) of which
a third party has commenced full-length cloning and notified CURAGEN thereof.

                                       4

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     1.25 "Project Data" shall mean all information obtained by CURAGEN from
the processing of BIOGEN Proprietary Material in a particular Research Project,
including QC data, expression data, sequence data and any other information
obtained or generated by CURAGEN in the performance of each Research Project in
the Research Program.

     1.26 "Project Data Set" shall mean all Project Data resulting from a
discrete Research Project.

     1.27 "Research Committee" or "RC" shall have the meaning set forth in
Section 2.2.1.

     1.28 "Research Plan" shall mean the written description of the research to
be performed by CURAGEN under this Agreement, as further described in Section
2.1.3. The Research Plan may specify one or more independent Research Projects.

     1.29 "Research Project" shall mean (i) a particular project to process and
analyze a specified set of samples in the Research Program, one of the primary
purposes of which is the discovery of novel genes or novel utilities of genes (a
"Discovery Project") or (ii) any other project mutually agreed to by the
Parties. Each individual Research Project shall involve the analysis of no more
than [XX] samples unless otherwise agreed by the Parties.
 
     1.30 "Research Project Invention" shall mean any discovery, invention,
know-how or trade secret conceived or made by employees of CURAGEN or BIOGEN or
jointly by employees of both, (a) in the performance of a Research Project
hereunder, or (b) in the course of evaluating or utilizing any Data Set, in each
case that is based on, incorporates or makes material inventive use of the
corresponding Project Data or CURAGEN Data.

     1.31 "Research Program" shall mean the research program to be performed
by CURAGEN under this Agreement as described in the Research Plan and amendments
thereto.

     1.32 "Research Term" shall have the meaning set forth in Section 2.3.1.

     1.33 "Term" shall have the meaning set forth in Section 8.1.

     1.34 "Territory" shall mean the world.

                              2. RESEARCH PROGRAM

     2.1  Implementation of Research Program.
          ----------------------------------   

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     2.1.1  Basic Provisions of Program.
            ---------------------------

     (a) The objective of the Research Program will be for CURAGEN to generate
and deliver to BIOGEN Project Data Sets by performing Research Projects
utilizing BIOGEN Proprietary Material. CURAGEN shall use commercially reasonable
efforts to perform such tasks as are set forth in the Research Plan, including
use of its functional genomics technologies (including GeneScape(R),
QEA/GeneCalling, MIM/PathCalling and all additional services provided by
CURAGEN) and the provision of such facilities and materials (other than BIOGEN
Proprietary Material), equipment and consultants as it deems necessary to the
achievement of such Research Plan and shall deliver each Project Data Set to
BIOGEN using the GeneScape(R) database and software. In carrying out the
Research Program, CURAGEN shall devote an average of at least [XXXXXXXX] FTEs
per year to the Research Program over its five year duration (the "Staffing
Level") unless BIOGEN and CURAGEN have agreed on a change in the Staffing Level
as provided in (b) below.
 
     (b)    BIOGEN may request an increase in the Staffing Level of up to [XXX
XXX] additional FTEs per year to be devoted to the Research Program, subject to
the agreement of CURAGEN. CURAGEN will use commercially reasonable efforts to
increase the staffing level if mutually agreed as promptly as practical. Once
the Staffing Level is increased, it may not be decreased during the following
[XXXXXXXXX] period without the consent of CURAGEN, which consent shall not be
unreasonably withheld.

     (c)    BIOGEN shall have the right, at BIOGEN's expense, to have an
independent certified public accountant review CURAGEN's accounting records for
the purpose of verifying the allocation of the required number of FTE's to the
Research Program.

     2.1.2  Collaborative Efforts and Reports.
            ---------------------------------

     (a)    The Parties agree that the successful execution of the Research
Program will require the collaborative use of both Parties' areas of expertise.
The Parties shall keep the RC fully informed about the status of the portions of
the Research Program they respectively perform. In particular, without
limitation, each Party shall furnish to the RC quarterly written reports within
thirty (30) days after the end of each quarterly period, describing the progress
of its activities in reasonable detail, including (x) a summary of Project Data
from ongoing Research Projects, (y) a summary of uses of Project Data and (z) a
description of Project Data Sets from 

                                       6

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<PAGE>
 
completed Research Projects. At any time, upon the reasonable request of BIOGEN,
CURAGEN will provide an update of the status of Research Projects to BIOGEN.
 
     (b) Scientists at CURAGEN and BIOGEN shall cooperate in the performance of
the Research Program and, subject to any confidentiality obligations to third
parties, shall exchange information and materials (including BIOGEN Proprietary
Material) as necessary to carry out the Research Program, subject to the
provisions of Section 4. Each Party will attempt to accommodate any reasonable
request of the other Party to send or receive personnel for purposes of
collaborating or exchanging information under the Research Program. Such visits
and/or access will have defined purposes and be scheduled in advance. The
requesting Party will bear the reasonable travel and lodging costs of any such
personnel.
 
     (c) CURAGEN will give written notice to BIOGEN and the RC upon completion
of the Project Data Set from each Research Project. "Completion" of a Project
Data Set shall occur upon generation of all QEA/GeneCalling data or
MIM/PathCalling data from a Research Project as contemplated by the Research
Plan.
 
     (d) CURAGEN shall set up and maintain, throughout the Research Term, a
secure partition of its GeneScape(R) database and software for the exclusive use
of BIOGEN and CURAGEN for the purpose of identifying genes from Exclusive Data
Sets, and shall provide online E-mail and telephone help during normal business
hours in the use thereof to BIOGEN. CURAGEN and BIOGEN shall jointly set up and
maintain a secure connection to said partition of the GeneScape(R) database and
software in order to give BIOGEN on-line access thereto. Through such
connection, BIOGEN shall have the right to utilize all features and functions of
the GeneScape(R) database and software (including, without limitation,
GeneTools(TM)) in connection with the Research Program.

     (e) BIOGEN will also receive access to CURAGEN's QEA/GeneCalling and
MIM/PathCalling subscription databases and to GeneTools(TM) pursuant to one or
more subscription agreements to be executed by the Parties, with terms
substantially as described in Appendix D hereto. Such subscriptions [XXXXXXXX
                              ----------
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXX] 

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<PAGE>
 
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] until the
expiration of the Research Term. Such subscription agreements may be terminated
by BIOGEN at any time, without affecting the Research Program, either in their
entirety or with respect to any database at BIOGEN's sole discretion upon three
(3) months prior written notice. BIOGEN shall have no rights to use the
GeneScape(R) database and software except as expressly set forth herein or in an
executed database subscription agreement.

     2.1.3  Research Plans.
            --------------

     The Research Plan for the first twelve months of the Research Program shall
be agreed upon by the Parties within thirty (30) days of the Effective Date and
shall include the initial Research Projects and plans to implement the
installation of access to the GeneScape(R) database and software for BIOGEN. The
initial Research Projects shall include a project on [XXXXXXXXXXXXXX
XXXXXXXXXXXXXX] and a project on [XXXXXXXXXX] as further described in Section
2.6. Every [XXXXXXXXXXXXXX] during the Research Term [XXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXX] the Research Plan shall be updated by BIOGEN in consultation
with CURAGEN to cover the next twelve months and shall be approved by the RC no
later than thirty (30) days before the end of each semi-annual period. The
Research Plan shall set forth specific Research Projects for the period covered
by the Research Plan. The RC will consider adjustments in the Research Plan at
any time upon the request of BIOGEN or CURAGEN. Notwithstanding the foregoing,
no project shall become a Research Project without the express consent of both
BIOGEN and CURAGEN; provided, however, that CURAGEN shall consent to any
reasonable proposed Discovery Project which is not substantially similar to a
project that is ongoing, planned, the subject of negotiation with a third party
or subject to a prior commitment to a third party, and which would not violate a
prior restriction under an agreement with a third party. The Parties shall
negotiate in good faith the terms to apply generally to any Research Project
that is not a Discovery Project, other than the [XXXXXXXXXX XXXXXXXX] which is
covered by Section 2.6.

     2.1.4  Exclusivity.
            -----------

     (a)    CURAGEN agrees that, during the conduct of a Research Project and
for the duration of any subsequent Exclusive Evaluation Period, CURAGEN shall
not undertake to perform a substantially similar research project with any third
party.

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<PAGE>
 
     (b)    CURAGEN agrees that during any Exclusive Evaluation Period, CURAGEN
will not grant access to any Exclusive Data Set to any other party and that
during any Option Period, CURAGEN shall not grant to any third party rights to
any Optioned Clone. In addition, CURAGEN shall not, during any Exclusive
Evaluation Period, grant a third party any exclusive rights to license a Clone
contained in the corresponding Exclusive Data Set (i) which BIOGEN has requested
CURAGEN to full-length clone or (ii) for which BIOGEN has commenced full-length
cloning and notified CURAGEN thereof. Notwithstanding the provisions of Article
4 and except as provided in Section 2.6 hereof, upon the expiration of any
Exclusive Evaluation Period for any Exclusive Data Set, CURAGEN shall have the
right, at its sole option, to make such Data Set and reasonable descriptions of
the data contained therein available to third parties or to put the Data Set and
such descriptions in the subscription portion of the GeneScape(R) database.
Nothing contained in this Agreement shall in any way restrict CURAGEN's right to
perform research or collaborate with third parties and to grant to third parties
the right to exploit the results of any such research or collaborations without
restriction other than as set forth above or as expressly provided in an
executed License Agreement. CURAGEN agrees that CURAGEN will not use and/or
replicate any BIOGEN Proprietary Material for any purpose other than as provided
herein.

     (c)    CURAGEN acknowledges that BIOGEN may, in the course of reviewing
Data Sets, obtain general information not specifically relating to any Clone or
to the utility thereof. BIOGEN shall be permitted to use any such general
information that is non-proprietary to CURAGEN in the course of conducting its
internal research programs, or as otherwise permitted herein, but for no other
purpose.

     (d)    BIOGEN agrees that, until any such information is in the public
domain, other than as a result of a disclosure by BIOGEN in violation of this
Agreement, an executed subscription agreement or an executed License Agreement,
BIOGEN will only utilize Project Data, CURAGEN Data, CURAGEN Proprietary
Material, Inventions or Patent Rights as expressly provided herein, in an
executed License Agreement or in an executed subscription agreement.

     2.1.5  Research License. CURAGEN hereby grants to BIOGEN a non-exclusive
            ----------------   
license under CURAGEN Background Inventions and CURAGEN's interest in any
Inventions solely 

                                       9
<PAGE>
 
during the Term hereof and to the extent necessary to allow BIOGEN to perform
its obligations under the Research Program and to exercise the rights granted
herein.
 
     2.1.6  Software License. Any access granted to the GeneScape(R) database
            ----------------   
and software hereunder, or any components thereof, is granted according to the
following terms:

     The GeneScape(R) database, software and display screeens are protected by
copyright, patent, trade secret and other intellectual property laws. CURAGEN
hereby grants to BIOGEN and its employees a non-exclusive non-transferrable
license to access the GeneScape(R) database and software solely for the purposes
of and during the Term of this Agreement. BIOGEN shall access Project Data Sets
and CURAGEN Data Sets only through the GeneScape(R) database and software
provided by CURAGEN. BIOGEN shall not copy the GeneScape(R) database, software
or display screens except as occurs during the normal course of CURAGEN-provided
access. In particular, BIOGEN will not retain such normal copies for a time not
reasonably related to CURAGEN-provided access. BIOGEN shall not reverse
engineer, decompile, or disassemble the GeneScape(R) software or display
screens. The GeneScape(R) database and software embody trade secrets of CURAGEN
that are considered Confidential Information of CURAGEN and subject to the
provisions of Article 6 hereof.

     2.2    Research Committee.
            ------------------

     2.2.1  Establishment and Functions of RC.
            ---------------------------------

     (a)    CURAGEN and BIOGEN shall establish a "Research Committee" (the
"RC"). The RC will be responsible for the planning and monitoring of the
Research Program. In particular, the activities of the RC shall include
reviewing progress in the Research Program and recommending necessary
adjustments to the Research Program, including any Research Project
substitutions deemed desirable based on results and on BIOGEN's commercial
interest, as the research and development progresses.

     (b)    In planning and monitoring the Research Program, the RC shall assign
tasks and responsibilities taking into account each Party's respective specific
capabilities and expertise in order in particular to avoid duplication and
enhance efficiency and synergies.

     2.2.2  RC Membership.
            -------------

     CURAGEN and BIOGEN each shall appoint, in their sole discretion, three
members to the RC, which shall include a Co-Chair to be designated by BIOGEN and
a Co-Chair to be 

                                       10
<PAGE>
 
designated by CURAGEN. Substitutes or alternates for the Co-Chairs or other RC
members may be appointed at any time by notice in writing to the other Party.
The Parties may mutually agree to change the size of the RC as long as there
shall be an equal number of representatives of each Party on the RC. The initial
Co-Chairs and other RC members shall be designated by the Parties upon execution
of this Agreement. CURAGEN shall appoint a Project Coordinator, who shall be
reasonably satisfactory to BIOGEN, to serve as the principal liaison with BIOGEN
for the Research Program. Such Project Coordinator will be one of CURAGEN's
members of the RC.

     2.2.3 Meetings.
           --------

     The RC shall meet at least quarterly, with such meetings to be held,
alternately, in New Haven, Connecticut, and Cambridge, Massachusetts unless the
Parties agree otherwise. Any additional meetings shall be held at places and on
dates selected by the Co-Chairs of the RC. In addition, the RC may act without a
formal meeting by a written memorandum signed by the Co-Chairs of the RC.
Whenever any action by the RC is called for hereunder during a time period in
which the RC is not scheduled to meet, the Co-Chairs of the RC shall cause the
RC to take the action in the requested time period by calling a special meeting
or by action without a meeting. Subject to the obligations set forth in Section
4, representatives of each Party or of its Affiliates, in addition to the
members of the RC, may attend RC meetings at the invitation of either Party with
the prior approval of the other Party, which shall not be unreasonably withheld.
 
     2.2.4 Minutes.
           -------
 
     The RC shall keep accurate minutes of its deliberations which record all
proposed decisions and all actions recommended or taken. Drafts of the minutes
shall be delivered to the Co-Chairs of the RC within twenty (20) days after the
meeting. The Party hosting the meeting shall be responsible for the preparation
and circulation of the draft minutes. Draft minutes shall be edited by the
Co-Chairs and shall be issued in final form only with their approval and
agreement as evidenced by their signatures on the minutes.
 
     2.2.5 Quorum; Voting; Decisions.
           -------------------------

     At each RC meeting, at least two (2) member(s) appointed by each Party
present in person or by telephone shall constitute a quorum and decisions shall
be made by majority vote. Each RC member shall have one vote on all matters
before the RC, provided that the member or members of each Party present at an
RC meeting shall have the authority to cast the votes of any 

                                       11
<PAGE>
 
of such Party's members on the RC who are absent from the meeting.
Notwithstanding the foregoing, the objective of the Parties to this Agreement is
that decisions of the RC shall be made by consensus. However, except as
otherwise set forth herein, in the event that the RC is unable to resolve any
matter before it as set forth above, such matter shall be resolved in good faith
by BIOGEN. Notwithstanding the foregoing, no project shall become a Research
Project without the express consent of both BIOGEN and CURAGEN; provided,
however, that CURAGEN shall consent to any reasonable proposed Discovery Project
which is not substantially similar to a project that is ongoing, planned, the
subject of negotiation with a third party or subject to a prior commitment to a
third party, and which would not violate a prior restriction under an agreement
with a third party.

     2.2.6 Expenses.
           --------
 
     CURAGEN and BIOGEN shall each bear all expenses of their respective RC
members related to their participation on the RC and attendance at RC meetings.

     2.3   Research and Development Term.
           -----------------------------

     2.3.1 Term of the R&D Program.
           -----------------------

     The Research Program shall expire five (5) years after the Effective Date
unless extended as provided below or unless earlier terminated by either Party
pursuant to the provisions in Section 2.3.3 and/or Article 8 (the "Research
Term").

     2.3.2 Extension of the Research Phase of the R&D Program. 
           --------------------------------------------------

     The Research Term may be extended upon six (6) months prior written
notice by mutual agreement of the Parties on terms to be agreed upon between the
Parties.

     2.3.3 Early Termination of the R&D Program.
           ------------------------------------

     (a)   BIOGEN may terminate the Research Program at its sole discretion upon
six (6) months prior written notice to CURAGEN, which notice may be given at any
time after the second anniversary of the Effective Date. Notwithstanding any
other provision of this Agreement, any such early termination of the Research
Program shall automatically terminate any ongoing Exclusive Evaluation Period or
Option Period, but shall not affect any License Agreement executed between the
Parties prior to such early termination or any Option that has been exercised
prior to such early termination.

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     (b)   Any termination of the Research Program under Section 2.3.3(a) shall
be without prejudice to the rights of either Party against the other, then
accruing or otherwise accrued under this Agreement and upon any such
termination, all remaining BIOGEN Proprietary Material provided to CURAGEN under
this Agreement shall be returned to BIOGEN or destroyed and all remaining
CURAGEN Proprietary Material provided to BIOGEN under this Agreement shall be
returned to CURAGEN or destroyed, except for any CURAGEN Proprietary Material
licensed pursuant to an executed License Agreement.
 
     2.4   Project Data Evaluations.
           ------------------------

     2.4.1 Exclusive Access. From the time at which a Research Project is begun
           ----------------
and continuing through a one-year period which shall commence on the first day
of the calendar quarter following the calendar quarter in which delivery of
a notice of a complete Project Data Set is made pursuant to Section 2.1.2(c)
(the "Exclusive Evaluation Period"), CURAGEN: (a) shall not use such Project
Data Set and related CURAGEN Proprietary Material resulting from such Research
Project for any purpose other than conducting the Research Program hereunder and
(b) shall keep such Project Data Set and related Inventions and CURAGEN
Proprietary Material confidential and will not disclose or transfer the Project
Data Set, or related Inventions and CURAGEN Proprietary Material, to third
parties by publication or otherwise, without the prior written consent of
BIOGEN.

     2.4.2 Extensions. BIOGEN may elect to extend the Exclusive Evaluation
           ----------
Period for any Project Data Set for up to two additional twelve (12) month 
periods from the end of the initial, unextended Exclusive Evaluation Period by
giving written notice to CURAGEN and making a payment of $500,000 per twelve 
(12) month period to CURAGEN prior to expiration of the then current Exclusive
Evaluation Period for such Project Data Set. An Exclusive Evaluation Period will
be automatically extended for [XXXXXXXXXXXXXX] for up to three months in order
to allow the completion of any reasonable requests for confirmation of data made
by BIOGEN during the primary twelve-month of such Exclusive Evaluation Period.

     2.4.3 Non-exclusive Access. Except with respect to any information which
           --------------------
becomes part of the public domain other than as a result of a disclosure by
BIOGEN in violation of this Agreement, an executed subscription agreement or an
executed License Agreement, following the expiration of the Exclusive Evaluation
Period for a Project Data Set, BIOGEN shall continue 

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<PAGE>
 
to have non-exclusive access to such Project Data Set solely through the
GeneScape(R) database and solely for the purpose of identifying Clones of
interest to BIOGEN in such Data Set, or to the extent expressly permitted in
Section 2.1.4(c), in an executed License Agreement or in an executed
subscription agreement.

     2.4.4. Data Annotations. Upon the expiration of the Exclusive Evaluation
            ----------------
Period for each Project Data Set, CURAGEN shall furnish to BIOGEN reasonable
descriptions of the Project Data Set to be included in the GeneScape(R) database
with the Project Data Set. BIOGEN shall have a period of [XXXXXXXXXXXXXX] to
review such descriptions and advise CURAGEN of reasonable objections. CURAGEN
shall not include in the GeneScape(R) database any descriptions, or portions
thereof, to which BIOGEN reasonably objects.
 
     2.5    CURAGEN Projects.
            ----------------

     2.5.1  Access. BIOGEN shall have the option, for such period or periods as
            ------
CURAGEN may specify, to obtain exclusive access to specified proprietary CURAGEN
Data Sets and related CURAGEN Project Inventions which are offered by CURAGEN in
its sole discretion to BIOGEN for review. Such option shall be exercisable as
set forth in Section 2.5.2 below.
  
     2.5.2  Exclusive Evaluation Option. Subject to any rights which CURAGEN may
            ---------------------------
grant or have granted to third parties, BIOGEN may request at any time during
the time period specified by CURAGEN that it receive exclusive access (as
described in Section 2.5.1) to any CURAGEN Data Set offered to BIOGEN pursuant
to Section 2.5.1. Such exclusive access to such CURAGEN Data Set shall be
granted to BIOGEN for an Exclusive Evaluation Period of [XXXXXXXXXX] commencing
upon CURAGEN's receipt of written notice from BIOGEN and payment of an exclusive
evaluation fee of [XXXXX] unless BIOGEN is notified by CURAGEN at any time
prior to CURAGEN's receipt of BIOGEN's written notice that exclusive access to
such CURAGEN Data Set is no longer available as a result of CURAGEN's agreements
with third parties existing at the time of the request.

     2.5.3  Extensions. BIOGEN may elect to extend the Exclusive Evaluation
            ----------
Period for any CURAGEN Data Set for up to [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXX] from the end of the initial unextended Exclusive Evaluation Period by
giving written notice to CURAGEN and making a second payment [XXXXXXXXXX
XXXXXXXXX] to CURAGEN prior to expiration of the then current
Exclusive Evaluation Period for such CURAGEN Data Set. An 

                                       14

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<PAGE>
 
Exclusive Evaluation Period will be automatically extended for [XXXXXXXXXXXX]
for up to [XXXXXXXXXXXX] in order to allow the completion of any reasonable
requests for confirmation of data made by BIOGEN during the primary [XXXXXXXXXX]
period of such Exclusive Evaluation Period. Following the expiration of the
Exclusive Evaluation Period for a CURAGEN Data Set, BIOGEN shall have no access
to or right to use such CURAGEN Data Set, other than as expressly permitted in
Section 2.1.4(c), in an executed License Agreement or in an executed
subscription agreement.
 
     2.6   [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXX]

                              3. FINANCIAL TERMS

     3.1   Equity Investment. BIOGEN agrees itself, or through one of its
           -----------------
Affiliates, to make an equity investment in CURAGEN in the amount of Five
Million Dollars ($5,000,000), such investment to be made in a transaction exempt
from registration under the Securities Act of 1933 contemporaneously with the
closing of the initial public offering of CURAGEN Common Stock at the public
offering price and pursuant to a mutually agreeable stock purchase agreement
containing reasonable and customary terms for the purchase of stock in such
circumstances and a 

                                       15

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<PAGE>
 
registration rights agreement providing for the filing of a registration
statement covering the resale of the purchased shares to be filed by CURAGEN
within twenty (20) days of the first anniversary of the effective date of the
registration statement pertaining such initial public offering. In the event
that CURAGEN has not closed an initial public offering within eighteen (18) 
months from the Effective Date, BIOGEN shall be released from its obligation
pursuant to this Section 3.1.

     3.2   Loan Commitment. As partial consideration for rights granted
           ---------------
hereunder, BIOGEN hereby commits to the following:

     (a)   BIOGEN shall itself, or through one of its Affiliates, subject to the
terms set forth below, make funds available to CURAGEN for general corporate
purposes in the form of a loan or loans to CURAGEN in an amount not to exceed
Ten Million Dollars ($10,000,000.00) (the "Loan"). Unless this Agreement has
been terminated for any reason, CURAGEN may, in such amounts and at such times
as CURAGEN, in it sole discretion, may determine, upon fifteen (15) days
written notice draw down the balance of the Loan over a period of five (5) Loan
Years (as defined below) following the Effective Date. For the purposes of this
section, a "Loan Year" commences on the Effective Date or an anniversary thereof
and terminates twelve months later. BIOGEN shall not be obligated to advance
more than Five Million Dollars ($5,000,000) in the first Loan Year or to advance
any funds under the Loan at any time during which (i) CURAGEN is in default
under any Note (defined below); or (ii) any proceeding, voluntary or
involuntary, in bankruptcy or insolvency, is pending against CURAGEN, or a
receiver is operating CURAGEN with or without the consent of CURAGEN. BIOGEN's
obligation to advance any funds under the Loan shall terminate upon the earlier
to occur of (i) the last day of the fifth Loan Year or (ii) termination or
expiration of the Research Program and the Research Term.

     (b)   On the Effective Date, CURAGEN shall execute and deliver to BIOGEN an
unsecured note, substantially in the form set forth in Appendix B attached
                                                       ----------
hereto and made a part hereof (the "Note"), evidencing the Loan. The schedule
attached to the Note shall be revised each time any amount is drawn down under
the Loan and each time any amount is repaid. Once any principal amount has been
repaid, BIOGEN shall not be obligated to advance such amount to CURAGEN during
the remainder of the term of the Loan. The Note shall be subordinated to (i)
all secured debt and liabilities of CURAGEN and (ii) all liabilities of CURAGEN
to institutional or
                                       16

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<PAGE>
 
commercial lenders and equipment lessors existing as of the date hereof or
incurred hereafter (including, without limitation any lease obligations) and
may be prepaid by CURAGEN at any time without premium or penalty on a date
specified by CURAGEN, in cash or at CURAGEN's option, in CURAGEN Common Stock
valued at its then Fair Market Value (as defined in Section 3.2(e) below).

     (c) The Note shall bear interest on the outstanding principal amount
thereof at a rate per annum equal to Prime (defined below) plus one (1%)
percent. Such interest shall accrue and be paid semi-annually commencing on the
six-month anniversary of the date first following any advance under the Loan and
continuing every six months thereafter until the Note is paid in full, unless
otherwise specified in this Section 3.2. Interest payments shall be made in cash
or at CURAGEN's option, in CURAGEN Common Stock valued at its then Fair Market
Value (as defined in Section 3.2(e) below). The applicable rate of interest for
the Note shall be adjusted semi-annually according to the Prime rate as
announced on each six-month anniversary date of the Effective Date.

     (d) Within fifteen (15) days of the expiration of the fifth Loan Year,
repayment in full of the principal amount and accrued interest, under the Note
shall be made in cash or, at CURAGEN's option, in CURAGEN Common Stock valued at
its then Fair Market Value (as defined in Section 3.2(e) below). Notwithstanding
the foregoing, if this Agreement is terminated by BIOGEN pursuant to Section
8.2(a), or if the Research Program is terminated pursuant to Section 2.3.3,
CURAGEN shall repay the principal and accrued interest owed under the Note
within twelve (12) months of the date the Agreement or the Research Program,
as the case may be, is terminated; provided, however, that any such repayment
may be made in cash or stock as set forth above, at CURAGEN's sole discretion.

     (e) For purposes of subsection (c) of this Section 3.2, "Prime" shall mean
the floating rate of interest reported by The Wall Street Journal as the
                                          -----------------------
prevailing base rate on corporate loans posted by at least 75% of the 30 largest
banks in the United States. In the event that the The Wall Street Journal ceases
                                                 -----------------------
to publish such a rate, or modifies its criteria for such rate, the term "Prime"
shall mean the generally prevailing base corporate lending rate of Fleet
National Bank. For purposes of subsections (b), (c), (d) and (f) of this
Section 3.2, "Fair Market Value" of CURAGEN Common Stock shall mean: the lower
of (i) the average of the closing prices as reported by

                                       17

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NASDAQ or, if not traded on NASDAQ, by such other principal securities exchange 
on which the shares are traded, as applicable, over the twenty (20) trading days
preceding the payment date specified by CURAGEN or the date on which the Loan is
otherwise due or payable, or (ii) the closing price on the last day on which 
shares are traded preceding such date if such price is more than twenty-percent 
(20%) below such average. Notwithstanding the foregoing, if CURAGEN Common Stock
is not publicly traded at the time of any repayment hereunder, Fair Market Value
shall mean the price at which CURAGEN issued shares in its most recent third 
party equity financing raising in excess of One Million Dollars. Delivery of
any shares of Common Stock shall take place no later than five (5) days after
the repayment date and shall be subject to execution by the Parties of an
agreement containing customary representations and provisions to comply with
Federal and State securities laws, as mutually agreed between the Parties.
Additionally, if CURAGEN Common Stock is not publicly traded at the time of any
such repayment, BIOGEN shall receive registration rights with respect to any
such shares on the same terms and conditions as set forth in the Registration
Rights Agreement between CURAGEN and Biotech Manufacturing Limited dated June
25, 1997.

     (f)   In the event that CURAGEN makes any repayment hereunder in CURAGEN
Common Stock and CURAGEN is eligible to file a registration statement on Form
S-3 (or successor short form) at the time of repayment, then within 20 days of
the repayment date, CURAGEN shall file a registration statement on Form S-3
covering the resale by BIOGEN of any shares so delivered to BIOGEN; provided,
however, that with respect to any repayment in CURAGEN Common Stock made under
subsection (c) hereof, to the extent not already included in any other
registration, CURAGEN shall annually during the month of April file a
registration statement on Form S-3 covering the resale by BIOGEN of any such
shares so delivered to BIOGEN. Notwithstanding anything herein to the contrary,
BIOGEN may require that CURAGEN repay the amounts borrowed under the Note in
cash and stock to the extent necessary to ensure that receipt of CURAGEN's
shares will not cause BIOGEN's holdings in CURAGEN to equal 19.9 percent or
more of CURAGEN's total Common Stock outstanding after the issuance of such
shares to BIOGEN.

     3.3   Research Funding.
           ----------------

                                       18

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<PAGE>
 
     During the Research Term, BIOGEN will pay CURAGEN non-refundable research
payments of [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] per year plus
the sum of [XXXXXX] per year per FTE in the Staffing Level above [XX]FTEs. Such
payments will be made quarterly in advance, commencing on the Effective Date,
and on or before the first day of each calendar quarter thereafter, with the
first and last payments prorated in the event that the Effective Date or the
expiration or termination date is not the first day or last day of a calendar
quarter, respectively. In the event that the Staffing Level is to change in any
calendar quarter, such payment shall be pro-rated accordingly, if necessary,
based on the above-specified level of funding per FTE. The first research
payment shall be made simultaneously with the execution of this Agreement and
shall include all amounts necessary to make BIOGEN current in research payments
due since the Effective Date. BIOGEN will fund its own activities under the
Research Program.

                   4. TREATMENT OF CONFIDENTIAL INFORMATION

     4.1   Confidential Information. During the course of the Research Program,
           ------------------------
or in discussions concerning Exclusive Data Sets, each Party may disclose to the
other proprietary technical and business information, including but not limited
to information contained in Data Sets (which information shall be deemed
Confidential Information of CURAGEN), (collectively, "Confidential
Information"). For a period of [XXXXXXXXXXX] after the receipt of any such
Confidential Information, except as expressly permitted hereunder, the receiving
Party shall keep confidential all such Confidential Information of the other
Party and will not disclose such Confidential Information of the other Party to
third parties by publication or otherwise. Each Party shall take reasonable
steps to ensure that all of its employees, consultants and RC members shall
protect and use Confidential Information of the other Party only in accordance
with the terms hereof. Each Party further agrees not to use Confidential
Information of the other Party for any purpose other than conducting or
evaluating research hereunder, evaluating and analyzing Data Sets or exercising
any rights granted to it or reserved by it hereunder, in an executed License
Agreement or executed subscription agreement, or as otherwise expressly
permitted hereunder. Notwithstanding the foregoing, it is understood and 

                                       19
 
                      [Confidential Treatment Requested]


<PAGE>
 
agreed that the receiving Party's obligations of confidentiality and nonuse
herein shall not apply to any information which:

           (a) is, at the time of disclosure by the disclosing Party hereunder,
           or thereafter becomes, a part of the public domain or publicly known
           or available through no fault or negligence of the receiving Party or
           any of its Affiliates; or

           (b) was otherwise in the receiving Party's lawful possession prior to
           disclosure by the disclosing Party, as demonstrated by the receiving
           Party's written records; or

           (c) is lawfully disclosed to the receiving Party or any of its
           Affiliates on a non-confidential basis by a third party who is not in
           violation of an obligation of confidentiality to the disclosing Party
           relative to such information.

     4.2   Publications. It is expected that each Party may wish to publish the
           ------------
results of its research under this Agreement. In order to safeguard intellectual
property rights, the Party wishing to publish or otherwise publicly disclose the
results of its research hereunder shall first submit a draft of the proposed
manuscripts to the Research Committee for review, comment and consideration of
appropriate patent action at least [XXXXXXXXXX] prior to any submission for
publication or other public disclosure. Within [XXXXXXXXXXXX] of receipt of
the prepublication materials, the Research Committee will advise the Party
seeking publication as to whether a patent application will be prepared and
filed or whether trade secret protection should be pursued and, if so, the
Research Committee will, in cooperation with both Parties, determine the
appropriate timing and content of any such publications.

     4.3   Press Release and Regulatory Filings. The Parties shall mutually
           ------------------------------------
agree on a press release announcing the execution of this Agreement and on any
confidential treatment request to be filed with the Securities and Exchange
Commission with respect to this Agreement. Once any written statement is
approved for disclosure by both Parties, either Party may make subsequent public
disclosures of the contents of such statement without the further approval of
the other Party.

                                       20

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<PAGE>
 
                        5. INTELLECTUAL PROPERTY RIGHTS

     5.1   BIOGEN Proprietary Material. mRNA pools extracted by CURAGEN from a
           ---------------------------
BIOGEN Proprietary Material in the performance of the Research Program shall
remain BIOGEN Proprietary Material. All other substances made by CURAGEN in the
performance of the Research Program shall be CURAGEN Proprietary Material.
BIOGEN Proprietary Material shall remain the property of BIOGEN and CURAGEN
shall use such BIOGEN Proprietary Material only for the purpose of conducting
the Research Program hereunder and shall not transfer BIOGEN Proprietary
Material to any other person or entity.

     5.2   CURAGEN Proprietary Material. Substances made by BIOGEN from CURAGEN
           ----------------------------
Proprietary Material shall remain CURAGEN Proprietary Material. CURAGEN
Proprietary Material shall remain the property of CURAGEN and BIOGEN shall use
such CURAGEN Proprietary Material only for purposes relating to performance of
the Research Program, evaluation of the Project Data, the exercise of the option
provided in Section 7.1, or pursuant to the terms of an executed License
Agreement. BIOGEN shall not transfer CURAGEN Proprietary Material to any other
person or entity except in connection with rights granted to BIOGEN pursuant to
an executed License Agreement.

     5.3   Inventions. Each Party shall promptly disclose to the other Party all
           ----------
Inventions. Except as set forth in Sections 5.1 and 5.2, (i) all Research
Project Inventions, and Patent Rights thereon, shall be owned jointly by CURAGEN
and BIOGEN; and (ii) all CURAGEN Project Inventions, and Patent Rights thereon,
shall be owned by CURAGEN. The rights and interests of CURAGEN and BIOGEN in
Inventions shall be subject to the provisions of Article 7.

              6. PROVISIONS CONCERNING THE FILING, PROSECUTION AND
                          MAINTENANCE OF PATENT RIGHTS

     6.1   Applicability. The provisions of this Section 6 shall be applicable
           -------------
to all Inventions and Patent Rights unless and until (i) they become subject to
a License Agreement, whereupon the License Agreement will govern the rights of
the Parties with respect to the subject matter thereof, or (ii) the relevant
Research Project is completed and the relevant Exclusive


                                      21
<PAGE>
 
Evaluation Period expires and the relevant Option Period, if any, expires,
whereupon this Section 6 shall cease to apply.
 
     6.2   Patent Filing.
           -------------
     (a)   CURAGEN shall have the first right (but not the obligation) to
prepare, file, prosecute, obtain and maintain patent applications and patents on
Inventions, at its sole expense. BIOGEN agrees to provide reasonable assistance
and cooperation to CURAGEN to facilitate such filing, prosecution and
maintenance. CURAGEN agrees that any such preparation, filing, prosecution and
maintenance shall be conducted diligently and that BIOGEN shall be kept fully
informed of the progress thereof and provided with copies of all material
documents pertaining thereto until the end of the Exclusive Evaluation Period,
and for any Invention which becomes subject to an Option, until the end of the
Option Period. BIOGEN shall, whenever possible, be given the opportunity to
review and comment in advance on any patent filings or other correspondence with
the patent office during such periods and CURAGEN shall consider incorporating
any comments provided by BIOGEN in good faith.

     (b)   CURAGEN may elect not to exercise its first right to prepare, file,
prosecute, obtain and maintain patent applications and patents on Inventions as
described in Section 6.2(a) above at any time for any such patent applications
and patents by giving written notice thereof to BIOGEN. Such notice shall
specifically identify the patent application(s) and/or patent(s) for which
CURAGEN wishes to relinquish such first right. Following the receipt of such
notice, BIOGEN shall have the right to prepare, file, prosecute, obtain and
maintain the patent application(s) and patent(s) identified in the notice, at
its sole expense, on behalf of the owner of the Invention, subject to the rights
granted herein, until the end of the Exclusive Evaluation Period, and for any
Invention which becomes subject to an Option, until the end of the Option
Period.
 
     (c)   The Parties shall mutually agree before permitting any patent
application or patent within Patent Rights to lapse as well as before
authorizing any amendment to any patent application or patent within Patent
Rights that would irrevocably limit the lawful scope of the Patent Rights, until
the end of the Exclusive Evaluation Period, and for any Invention which becomes
subject to an option, until the end of the Option Period.


                                      22
<PAGE>
 
     (d)   No Party shall have any obligation under this Agreement to pay any
fees or costs: (i) for bringing a lawsuit or other action to enforce any of the
Patent Rights against an actual or suspected infringement or (ii) for any other
Party to obtain for its own benefit independent business or legal advice
concerning any of the Patent Rights.

     6.3   Notice of Infringement. If either Party learns of any infringement or
           ----------------------
threatened infringement by a third party of the patents within Patent Rights,
such Party shall promptly notify the other Party and shall provide such other
Party with available evidence of such infringement.
 
     6.4   Infringement. CURAGEN shall have all rights, at its own expense, to
           ------------
bring suit (or other appropriate legal action) against any actual or suspected
infringement of the Patent Rights.
 
     6.5   Cooperation. BIOGEN shall execute all papers and perform such other
           -----------
acts as may be reasonably required to maintain any infringement suit brought in
accordance with Section 6.4 above (including giving legal consent for bringing
such suit, and agreeing to be named as a plaintiff or otherwise joined in such
suit). BIOGEN shall be reimbursed by CURAGEN for any out of pocket expenses
incurred in connection with the foregoing. BIOGEN, at its option and expense,
may be represented in such suit by counsel of its choice.

                              7. OPTION TO BIOGEN

     7.1   Option Grant.
           ------------

     7.1.1 Option. Subject to rights third parties have obtained by virtue of
           ------
access to other CURAGEN Data Sets, data sets resulting from agreements between
CURAGEN and third parties, or the subscription portion of the GeneScape(R)
database prior to BIOGEN's election, CURAGEN hereby grants to BIOGEN the right
to elect an exclusive option (the "Option") to license all Inventions and other
CURAGEN patents or patent applications as described in Section 2.3 of the
License Agreement relating to any Clone whose sequence or utility is determined
in whole or in part from the use of an Exclusive Data Set which is not a
Previously Committed Clone. Such Option shall give BIOGEN the right to obtain,
at BIOGEN's sole discretion, either (a) subject to the rights reserved by
CURAGEN in Section 7.1.3, an exclusive license to the Clone specified in
BIOGEN's notice of exercise (the "Optioned Clone") and to all Patent Rights 


                                      23
<PAGE>
 
and Inventions to the extent that they relate to such Optioned Clone including
but not limited to Patent Rights claiming whole or partial sequences or utility,
to develop, make, have made, use, have used, sell, offer for sale, have sold,
import and have imported products (i) incorporating or derived from such
Optioned Clone, or (ii) discovered or developed using such Optioned Clone, in
the Territory, for any and all human uses, under the terms and conditions set
forth in the License Agreement; (b) a non-exclusive license to the Optioned
Clone and to all Patent Rights and Inventions to the extent that they relate to
such Optioned Clone, solely for use of the Optioned Clone as a target to develop
small molecule products; or (c) subject to the rights reserved by CURAGEN in
Section 7.1.3, an exclusive license to all Patent Rights and Inventions claiming
utility of a known Optioned Clone, as further described in the License
Agreement. Such Option shall be exercisable at any time during the Option Period
specified in Section 7.3.

     7.1.2 Option Election.
           ---------------
     Such Option shall be elected by BIOGEN by giving written notice to CURAGEN
within the Exclusive Evaluation Period for such Exclusive Data Set, which shall
specify in detail the Optioned Clone to be included within the terms of any such
Option and which shall be accompanied by the payment of any Option Fee as
specified in Section 7.2. Each Optioned Clone, and the term of the corresponding
Option Period, shall be listed on Appendix A hereto from time to time.
Notwithstanding the foregoing, for Project Data Sets, BIOGEN may request such an
Option after expiration of the Exclusive Evaluation Period, which Option shall
be granted by CURAGEN upon payment of the Option Fee specified in Section 7.2,
unless prohibited by agreements with third parties.

     7.1.3 Reservation of Rights. Notwithstanding the foregoing, in any
           ---------------------
exclusive license granted pursuant to the exercise of an Option, CURAGEN shall
retain for itself the right to use the Optioned Clone or the protein derived
therefrom as part of a general library of nucleic acids, which library is used
for research purposes.
 
     7.2 Option Fee. An Option Fee of [XXXXXX] per Optioned Clone shall be due
         ----------
upon the election of an Option with respect to any Clone from any Exclusive Data
Set; [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXX]


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     7.3   Option Period. Each Option shall remain in effect for a period of
           -------------
[XXXXXXXXXXXX] from receipt by CURAGEN of BIOGEN's written notice of its
election of such Option and payment of any required Option Fee (the "Option
Period"); provided, however, that any Option Period may be extended for [XXX
XXXXXXXXXXXXXXXXXXXXXXXX] period upon payment by BIOGEN of [XXXXXXXXXXXXXX]
per Optioned Clone.

     7.4   Option Exercise. During each Option Period, upon notice to CURAGEN
           ---------------
and upon payment of the corresponding license fee, BIOGEN shall have the right
to receive a license to the Optioned Clone under the terms and conditions set
forth in an executed License Agreement. The license fee for a license described
in Section 7.1.1, clause (a) shall be [XXXXXX] and the license fee for a license
described in Section 7.1.1, clause (b) or (c), shall be [XXXXXX]
Notwithstanding the foregoing, [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]The License Agreement shall be executed in
substantially the form attached hereto upon exercise of the first Option, unless
previously executed pursuant to Section 7.5, and shall be amended from time to
time in accordance with the terms hereof and thereof as additional Options are
exercised.

     7.5  [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]

     7.6   Reversion of Rights. CURAGEN shall retain all rights to all Project
           -------------------
Data, CURAGEN Data, CURAGEN Proprietary Material, Inventions and Patent Rights
not expressly granted to BIOGEN hereunder. Upon expiration of any Exclusive
Evaluation Period, 


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CURAGEN shall recover and retain all of CURAGEN's rights to the corresponding
Exclusive Data Set and related Inventions and Patent Rights thereon other than
such rights as BIOGEN may have as provided in Sections 2.1.4, 2.1.5, 2.4.3 and
2.6 or with respect to Optioned Clones. In the event that upon the expiration of
any Option Period the corresponding Option has not been exercised by BIOGEN, all
of CURAGEN's rights in the corresponding Optioned Clone and related Inventions
and Patent Rights thereon shall revert to CURAGEN. Notwithstanding the
foregoing, nothing contained in this Section 7.6 shall be deemed to limit any
rights of BIOGEN expressly provided in an executed License Agreement or an
executed subscription agreement. In addition, BIOGEN shall (a) upon the
expiration of each Exclusive Evaluation Period, without any further action on
its part, be deemed to have granted to CURAGEN an exclusive (except for uses by
BIOGEN permitted in Section 2.4.3), royalty-free license for all purposes under
BIOGEN's rights in Inventions or Patent Rights claiming (i) any Clones other
than [XXXXXXXXXXX] whose sequence or utility is determined in whole or in part
from the use of the corresponding Exclusive Data Set and which are not the
subject of any Option or License Agreement, or (ii) any uses of such Clones, and
(b) upon the expiration of each Option Period, without any further action on its
part, be deemed to have granted to CURAGEN a license as set forth in (a) above
with respect to each Optioned Clone for which an Option has not been exercised.
Prior to any disposition of rights as set forth above or in an executed License
Agreement, BIOGEN shall not assign, encumber or otherwise limit its ownership
interest in any Invention or Patent Right.

     7.7   No Other Rights. BIOGEN shall receive no rights to Data Sets or
           ---------------
Clones under CURAGEN Patent Rights or Inventions except as expressly set forth
herein or in an executed License Agreement.

                            8. TERM AND TERMINATION

     8.1   Term. Unless earlier terminated as provided in this Section 8, the
           ----
term of this Agreement shall be for five (5) years following the Effective Date
plus the length of any available Exclusive Evaluation Periods and any permitted
extensions thereof and the length of

                                      26

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<PAGE>
 
any Options and any permitted extensions thereof, or until the date on which
BIOGEN no longer has access to Project Data Sets, whichever is later (the
"Term").

     8.2   Termination.
           -----------
     (a)   This Agreement and the options granted herein may be terminated by
either Party upon any breach by the other Party of any material obligation or
condition, effective thirty (30) days after giving written notice to the
breaching Party of such termination in the case of a payment breach and sixty
(60) days after giving written notice to the breaching Party of such termination
in the case of any other breach, which notice shall describe such breach in
reasonable detail. The foregoing notwithstanding, if the default or breach is
cured or shown to be non-existent within the aforesaid thirty (30) or sixty (60)
day period, the notice shall be deemed automatically withdrawn and of no effect.

     (b)   If either Party files for protection under bankruptcy laws, makes an
assignment for the benefit of creditors, appoints or suffers appointment of a
receiver or trustee over its property, files a petition under any bankruptcy or
insolvency act or has any such petition filed against it which is not discharged
within sixty (60) days of the filing thereof, then the other Party may terminate
this Agreement by notice to such Party.
 
     8.3   Remedies. If either Party shall fail to perform or observe or
           --------
otherwise breaches any of its material obligations under this Agreement, in
addition to any right to terminate this Agreement, the non-defaulting Party may
elect to obtain other relief and remedies available under law.

     8.4   Surviving Provisions. Notwithstanding any provision herein to the
           --------------------
contrary, the rights and obligations set forth in Sections 2.1.4, 2.1.6 and
2.3.3(b), Articles 4, 5, and 6, Sections 7.6 and 8.4, and Article 9 hereof, as
well as any rights and obligations otherwise accrued, shall survive the
expiration or termination of the Term of this Agreement.

                               9. MISCELLANEOUS

     9.1   CURAGEN Representations and Covenants. CURAGEN represents and
warrants that: (a) the execution and delivery of this Agreement and the
performance of the transactions contemplated hereby have been duly authorized by
all appropriate CURAGEN 


                                      27
<PAGE>
 
corporate action; (b) CURAGEN is under no obligation which is inconsistent with
this Agreement, (c) CURAGEN is not aware of any patent held by any third party
which would prevent CURAGEN's use of its technology in the performance of the
Research Program, and (d) CURAGEN has the full right and legal capacity to grant
the rights to BIOGEN pursuant to Article 7 without violating the rights of any
third party. CURAGEN covenants that (a) CURAGEN will obtain from its employees
and consultants rights of assignment with respect to all Inventions and (b)
CURAGEN will not enter into any agreement with any third party that is
inconsistent with the terms of this Agreement. Nothing in this Agreement shall
be interpreted as obligating either Party to commercialize technology made
hereunder or to perform any additional work beyond that set forth in the
Research Plan.

     9.2   BIOGEN Representations. BIOGEN represents and warrants that: (a) the
           ----------------------  
execution and delivery of this Agreement and the performance of the transactions
contemplated hereby have been duly authorized by all appropriate BIOGEN
corporate action; (b) BIOGEN is under no obligation which is inconsistent with
this Agreement, and (c) BIOGEN has the full right and legal capacity to grant
the rights to CURAGEN pursuant to Article 7 without violating the rights of any
third party. Nothing in this Agreement shall be interpreted as obligating either
Party to commercialize technology made hereunder or to perform any additional
work beyond that set forth in the Research Plan.
 
     9.3   No Warranties.
           -------------
     (a)   Nothing in this Agreement is or shall be construed as:

                         (i)   a warranty or representation by CURAGEN as to the
                 validity or scope of any application or patent within the
                 Patent Rights;

                        (ii)   a warranty or representation that anything made,
                 used, sold or otherwise disposed of under any license granted
                 pursuant to this Agreement is or will be free from infringement
                 of patents, copyrights, and other rights of third parties,
                 except as expressly set forth in Section 9.1.

     (b)   Except as expressly set forth in this Agreement, NEITHER PARTY MAKES
ANY REPRESENTATIONS OR EXTENDS ANY WARRANTIES OF ANY KIND, EITHER EXPRESS OR
IMPLIED. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE, OR OF NON-


                                      28
<PAGE>
 
INFRINGEMENT OF ANY PATENT, COPYRIGHT, TRADEMARK, OR OTHER RIGHTS, OR ANY OTHER
EXPRESS OR IMPLIED WARRANTIES.

     9.4   Liability. NOTWITHSTANDING ANYTHING ELSE IN THIS AGREEMENT OR
           ---------
OTHERWISE, NEITHER PARTY WILL BE LIABLE WITH RESPECT TO ANY SUBJECT MATTER OF
THIS AGREEMENT UNDER ANY CONTRACT, NEGLIGENCE, STRICT LIABILITY OR OTHER LEGAL
OR EQUITABLE THEORY FOR (I) ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL OR PUNITIVE
DAMAGES OR LOST PROFITS OR (II) COST OF PROCUREMENT OF SUBSTITUTE GOODS,
TECHNOLOGY OR SERVICES

     9.5   Notices. Any notices, requests, deliveries, approvals or consents
           -------
required or permitted to be given under this Agreement to BIOGEN or CURAGEN
shall be in writing and shall be personally delivered or sent by telecopy (with
written confirmation to follow via United States first class mail), overnight
courier providing evidence of receipt or certified mail, return receipt
requested, postage prepaid, in each case to the respective address specified
below (or to such address as may be specified in writing to the other Party
hereto):

           CURAGEN:          555 Long Wharf, 11th Floor
                             New Haven, CT   06511
                             Attn: Executive Vice President
                             Telecopy: (203) 401-3333

           BIOGEN:           14 Cambridge Center
                             Cambridge, MA 02142
                             Attn: Director, Marketing and Business Development
                             Telecopy: (617) 679-2804

           with copies to:   Vice President - General Counsel
                             Telecopy:  (617) 679-2838

     Such notices shall be deemed to have been sufficiently given on: (a) the
date sent if delivered in person or transmitted by telecopy, (b) the next
business day after dispatch in the case of overnight courier or (c) five (5)
business days after deposit in the U.S. mail in the case of certified mail.

     9.6   Governing Law. This Agreement will be construed, interpreted and
           -------------
applied in accordance with the laws of the State of Connecticut (excluding its
body of law controlling conflicts of law).

                                      29
<PAGE>
 
     9.7   Limitations. Except as set forth elsewhere in this Agreement, neither
           -----------
Party grants to the other Party any right or license to any of its intellectual
property.
 
     9.8   Entire Agreement. This is the entire Agreement between the Parties
           ----------------
with respect to the subject matter hereof and supersedes all prior agreements
between the Parties with respect to the subject matter hereof. No modification
shall be effective unless in writing with specific reference to this Agreement
and signed by the Parties.

     9.9   Waiver. The terms or conditions of this Agreement may be waived only
           ------
by a written instrument executed by the Party waiving compliance. The failure of
either Party at any time or times to require performance of any provision hereof
shall in no manner affect its rights at a later time to enforce the same. No
waiver by either Party of any condition or term shall be deemed as a continuing
waiver of such condition or term or of another condition or term.

     9.10  Headings. Section and subsection headings are inserted for
           --------
convenience of reference only and do not form part of this Agreement.

     9.11  Assignment. This Agreement may not be assigned by either Party
           ----------
without the consent of the other, except that each Party may, without such
consent, assign this Agreement and the rights, obligations and interests of such
Party, in whole or in part, to any of its Affiliates, to any purchaser of all or
substantially all of its assets in the line of business to which this Agreement
pertains or to any successor corporation resulting from any merger or
consolidation of such Party with or into such corporations.

     9.12  Force Majeure. Neither Party shall be liable for failure of or delay
           -------------
in performing obligations set forth in this Agreement, and neither shall be
deemed in breach of its obligations, if such failure or delay is due to natural
disasters or any causes beyond the reasonable control of such Party. In event of
such force majeure, the Party affected thereby shall use reasonable efforts to
cure or overcome the same and resume performance of its obligations hereunder.

     9.13  Construction. The Parties hereto acknowledge and agree that: (i) each
           ------------
Party and its counsel reviewed and negotiated the terms and provisions of this
Agreement and have contributed to its revision; (ii) the rule of construction to
the effect that any ambiguities are resolved against the drafting Party shall
not be employed in the interpretation of this Agreement; and (iii) the terms and
provisions of this Agreement shall be construed fairly as to all Parties 


                                      30
<PAGE>
 
hereto and not in a favor of or against any Party, regardless of which Party was
generally responsible for the preparation of this Agreement.

     9.14  Severability. If any provision(s) of this Agreement are or become
           ------------
invalid, are ruled illegal by any court of competent jurisdiction or are deemed
unenforceable under then current applicable law from time to time in effect
during the Term hereof, it is the intention of the Parties that the remainder of
this Agreement shall not be affected thereby provided that a Party's rights
under this Agreement are not materially affected. The Parties hereto covenant
and agree to renegotiate any such term, covenant or application thereof in good
faith in order to provide a reasonably acceptable alternative to the term,
covenant or condition of this Agreement or the application thereof that is
invalid, illegal or unenforceable, it being the intent of the Parties that the
basic purposes of this Agreement are to be effectuated.

     9.15  Status. Nothing in this Agreement is intended or shall be deemed to
           ------
constitute a partner, agency, employer-employee, or joint venture relationship
between the Parties.
 
     9.16  Indemnification.
           ---------------

     (a)   BIOGEN shall indemnify, defend and hold harmless CURAGEN, its
Affiliates and their respective directors, officers, employees, and agents and
their respective successors, heirs and assigns (the "CURAGEN Indemnitees"),
against any liability, damage, loss or expense (including reasonable attorneys'
fees and expenses of litigation) incurred by or imposed upon the CURAGEN
Indemnitees, or any of them, in connection with any claims, suits, actions,
demands or judgments of third parties, including without limitation personal
injury matters (except to the extent such claims, suits, actions, demands or
judgments result from a material breach of this Agreement, or the negligence or
willful misconduct on the part of CURAGEN or are the subject matter of CURAGEN's
indemnification of BIOGEN as set forth in Section 9.16(b)) arising out of or
relating to any actions of BIOGEN under this Agreement including, without
limitation, the supply of samples for use in the Research Program.
 
     (b)   CURAGEN shall indemnify, defend and hold harmless BIOGEN, its
Affiliates and their respective directors, officers, employees, and agents and
their respective successors, heirs and assigns (the "BIOGEN Indemnitees"),
against any liability, damage, loss or expense (including reasonable attorneys'
fees and expenses of litigation) incurred by or imposed upon the BIOGEN
Indemnitees, or any of them, in connection with any claims, suits, actions,
demands or judgments of third parties, including without limitation personal
injury matters (except to the extent such claims, suits, actions, demands or

                                       31
<PAGE>
 
judgments result from a material breach of this Agreement, or the negligence or
willful misconduct on the part of BIOGEN) arising out of the performance of the
Research Program by CURAGEN, except to the extent such claims, suits, actions,
demands or judgments are based on the use of the samples or information provided
to CURAGEN by BIOGEN under this Agreement.





                   REMAINDER OF PAGE INTENTIONALLY LEFT BLANK

                                       32
<PAGE>
 
     IN WITNESS WHEREOF, the Parties have caused this Agreement to be executed
by their duly authorized representative in two (2) originals.

BIOGEN, INC.                           CURAGEN CORPORATION

By:                                    By:
   /s/ James R. Tobin                      /s/ Gregory Went
   ---------------------------------       -----------------------------------
Title: President and CEO               Title: Executive Vice President
      ------------------------------         --------------------------------   

                                       33
<PAGE>
 
                                  APPENDIX A

                                Optioned Clones

                                       34
<PAGE>
 
                                  APPENDIX B

                                     Note

                                       35
<PAGE>
 
                                PROMISSORY NOTE

Up to $10,000,000.00                                           __________, 1997


     FOR VALUE RECEIVED, the undersigned, CURAGEN CORPORATION (the "Borrower"),
having an address of 555 Long Wharf Drive, 11th Floor, New Haven, Connecticut
06511, hereby promises to pay to BIOGEN, INC., having an address at 14 Cambridge
Center, Cambridge, MA 02142 (the "Lender"), the principal sum of

                       TEN MILLION DOLLARS ($10,000,000)

or such lesser sum which may from time to time be advanced pursuant to the terms
of the section of the Research and Option Agreement dated October 1, 1997
between the Borrower and the Lender (the "Agreement") entitled "Section 3.2-Loan
Commitment". Capitalized terms used herein and not defined herein have the
meanings assigned to them in the Agreement.

     Payments
     --------

     (a) The Borrower shall pay the accrued interest and principal balance of
this Note, which represents the Loan, in full within fifteen (15) days of the
last day of the Fifth Loan Year, or within one year after any earlier
termination of the Research Program or the Agreement, whichever shall first
occur.

     (b) This Note may be prepaid by Borrower at any time without premium or
penalty.

     (c) Payments pursuant to paragraph (a) or (b) shall be paid in cash or, at
the option of Borrower, in CuraGen Common Stock, valued at its then Fair Market
Value, as set forth in the Agreement.

     Interest
     --------

     (a) Interest shall accrue on the outstanding principal balance hereunder at
a rate per annum equal to Prime plus one percent (1%). Prime shall be determined
and adjusted in accordance with Section 3.2(c) and 3.2(e) of the Agreement.
Interest shall accrue and be paid semi-annually commencing on the six-month
anniversary date of the first advance under the Loan and continuing every six
months thereafter until all amounts due hereunder have been paid in full.

     (b) Payments pursuant to paragraph (a) shall be made in cash or, at the
option of Borrower, in CuraGen Common Stock, valued at its then Fair Market
Value, as set forth in the Agreement.

 
                      [Confidential Treatment Requested]


<PAGE>
 
     Recording of Advances and Repayments
     ------------------------------------

     The advances described in the Agreement and made by the Lender to the
Borrower, and all repayments made on the account of principal thereof, shall be
recorded by the Lender on the Schedule attached hereto which is a part of this
Note; provided, however, that the failure of the Lender so to record on this
Note (or any error in recording on this Note) shall not affect the Borrower's
obligations hereunder.

     Subordination
     -------------

     This Note shall be Subordinated to (i) all secured debt and liabilities of
the Borrower and (ii) all liabilities of the Borrower to institutional or
commercial lenders and equipment lessors existing as of the date hereof or
incurred hereafter (including, without limitation any lease obligations).

     General
     -------

     The Borrower hereby waives presentment, demand, protest or notice of
any kind in connection with this Note. No failure on the part of the Lender in
exercising any right or remedy hereunder, and no single, partial or delayed
exercise by the Lender of any right or remedy shall preclude the full and timely
exercise by the Lender at any time of any right or remedy of the Lender
hereunder without notice. No course of dealing or other conduct, no oral
agreement or representation made by the Lender or usage of trade shall operate
as a waiver of any right or remedy of the Lender. This Note and the Agreement
contain the entire agreement between the parties with respect to the subject
matter hereof, and supersedes every course of dealing, other conduct, oral
agreement or representation previously made by the Lender. In the event that any
court of competent jurisdiction shall determine that any provision, or portion
thereof, contained in this Note shall be unenforceable in any respect, then such
provision shall be deemed limited to the extent that such court deems it
enforceable, and the remaining provisions of this Note shall nevertheless remain
in full force and effect.

     None of the terms or provisions of this Note may be excluded, modified, or
amended except by a written instrument duly executed on behalf of both the
Borrower and the Lender expressly referring hereto and setting forth the
provision so excluded, modified or amended. No waiver or forbearance of any of
the rights and remedies of the Lender hereunder shall be effective unless made
specifically in a writing signed by the Lender, and any such waiver or
forbearance shall be effective only in the specific instance and for the
specific purpose for which given.

     This Note is the "Note" referred to in the Agreement and is entitled to all
of the rights and benefits referred to therein.

     This note is delivered to the Lender at its principal office in
Cambridge, Massachusetts, shall be governed by, and construed and enforced in
accordance with, the laws of the state of 

                                     - 2 -
 
                      [Confidential Treatment Requested]


<PAGE>
 
Connecticut, without regard to its principles of conflicts of laws and shall
take effect as a sealed instrument.

     IN WITNESS WHEREOF, the Borrower has caused this Note to be executed as an
instrument under seal by its duly authorized officer as of the date first above
written.

Witness:                                    CURAGEN CORPORATION


                                    by:
- -------------------------              -------------------------------
                                       (Signature)

                                      ----------------------------
                                      (Print or type name)
                                      its:
                                          ----------------------------
                                      (Title or Capacity)


                                     - 3 -
<PAGE>
 
                          Schedule to Promissory Note
                            dated October ___, 1997
                           from CURAGEN CORPORATION
                                to BIOGEN, INC.
                      in the amount of up to $10,000,000

<TABLE> 
<CAPTION> 

                                            Biogen            CuraGen
Date     Amount Drawn      Amount Repaid    Acknowledgement   Acknowledgement
- ----     ------ -----      ------ ------    ---------------   ---------------
<S>      <C>               <C>              <C>               <C> 





</TABLE> 

                                     - 4 -
<PAGE>
 
                                  APPENDIX C

                           Form of License Agreement

                                       40
<PAGE>
 
                                LICENSE AGREEMENT

     This License Agreement ("Agreement") is made effective as of _________,
_____ (the "Effective Date") by and between BIOGEN, INC., a Massachusetts
corporation having its principal business office at 14 Cambridge Center,
Cambridge, MA 02142 ("BIOGEN"), and CURAGEN CORPORATION, a Delaware corporation
with its principal place of business at 555 Long Wharf Drive, 11th Floor, New
Haven, Connecticut 06511 ("CURAGEN"). BIOGEN and CURAGEN are each hereafter
referred to individually as a "Party" and together as the "Parties".

     WHEREAS, BIOGEN wishes to obtain a license to certain inventions made by
CURAGEN as provided in the Research and Option Agreement between the Parties
hereto dated as of _______, 1997 (the "Research Agreement");

     WHEREAS, CURAGEN has agreed to provide such license under the terms and
conditions set forth herein.

     NOW, THEREFORE, in consideration of the mutual covenants contained herein,
and for other good and valuable consideration, the receipt and adequacy of which
are hereby acknowledged, the Parties hereby agree as follows:

                                 1. DEFINITIONS

     Whenever used in the Agreement with an initial capital letter, the terms
defined in this Section 1 shall have the meanings specified.

     1.1 "Affiliate" shall mean any corporation, firm, limited liability
company, partnership or other entity which directly or indirectly controls or is
controlled by or is under common control with a Party to this Agreement.
"Control" means ownership, directly or through one or more Affiliates, of fifty
percent (50%) or more of the shares of stock entitled to vote for the election
of directors, in the case of a corporation, or fifty percent (50%) or more of
the equity interests in the case of any other type of legal entity, status as a
general partner in any partnership, 

                                       1
<PAGE>
 
or any other arrangement whereby a Party controls or has the right to control
the Board of Directors or equivalent governing body of a corporation or other
entity.

     1.2 "Clone" shall mean a segment of DNA representing a whole or partial
gene whose sequence or utility is determined from the use of one or more Data
Sets.

     1.3 "CURAGEN Background Inventions" shall mean all patent rights and
know-how of CURAGEN, other than those relating primarily to Inventions, which
CURAGEN has the right to license as of the Effective Date or at any time during
the term hereof and which would be infringed by the development, manufacture,
use, sale or importation of a Licensed Product; provided, however, that CURAGEN
Background Inventions shall expressly exclude any patent rights or know-how
specifically relating to Clones or genes not licensed by BIOGEN pursuant to this
Agreement and any patent rights or know-how arising from any CURAGEN
collaboration with a third party, except to the extent permitted thereby.

     1.4 "CURAGEN Data" shall mean, with respect to a Licensed Clone, all
information pertaining to such Licensed Clone obtained by CURAGEN from the
processing of specified CURAGEN samples, including QC data, expression data,
sequence data and any other information obtained or generated by CURAGEN in the
performance of the CURAGEN Project relating to such Licensed Clone.

     1.5 "CURAGEN Data Set" shall mean all CURAGEN Data resulting from a
discrete CURAGEN Project.

     1.6 "CURAGEN Project" shall mean a particular project undertaken by CURAGEN
outside the Research Program to process and analyze a specified set of samples
which do not contain BIOGEN Proprietary Material, and as to which CURAGEN is
free to grant rights to BIOGEN hereunder.

     1.7 "CURAGEN Project Invention" shall mean any discovery, invention,
know-how or trade secret conceived or made by employees of CURAGEN (i) in the
performance of a CURAGEN Project that results in CURAGEN Data that becomes part
of an Exclusive Data Set, 

                                       2
<PAGE>
 
that is based on, incorporates or makes material use of the corresponding
CURAGEN Data or (ii) relating to a Lead.

     1.8 "CURAGEN Proprietary Material" shall mean, with respect to a Licensed
Clone, all substances made by CURAGEN in the performance of the Research Project
relating to such Licensed Clone other than mRNA pools extracted from BIOGEN
Proprietary Material. CURAGEN Proprietary Material shall also mean, with respect
to a Licensed Clone, all substances made by CURAGEN in the performance of the
CURAGEN Project relating to such Licensed Clone, including mRNA pools. CURAGEN
Proprietary Materials shall include, without limitation, QEA fragments and
materials derived or constructed from QEA fragments, including, without
limitation, fragment and full length cDNA clones.

     1.9 "Data Set," which may be either a Project Data Set or a CURAGEN Data
Set, with respect to a Licensed Clone, shall mean all Project Data resulting
from the discrete Research Project relating to the Licensed Clone or all CURAGEN
Data resulting from the discrete CURAGEN Project relating to the Licensed Clone,
respectively.

     1.10 [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXX]

     1.11 "Exclusive Data Set" shall mean any Project Data Set during the
corresponding Exclusive Evaluation Period as provided in Section 2.4 of the
Research Agreement or any CURAGEN Data Set during the corresponding Exclusive
Evaluation Period as provided in Section 2.5.2 of the Research Agreement.

     1.12 "Exclusive Evaluation Period" shall have the meaning set forth in
Section 2.4 or 2.5.2 of the Research Agreement.

     1.13 "Extended License" shall have the meaning set forth in Section 2.3.

     1.14 "Invention," as to each Licensed Clone, shall mean any CURAGEN Project
Invention or Research Project Invention that is based on, incorporates or makes
material use of the Project Data or CURAGEN Data corresponding to the Licensed
Clone.

                                       3
 
                      [Confidential Treatment Requested]


<PAGE>
 
     1.15 [XXXXXXXX] shall have the meaning set forth in Section 2.1.3 of the 
Research Agreement.

     1.16 "Lead" shall mean a lead compound discovered or developed by CURAGEN
outside of the Research Program using a Licensed Clone or the protein expressed
thereby as a target, which lead compound is accepted by BIOGEN for use pursuant
to the terms of this Agreement.

     1.17 "Licensed Clone" shall have the meaning set forth in Section 2.1.

     1.18 "Licensed Product," as to each Licensed Clone, shall have the meaning
set forth in the relevant subsection of Section 2.1.

     1.19 "Net Sales" shall mean [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.

           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXX

           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXX

           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
           XXX

           XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]

                                       4
 
                      [Confidential Treatment Requested]


<PAGE>
 
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXX]

     [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXX]

    1.20 "Optioned Clone" shall have the meaning set forth in Section 7.1 of
the Research Agreement.

     1.21 "Patent Rights," as to each Licensed Clone, mean the rights and
interests in and to issued patents and pending patent applications in any
country, including, but not limited to, all provisional applications,
substitutions, continuations, continuations-in-part, divisions, and renewals,
all letters patent granted thereon, and all reissues, reexaminations and
extensions thereof, whether owned solely or jointly by a Party or licensed in by
a Party, with the right to sublicense, now or in the future, wherein at least
one claim of such patent right is to an Invention. "CURAGEN Patent Rights" shall
mean Patent Rights owned solely or jointly by CURAGEN or licensed in by CURAGEN.

     1.22 "Project Data" shall mean all information obtained by CURAGEN from the
processing of BIOGEN Proprietary Material in a particular Research Project,
including QC data, 

                                       5

                      [Confidential Treatment Requested]


<PAGE>
 
expression data, sequence data and any other information obtained or generated
by CURAGEN in the performance of the Research Project relating to such Licensed
Clone.

     1.23 "Project Data Set" shall mean all Project Data resulting from a
discrete Research Project.

     1.24 "Research Program" shall mean the Research Program to be performed by
CURAGEN under the Research Agreement.

     1.25 "Research Project" shall mean a particular project to process and
analyze a specified set of samples in the Research Program.

     1.26 "Research Project Invention" shall mean any discovery, invention,
know-how or trade secret conceived or made by employees of CURAGEN or BIOGEN or
jointly by employees of both, (a) in the performance of a Research Project
hereunder, or (b) in the course of evaluating any Exclusive Data Set, in each
case that is based on, incorporates or makes material inventive use of the
corresponding Project Data or CURAGEN Data.

     1.27 "Sublicensee" shall mean any non-Affiliate third party expressly
sublicensed by BIOGEN under the license granted to BIOGEN hereunder, to make,
have made, use, have used, offer to sell, sell, have sold, import or have
imported any Licensed Product.

     1.28 "Territory" shall mean the world.

     1.29 "Valid Claim(s)" shall mean an unexpired claim of (i) any issued
patent within Patent Rights which has not been finally declared invalid or
unenforceable by a patent office or by a court or other body of competent
jurisdiction in any unappealed or unappealable decision and which has not been
lost through an interference or opposition proceeding or (ii) any pending patent
application within Patent Rights which has not been finally rejected by a patent
office of competent jurisdiction in any unappealed or unappealable decision and
which has not been pending for more than seven (7) years.

                                       6
<PAGE>
 
                                2. LICENSE GRANT

     2.1. License Grant. Upon exercise of an Option pursuant to Section 7.4 of
          -------------
the Research Agreement for any Optioned Clone, BIOGEN shall elect one of the
following license types and the Parties shall indicate such election on Schedule
I attached hereto and shall complete the information on Schedule I for such
Optioned Clone and sign such Schedule I. Such Optioned Clone shall thereafter be
deemed a Licensed Clone. Additionally, upon written request of BIOGEN made
pursuant to Section 7.5 of the Research Agreement for any [XXXXXXXXXXX], BIOGEN
shall elect one of the following license types and the Parties shall indicate
such election on Schedule I attached hereto and shall complete the information
on Schedule I for such [XXXXXXXXXXXXXX] and sign such Schedule I. Such [XXXXXXX
XXXXX] shall thereafter be deemed a Licensed Clone.

     (a) For each Licensed Clone listed on Schedule I for which a Section 2.1(a)
exclusive license is elected subject to the rights reserved to CURAGEN in
Section 2.5 below, CURAGEN hereby grants to BIOGEN an exclusive license (even as
to CURAGEN) in the Territory, to develop, make, have made, use, have used, sell,
have sold, offer for sale, import and have imported products (i) incorporating
or derived from such Licensed Clone or the protein expressed thereby, (ii)
discovered or developed using any such Licensed Clone or the protein expressed
thereby as a target or (iii) discovered or developed using a Lead which was
itself discovered or developed using such Licensed Clone or the protein
expressed thereby as a target ("Licensed Products"), for any and all human uses,
under (x) all Patent Rights, Inventions, and CURAGEN Proprietary Material
pertaining to such Licensed Clone or the uses thereof, including but not limited
to Patent Rights claiming whole or partial sequences or utility and (y) all
Patent Rights and know-how of CURAGEN which CURAGEN has the right to license to
BIOGEN relating to Leads discovered or developed using the Licensed Clone or the
protein expressed thereby as a target. Such license shall be perpetual unless
terminated as set forth herein.

     (b) For each Licensed Clone listed on Schedule I for which a Section 2.1(b)
exclusive license is elected and which was "known" by third parties prior to the
exercise of the corresponding Option as determined pursuant to subsection (d)
below, subject to the rights reserved to CURAGEN in Section 2.5 below, CURAGEN
hereby grants to BIOGEN an 

                                       7
 
                      [Confidential Treatment Requested]


<PAGE>
 
exclusive license (even as to CURAGEN) in the Territory, to develop, make, have
made, use, have used, sell, have sold, offer for sale, import and have imported
products (i) incorporating or derived from such Licensed Clone or the protein
expressed thereby, (ii) discovered or developed using any such Licensed Clone or
the protein expressed thereby as a target or (iii) discovered or developed using
a Lead which was itself discovered or developed using such Licensed Clone or the
protein expressed thereby as a target ("Licensed Products"), for any and all
human uses, under (x) all Patent Rights, Inventions, and CURAGEN Proprietary
Material pertaining to such Licensed Clone or the uses thereof, including but
not limited to Patent Rights claiming whole or partial sequences or utility and
(y) all Patent Rights and know-how of CURAGEN which CURAGEN has the right to
license to BIOGEN relating to Leads discovered or developed using the Licensed
Clone or the protein expressed thereby as a target. Such license shall be
perpetual unless terminated as set forth herein.

     (c) For each Licensed Clone listed on Schedule I for which a Section 2.1(c)
non-exclusive license is elected, CURAGEN hereby grants to BIOGEN a
non-exclusive license in the Territory to use such Licensed Clone or the protein
expressed thereby as a target for discovering or developing small molecule drugs
and to develop, make, have made, use, have used, sell, have sold, offer for
sale, import and have imported any small molecule discovered or developed by
BIOGEN using such Licensed Clone or the protein expressed thereby as a target
("Licensed Products"), for any and all human uses, under all Patent Rights,
Inventions, and CURAGEN Proprietary Materials pertaining to such Licensed Clone
or the uses thereof, including but not limited to Patent Rights claiming whole
or partial sequences or utility. Such license shall be perpetual unless
terminated as set forth herein.

     (d) The Parties shall mutually agree in good faith on whether any Licensed
Clone is "known" by third parties prior to the exercise of an Option, based
primarily on the availability of the whole or substantially whole coding domains
identical to such Licensed Clone in publicly available literature or databases.
Licensed Clones which are "known" only as a result of either a previous Research
Project or a CURAGEN Project from which BIOGEN received access to an Exclusive
Data Set from which the Licensed Clone was optioned, and are not "known" to
third 

                                       8
<PAGE>
 
parties other than through any disclosure of research results related to such
Research Project or CURAGEN Project, shall not be deemed "known" for the
purposes hereof.

     (e) A Licensed Product will be deemed to be discovered or developed using a
Licensed Clone or the protein expressed thereby as a target if the Licensed
Clone or the whole or partial sequence thereof or the protein expressed thereby
is utilized in any material way in the discovery, development, modification or
testing of the Licensed Product, or of analogs thereof or of molecules used in
the discovery, development or modification thereof.

     2.2 Non-exclusive License. CURAGEN hereby grants to BIOGEN a non-exclusive
         ---------------------
license, coterminus with each license grant in Section 2.1, under CURAGEN
Background Inventions solely to the extent necessary to allow BIOGEN to practice
the license granted in Section 2.1 and for no other purpose.
 
     2.3 Extended License. In the event that (a) CURAGEN is the owner of any
         ----------------
patent or patent application resulting from any activities other than the
Research Program that claims (i) any Licensed Clone, (ii) the protein expressed
by such Licensed Clone, (iii) any product discovered or developed using any such
Licensed Clone or the protein expressed thereby as a target, or (iv) a human
gene functionally equivalent to such Licensed Clone [XXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] and (b) CURAGEN is not utilizing
the invention or inventions claimed in such patent or application in a research
or development project then being actively planned or conducted by CURAGEN
(alone or in collaboration with any third party), and (c) CURAGEN has the right
to grant a license thereunder to BIOGEN, then any license granted to BIOGEN
under Section 2.1(a) or (b) shall include a license to such patent or patent
applications (an "Extended License").

     2.4 Due Diligence. BIOGEN shall use commercially reasonable efforts, at
         -------------
least equivalent to those efforts which BIOGEN uses with respect to its own
products, to develop, test, obtain regulatory approval of, market and sell
Licensed Products with respect to each Licensed Clone; provided, however, that
BIOGEN shall not be required hereby to be actively developing [XXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] at any
one time. Failure to use 

                                       9

                      [Confidential Treatment Requested]

<PAGE>
 
diligent efforts as set forth herein for a given Licensed Clone shall give
CURAGEN the right, but not the obligation, to terminate BIOGEN's license
hereunder with respect to such Licensed Clone.

     2.5 Reservation of Rights. Notwithstanding anything in this Agreement to
         ---------------------
the contrary, CURAGEN hereby retains for itself the right to use each Licensed
Clone and the proteins derived therefrom for as part of a general library of
nucleic acids, which library is used for research purposes.

     2.6 Sublicenses. BIOGEN shall have the right to grant sublicenses to all or
         -----------
any portion of its rights under any license granted herein to any Affiliate or
Sublicensee, provided, however, that BIOGEN shall remain obligated to ensure
payment of royalty and milestone obligations as set forth in Article 3.

                                3. CONSIDERATION

     3.1 License Fees. Upon exercise of an Option pursuant to Section 7.1.2 of
         ------------
the Research Agreement for any Optioned Clone, BIOGEN shall pay to CURAGEN the
license fee specified in the Research Agreement which shall be as set forth
below:
<TABLE> 
<CAPTION> 

     License Type                                          $ (thousands)
     ------------                                          -------------
     <S>                                                   <C> 
     Exclusive license under Section 2.1(a)                       [XXX]
     Exclusive license under Section 2.1(b)                       [XXX]
     Non-exclusive license under Section 2.1(c)                   [XXX]
</TABLE> 

No license fees shall be due with respect to [XXXXXXXXXXXX] licensed during the
Exclusive Evaluation Period of the [XXXX] [XXXXXX]. Additionally, [XXXXXXXX]
fees shall be due with respect to the [XXXXXXXXX] Optioned Clones which are
licensed hereunder.

     3.2 Milestone Payments for Therapeutic or Prophylactic Products.
         -----------------------------------------------------------

                                      10

                      [Confidential Treatment Requested]

<PAGE>
 
     3.2.1 Milestone Payments under Exclusive License. BIOGEN shall make the
           ------------------------------------------
following milestone payments to CURAGEN for each therapeutic or prophylactic
Licensed Product under an exclusive license under Section 2.1(a) or Section
2.1(b):

           (a) [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days following
           the date BIOGEN or an Affiliate or Sublicensee files the first
           Investigational New Drug application (or foreign equivalent) with the
           FDA (or equivalent foreign regulatory agency) for the Licensed
           Product ("IND");

           (b) [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days following
           the date BIOGEN or an Affiliate or Sublicensee commences the first
           Phase III or Phase II/III clinical trial in any country for the
           Licensed Product;

           (c) [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days following
           the date BIOGEN or an Affiliate or Sublicensee submits the first
           Biologics License Application, Product License Application, New Drug
           Application or other application for approval to sell the Licensed
           Product to the FDA (or equivalent foreign regulatory agency) for the
           Licensed Product;

           (d)  [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days following
           the date BIOGEN or an Affiliate or Sublicensee receives FDA (or
           equivalent foreign regulatory agency) approval of the Licensed
           Product for commercial sale; and

           (e) [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within
           forty-five (45) days following the end of the first calendar year in
           which annual gross sales of such Licensed Product exceed [XXXXX
           XXXXXXXX] provided that such event has occurred prior to the end of
           the fifth full calendar year following first commercial sale in the
           United States or Europe of such Licensed Product.

     3.2.2 Milestone Payments under Non-exclusive License. BIOGEN shall make the
           ----------------------------------------------
following milestone payments to CURAGEN for each therapeutic or prophylactic
Licensed Product covered by a non-exclusive license under Section 2.1(c):

                                      11

                      [Confidential Treatment Requested]

<PAGE>
 
           (a)   [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10)
           days following the date BIOGEN or an Affiliate or Sublicensee files
           the first Investigational New Drug application (or foreign
           equivalent) with the FDA (or equivalent foreign regulatory agency)
           for the Licensed Product ("IND");

           (b)   [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days
           following the date BIOGEN or an Affiliate or Sublicensee commences
           the first Phase III or Phase II/III clinical trial in any country for
           the Licensed Product;

           (c)   [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10)
           days following the date BIOGEN or an Affiliate or Sublicensee submits
           the first Biologics License Application, Product License Application,
           NDA or other application for approval to sell the Licensed Product to
           the FDA (or equivalent foreign regulatory agency) for the Licensed
           Product;

           (d)   [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days following
           the date BIOGEN or an Affiliate or Sublicensee receives FDA (or
           equivalent foreign regulatory agency) approval of the Licensed
           Product for commercial sale; and

           (e)   [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10) days following
           the end of the first calendar year in which annual gross sales of
           such Licensed Product exceed [XXXXXXXXXXX] provided that such event
           has occurred prior to the end of the fifth full calendar year
           following first commercial sale in the United States or Europe of
           such Licensed Product.

           3.2.3 [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
                 ---------------
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
[XXXXXXXXXXXXXXX]

     3.3   Milestone Payments for Diagnostic Products. BIOGEN shall make the
           ------------------------------------------
following milestone payment to CURAGEN for each diagnostic Licensed Product
under an exclusive license under Section 2.1(a) or Section 2.1(b):

                                      12

                      [Confidential Treatment Requested]

<PAGE>
 
          [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] within ten (10)
          days following the date BIOGEN or an Affiliate or Sublicensee
          receives FDA (or equivalent foreign regulatory agency)
          approval of the Licensed Product for commercial sale.

     Notwithstanding the foregoing, the milestone payment set forth above shall
not be due with respect to any Licensed Product with a substantially similar
purpose and format to one for which such milestone has already been paid to
CURAGEN.

     3.4   Royalties on Licensed Products from Research Project Inventions.
           ---------------------------------------------------------------
BIOGEN shall pay to CURAGEN a royalty on Net Sales of Licensed Products if the
sequence and/or utility of the relevant Licensed Clone is a Research Project
Invention or if the Licensed Product results from a Research Project Invention
or a Lead using a Licensed Clone which is a Research Project Invention as
follows:

     (a)   If the Licensed Product is: (1) a recombinant protein form of a
naturally occurring protein or a modified form or fragment thereof ("Protein
Product"), (2) a product involving insertion of nucleic acid into a human host
in order to induce cells in such host to express the protein encoded by such
nucleic acid for therapeutic benefit, or a product involving ex vivo insertion
of nucleic acid into human cells where such cells are then reimplanted into a
human to express the protein encoded by such nucleic acid for therapeutic
benefit ("Gene Therapy Product"), (3) a product designed to activate the
expression of an endogenous gene ("Gene Activation Product"), (4) a product
which is an oligonucleotide which binds to mRNA in vivo to inhibit or block
                                                -------
protein production ("Anti-sense/ribozyme Product"), or (5) an antibody to the
protein encoded by a Licensed Clone ("Antibody Product"), the royalty rate on
Net Sales of such Licensed Product shall be as follows:

                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXX
 
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXX]

                                      13

                      [Confidential Treatment Requested]

<PAGE>
 
                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXX]

     (b)   If the Licensed Product is a small molecule discovered or developed
using a Licensed Clone or the protein expressed thereby as a target, which
target is non-exclusively licensed by BIOGEN pursuant to the provisions of
Section 2.1(c), the royalty rate on Net Sales of such Licensed Product shall be:

                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXX    
      
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXX]          

     (c)   If the Licensed Product is a small molecule discovered or developed
using a Licensed Clone or the protein expressed thereby as a target (and is not
derived from, or a chemical, structural or functional analog of, a Lead), which
target is exclusively licensed by BIOGEN pursuant to the provisions of Sections
2.1(a) or (b), the royalty rate on Net Sales of 


                                      14

                      [Confidential Treatment Requested]

<PAGE>
 
such Licensed Product shall be negotiated in good faith by the Parties prior to
the commencement of pre-clinical regulatory testing of such Licensed Product;
provided, however, that in no event shall the negotiated royalty rates be less
than those set forth in Section 3.4(b) above.

     (d)   If the Licensed Product is derived from, or is a chemical, structural
or functional analog of, a Lead identified by CURAGEN and provided to BIOGEN
pursuant to an exclusive license granted pursuant to the provisions of Section
2.1 (a) or (b), the royalty rate on Net Sales of such Licensed Product shall be:

                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXX
 
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                                    
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXX
                 
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
                 

     (e)   If the Licensed Product is a diagnostic product or any product other
than one whose royalty rate is set forth in Section 3.4(a), (b), (c) or (d)
above, then the royalty rate on Net Sales of such Licensed Product shall be:

                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]


                                      15

                      [Confidential Treatment Requested]

<PAGE>
 
                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXX]
 

     Notwithstanding the foregoing, in no event shall BIOGEN be obligated
pursuant to this subsection (e) to pay to CURAGEN more than [XXXXXXXXXXXXXXXXX]
of the running royalties received by BIOGEN or its Affiliates from a Sublicensee
with respect to any such Licensed Product.

     (f)   Royalties due to CURAGEN pursuant to subsections (a), (b), (c), (d)
or (e) above for a given Licensed Product [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] may be reduced by (i) [XXXXXXXXXXXXXXXXX] of
any royalties paid to third parties by BIOGEN on net sales of such Licensed
Product under licenses that are required [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] and
(ii) [XXXXXXXXXXXXX] of any royalties in excess of a total of [XXXXXXXXXX
XXXX] paid to third parties by BIOGEN on net sales of such Licensed Product 
under licenses [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]. Royalties due
to CURAGEN pursuant to subsections (a), (b), (c), (d) or (e) above for a given
Licensed Product [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] of any royalties paid to third parties by
BIOGEN on net sales of such Licensed Product under licenses [XXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]. [XXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]



                                      16

                      [Confidential Treatment Requested]

<PAGE>
 
     3.5   Royalties on Licensed Products from CURAGEN Project Inventions.
           --------------------------------------------------------------
BIOGEN shall pay to CURAGEN a royalty on Net Sales of Licensed Products if (i)
the sequence and/or utility of the relevant Licensed Clone is a CURAGEN Project
Invention or if the Licensed Product results from a CURAGEN Project Invention or
a Lead developed using a Licensed Clone which is a CURAGEN Project Invention, or
(ii) the manufacture, use or sale of the Licensed Product is covered by an
Extended License, as follows:

     (a)   If the Licensed Product is: (1) a recombinant protein form of a
naturally occurring protein or a modified form or fragment thereof ("Protein
Product"), (2) a product involving insertion of nucleic acid into a human host
in order to induce cells in such host to express the protein encoded by such
nucleic acid for therapeutic benefit, or a product involving ex vivo insertion
of nucleic acid into human cells where such cells are then reimplanted into a
human to express the protein encoded by such nucleic acid for therapeutic
benefit ("Gene Therapy Product"), (3) a product designed to activate the
expression of an endogenous gene ("Gene Activation Product"), (4) a product
which is an oligonucleotide which binds to mRNA in vivo to inhibit or block
                                                -------
protein production ("Anti-sense/ribozyme Product"), or (5) an antibody to the
protein encoded by a Licensed Clone ("Antibody Product"), the royalty rate on
Net Sales of such Licensed Product shall be as follows:

                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXX 
                 
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXX]


     (b)   If the Licensed Product is a small molecule discovered or developed
using a Licensed Clone or the protein expressed thereby as a target, which
target is non-exclusively licensed by BIOGEN pursuant to the provisions of
Section 2.1(c), the royalty rate on Net Sales of such Licensed Product shall be:



                                      17

                      [Confidential Treatment Requested]

<PAGE>
 
                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXX]


     (c)   If the Licensed Product is a small molecule discovered or developed
using a Licensed Clone or the protein expressed thereby as a target (and is not
derived from, or a chemical, structural or functional analog of, a Lead), which
target is exclusively licensed by BIOGEN pursuant to the provisions of Sections
2.1(a) or (b), the royalty rate on Net Sales of such Licensed Product shall be
negotiated in good faith by the Parties prior to the commencement of
pre-clinical regulatory testing of such Licensed Product; provided, however,
that in no event shall the negotiated royalty rates be less than those set forth
in Section 3.5(b) above.

     (d)   If the Licensed Product is derived from, or is a chemical, structural
or functional analog of, a Lead identified by CURAGEN and provided to BIOGEN
pursuant to an exclusive license granted pursuant to the provisions of Section
2.1 (a) or (b), the royalty rate on Net Sales of such Licensed Product shall be:

                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXX]
 


                                      18

                      [Confidential Treatment Requested]

<PAGE>
 
                    [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
  
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXX
             
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]

     (e)   If the Licensed Product is a diagnostic product or any product other
than one whose royalty rate is set forth in Section 3.5(a), (b), (c) or (d)
above, then the royalty rate on Net Sales of such Licensed Product shall be:

                 [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]

     Notwithstanding the foregoing, in no event shall BIOGEN be obligated
pursuant to this subsection (e) to pay to CURAGEN more than [XXXXXXXXXXXXXXXXX]
of the running royalties received by BIOGEN or its Affiliates from a Sublicensee
with respect to any such Licensed Product.

     (f)   Royalties due to CURAGEN pursuant to subsections (a), (b), (c), (d)
or (e) above for a given Licensed Product [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] may be reduced by (i) [XXXXXXXXXXXXXXXXXX] of
any royalties paid to third parties by BIOGEN on net sales of such Licensed
Product under licenses that are required [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] and
(ii) [XXXXXXXXXXXXX] of any royalties in excess of a total of [XXXXXXXXXXX
XXX] paid to third parties by BIOGEN on net sales of such Licensed Product under
licenses [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]. Royalties due to CURAGEN
pursuant to subsections (a), (b), (c), (d) or 



                                      19

                      [Confidential Treatment Requested]

<PAGE>
 
(e) above for a given Licensed Product [XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX] of any royalties paid
to third parties by BIOGEN on net sales of such Licensed Product under licenses
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXX]

     3.6   One Royalty. Only one royalty, calculated at the highest applicable
           -----------
royalty rate hereunder, shall be payable to CURAGEN hereunder for each sale of a
Licensed Product.

     3.7   Payment Terms.
           -------------
     (a)   Royalty payments shall be made to CURAGEN in United States Dollars
[XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXX]  Each royalty payment shall be accompanied by a
report summarizing the total Net Sales for each Licensed Product [XXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXX]

     (b)   All royalties shall be payable in full in the United States in United
States Dollars, regardless of the countries in which sales are made. For the
purpose of computing Net Sales for Licensed Products sold in a currency other
than United States dollars, such currency shall be converted into United States
dollars at the exchange rate for buying U.S. dollars set forth in The Wall
                                                                  -------- 
Street Journal for the last business day of the calendar quarter.
- --------------

     3.8   Royalty Term. BIOGEN shall pay royalties with respect to each
           ------------
Licensed Product on a country by country basis until (i) the expiration or
revocation or complete rejection of the last to expire or to be revoked or to be
completely rejected of any Valid Claim of a Patent Right covering such Licensed
Product in such country, or (ii) ten (10) years from the first commercial sale
of such Licensed Product in such country, whichever is later. Following such
period, BIOGEN shall have a fully paid-up, irrevocable license in such country
under the relevant Patent Rights and Inventions and CURAGEN Background
Inventions, to make, have made, use,

                                      20

                      [Confidential Treatment Requested]


<PAGE>
 
have used, sell, have sold, offer for sale, import and have imported such
Licensed Product in such country.

     3.9   Overdue Royalties. Royalties not paid within the time period set
           -----------------
forth in this Article 3 shall bear interest at a rate of [XXXXXXXXXXXXXXXXXX
XXXXXXX] from the due date until paid in full.

    3.10   Records Retention. Audits. BIOGEN, its Affiliates and Sublicensees
           -------------------------
shall keep for three (3) years from the date of each payment of royalties
complete and accurate records of sales by BIOGEN and its Affiliates and
Sublicensees of each Licensed Product in sufficient detail to allow the accruing
royalties to be determined accurately. CURAGEN shall have the right for a period
of three (3) years after receiving any report or statement with respect to
royalties due and payable to appoint an independent certified public accountant
reasonably acceptable to BIOGEN to inspect the relevant records of BIOGEN and
its Affiliates and Sublicensees to verify such report or statement. BIOGEN and
its Affiliates and Sublicensees shall each make its records available for
inspection by such independent certified public accountant during regular
business hours at such place or places where such records are customarily kept,
upon reasonable notice from CURAGEN, solely to verify the accuracy of the
reports and payments. Such inspection right shall not be exercised more than
once in any calendar year nor more than once with respect to sales of any
Licensed Product in any given payment period. CURAGEN agrees to hold in strict
confidence all information concerning royalty payments and reports, and all
information learned in the course of any audit or inspection, except to the
extent necessary for CURAGEN to reveal such information in order to enforce its
rights under this Agreement or if disclosure is required by law, regulation or
judicial order. The results of each inspection, if any, shall be binding on both
Parties. CURAGEN shall pay for such inspections, except that in the event there
is any upward adjustment in aggregate royalties payable for any year shown by
such inspection of more than [XXXXXXXXXXXXXX] of the amount paid, BIOGEN shall
pay for such inspection.

     3.11  Tax Withholding. CURAGEN agrees that any tax burden levied by any
           --------------- 
countries foreign to the United States covered by this Agreement on receipt by
CURAGEN of royalties from BIOGEN under this Agreement shall be borne by CURAGEN.
In the event that 


                                      21

                      [Confidential Treatment Requested]

<PAGE>
 
such tax is required to be withheld by BIOGEN, its Affiliates, licensees or
Sublicensees, it shall deliver to CURAGEN a statement including the amount of
tax withheld and justification therefor, and such other information as may be
necessary for United States foreign tax credit purposes.

                   4. TREATMENT OF CONFIDENTIAL INFORMATION

     4.1   Confidential Information. During the term of this Agreement, each
           ------------------------
Party may disclose to the other proprietary technical and business information
(collectively, "Confidential Information"). For a period of [XXXXXXXXXX] after
the receipt of any such Confidential Information, the receiving Party shall keep
confidential all such Confidential Information of the other Party and will not
disclose such Confidential Information of the other Party to third parties by
publication or otherwise. Each Party further agrees not to use Confidential
Information of the other Party for any purpose other than exercising any rights
granted to it or reserved by it hereunder. Notwithstanding the foregoing, it is
understood and agreed that the receiving Party's obligations of confidentiality
and nonuse herein shall not apply to any information which:

           (a)   is, at the time of disclosure by the disclosing Party
           hereunder, or thereafter becomes, a part of the public domain or
           publicly known or available through no fault or negligence of the
           receiving Party or any of its Affiliates; or

           (b)   was otherwise in the receiving Party's lawful possession prior
           to disclosure by the disclosing Party, as demonstrated by the
           receiving Party's written records; or

           (c)   is lawfully disclosed to the receiving Party or any of its
           Affiliates on a non-confidential basis by a third party who is not in
           violation of an obligation of confidentiality to the disclosing Party
           relative to such information.

     4.2   Press Release and Regulatory Filings. The Parties shall mutually
           ------------------------------------
agree on a press release announcing the execution of this Agreement and on any
confidential treatment request to be filed with the Securities and Exchange
Commission with respect to this Agreement.

                                      22

                      [Confidential Treatment Requested]

<PAGE>
 
Once any written statement is approved for disclosure by both Parties, either
Party may make subsequent public disclosures of the contents of such statement
without the further approval of the other Party.


              5. PROVISIONS CONCERNING THE FILING, PROSECUTION AND
                          MAINTENANCE OF PATENT RIGHTS
 
     5.1 Patent Filing. During the term of this Agreement, with respect to any
         -------------
Patent Rights or Inventions licensed hereunder:

     (a) Upon inclusion of a Licensed Clone or Lead under the terms of this
Agreement, CURAGEN and BIOGEN shall meet to discuss the feasibility of filing
requests for divisional patent applications in order to create Patent Rights
relating solely to Licensed Clones or Leads which are exclusively licensed
hereunder and not to other Clones or Inventions. CURAGEN shall cause such
actions to be taken if the Parties reasonably agree that such actions are
feasible and desirable.

     (b) BIOGEN shall have the right to prepare, file, prosecute, obtain and
maintain, at its expense, all Patent Rights relating solely to Licensed Clones
or Leads which are exclusively licensed hereunder. CURAGEN agrees to provide
reasonable assistance and cooperation to BIOGEN to facilitate such filing,
prosecution and maintenance. BIOGEN agrees that any such preparation, filing,
prosecution and maintenance shall be conducted with reasonable diligence and
that CURAGEN shall be kept fully informed of the progress thereof and provided
with copies of all material documents pertaining thereto. CURAGEN shall,
whenever possible, be given the opportunity to review and comment in advance on
any patent filings or other correspondence with the patent office during such
periods and BIOGEN shall consider incorporating any comments provided by CURAGEN
in good faith.

     (c) Except as provided in (b) above, CURAGEN shall have the first right
(but not the obligation) to prepare, file, prosecute, obtain and maintain patent
applications and patents on Inventions relating to the Licensed Clones or Leads
which are licensed hereunder at its sole expense. BIOGEN agrees to provide
reasonable assistance and cooperation to CURAGEN to 

                                      23
<PAGE>
 
facilitate such filing, prosecution and maintenance. CURAGEN agrees that any
such preparation, filing, prosecution and maintenance shall be conducted with
reasonable diligence and that BIOGEN shall be kept fully informed of the
progress thereof and provided with copies of all material documents pertaining
thereto during the term of this agreement. BIOGEN shall, whenever possible, be
given the opportunity to review and comment in advance on any patent filings or
other correspondence with the patent office during such periods and CURAGEN
shall consider incorporating any comments provided by BIOGEN in good faith.

     (d) CURAGEN may elect not to exercise its first right to prepare, file,
prosecute, obtain and maintain patent applications and patents on Inventions as
described in Section 5.1(c) above at any time for any such patent applications
and patents by giving written notice thereof to BIOGEN. Such notice shall
specifically identify the patent application(s) and/or patent(s) for which
CURAGEN wishes to relinquish such first right. Following the receipt of such
notice, BIOGEN shall have the right to prepare, file, prosecute, obtain and
maintain the patent application(s) and patent(s) identified in the notice, at
its sole expense, on behalf of the owner of the Invention, subject to the rights
granted herein, during the term of this Agreement.

     (e) The Parties shall mutually agree before permitting any patent
application or patent within Patent Rights exclusively licensed hereunder to
lapse as well as before authorizing any amendment to any patent application or
patent within such Patent Rights that would irrevocably limit the lawful scope
of the Patent Rights.

     (f) BIOGEN may elect not to exercise its right to prepare, file, prosecute,
obtain and maintain patent applications and patents on Inventions or Leads as
described in Section 5.1(b) above at any time for any such Patent Rights by
giving written notice thereof to CURAGEN. Such notice shall specifically
identify the patent application(s) and/or patent(s) for which BIOGEN wishes to
relinquish such right. Following the receipt of such notice, CURAGEN shall have
the right to prepare, file, prosecute, obtain and maintain the patent
application(s) and patent(s) identified in the notice, at its sole expense, and
CURAGEN shall thereafter be deemed the sole owner of any such application or
patent, and any such patents and patent applications shall be removed from
operation of this Agreement.

     (g) No Party shall have any obligation under this Agreement to pay any fees
or costs: (i) for bringing a lawsuit or other action to enforce any of the
Patent Rights against an actual or 

                                      24
<PAGE>
 
suspected infringement or (ii) for any other Party to obtain for its own benefit
independent business or legal advice concerning any of the Patent Rights.

     5.2 Notice of Infringement. If, during the term of this Agreement or the
         ----------------------
term of any license hereunder, either Party learns of any infringement or
threatened infringement by a third party of the patents within Patent Rights,
such Party shall promptly notify the other Party and shall provide such other
Party with available evidence of such infringement.
 
     5.3 Infringement. BIOGEN shall have the first right (but not the
         ------------ 
obligation), at its own expense, to bring suit (or other appropriate legal
action) against any actual or suspected infringement of the Patent Rights
licensed hereunder provided that BIOGEN has an exclusive license to the
infringed claim(s) of any such Patent Right pursuant to Article 2. If BIOGEN
does not take such action within one hundred twenty (120) days after written
notice from CURAGEN of the infringement, CURAGEN shall have the right (but not
the obligation), at its own expense, to bring suit against such infringement.
Any amount recovered, whether by judgment or settlement, shall first be applied
to reimburse the costs and expenses (including attorneys' fees) of the Party
bringing suit, then to the costs and expenses (including attorneys' fees), if
any, of the other Party. Any amounts remaining shall be allocated [XXXXXXXXXXX
XXXXXX] to the Party bringing suit and [XXXXXXXXXX] to the other Party or
shall be allocated one-half to each Party if the suit is brought jointly.

     5.4 Cooperation. Each Party shall, at the expense of the other Party,
         -----------
execute all papers and perform such other acts as may be reasonably required to
maintain any infringement suit brought in accordance with Section 5.3 above
(including giving legal consent for bringing such suit, and agreeing to be named
as a plaintiff or otherwise joined in such suit), and at its option and expense,
may be represented in such suit by counsel of its choice.

                             6. TERM AND TERMINATION

     6.1. Termination Provisions.
          ----------------------
     (a) This Agreement and the licenses granted herein may be terminated by
CURAGEN upon any breach by BIOGEN of any material obligation or condition,
effective thirty (30) days 

                                      25

                      [Confidential Treatment Requested]

<PAGE>
 
after giving written notice to BIOGEN of such termination in the case of a
payment breach and sixty (60) days after giving written notice to BIOGEN of such
termination in the case of any other breach, which notice shall describe such
breach in reasonable detail; provided, however, that a breach of Section 2.4
shall only give rise to the termination rights specified therein. The foregoing
notwithstanding, if the default or breach is cured or shown to be non-existent
within the aforesaid thirty (30) or sixty (60) day period, the notice shall be
deemed automatically withdrawn and of no effect.

     (b) If either Party files for protection under bankruptcy laws, makes an
assignment for the benefit of creditors, appoints or suffers appointment of a
receiver or trustee over its property, files a petition under any bankruptcy or
insolvency act or has any such petition filed against it which is not discharged
within sixty (60) days of the filing thereof, then the other Party may terminate
this Agreement by notice to such Party.

     6.2 Effect of Termination.
         ---------------------

     (a) Upon termination of this Agreement under Section 6.1, all relevant
licenses and sublicenses granted by CURAGEN to BIOGEN hereunder shall terminate
automatically and BIOGEN shall promptly transfer to CURAGEN all related Licensed
Clones, Leads, Data Sets and CURAGEN Proprietary Material in its possession
without retaining any copies thereof, as well as any full-length sequence data
relating to such Licensed Clone(s) and a summary of any safety information
generated by or at the direction of BIOGEN with respect to products derived from
such Licensed Clone(s) or Leads. In addition, upon any termination pursuant to
Section 6.1(a), BIOGEN shall be deemed without any further action to have
granted to CURAGEN an exclusive, worldwide, royalty-free license (including the
right to grant sublicenses), under BIOGEN's ownership interest in any Inventions
and Patent Rights covering or related to the relevant Licensed Clone(s) or Leads
to develop, have developed, make, have made, use, have used, offer for sale,
sell, have sold, import and have imported any and all products in all fields.

     (b) Documentation. At the request of CURAGEN, BIOGEN shall execute and
         -------------
deliver such bills of sale, assignments and licenses and other documents, if
any, as may be 

                                      26
<PAGE>
 
necessary to fully vest in CURAGEN all right, title and interest to which it is
entitled as aforesaid pursuant to this Section 6.2.

     (c) Payment Obligations. BIOGEN shall have no obligation to make any
milestone or royalty payment to CURAGEN that has not accrued prior to the
effective date of such termination, but shall remain liable for all obligations
accruing prior to termination.

     6.3 Termination by BIOGEN. BIOGEN may terminate this Agreement, and the
         ---------------------
rights and obligations hereunder, or may remove any Licensed Clone and the
licenses related thereto from operation of this Agreement, in its sole
discretion at any time by giving written notice thereof to CURAGEN. Such
termination shall be effective fifteen (15) days following the date such
notice is received by CURAGEN and shall have all consequences as set forth in
Section 6.2 above, but only with respect to the specified Licensed Clone(s), as
if this Agreement had been terminated pursuant to Section 6.1(a).

     6.4 Remedies. If either Party shall fail to perform or observe or otherwise
         --------
breaches any of its material obligations under this Agreement, in addition to
any right to terminate this Agreement, the non-defaulting Party may elect to
obtain other relief and remedies available under law.
 
     6.5 Surviving Provisions. Notwithstanding any provision herein to the
         -------------------- 
contrary, the rights and obligations set forth in Article 4, Sections 6.2 and
6.4, and Article 7 hereof, as well as any rights or obligations otherwise
accrued, shall survive the expiration or termination of the term of this
Agreement.

                                7. MISCELLANEOUS
 
     7.1 CURAGEN Representations. CURAGEN represents and warrants that: (a) the
         -----------------------
execution and delivery of this Agreement and the performance of the transactions
contemplated hereby have been duly authorized by all appropriate CURAGEN
corporate action; (b) CURAGEN is under no obligation which is inconsistent with
this Agreement; and (c) CURAGEN has the full right and legal capacity to grant
the rights to BIOGEN pursuant to Article 2 above without violating the rights of
any third party.

                                      27

                      [Confidential Treatment Requested]


<PAGE>
 
     7.2 BIOGEN Representations. BIOGEN represents and warrants that: (a) the
         ----------------------
execution and delivery of this Agreement and the performance of the transactions
contemplated hereby have been duly authorized by all appropriate BIOGEN
corporate action; and (b) BIOGEN is under no obligation which is inconsistent
with this Agreement.
 
     7.3 No Warranties.
         -------------
     (a) Nothing in this Agreement is or shall be construed as:

           (i) a warranty or representation by CURAGEN as to the validity or
           scope of any application or patent within the Patent Rights;

           (ii) a warranty or representation that anything made, used, sold or
           otherwise disposed of under any license granted in this Agreement is
           or will be free from infringement of patents, copyrights, and other
           rights of third parties.

     (b) Except as expressly set forth in this Agreement, NEITHER PARTY MAKES
ANY REPRESENTATIONS OR EXTENDS ANY WARRANTIES OF ANY KIND, EITHER EXPRESS OR
IMPLIED. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE, THAT ANY LICENSED PRODUCT WILL BE SUCCESSFULLY
DEVELOPED OR MARKETED, OR THAT THE DEVELOPMENT, MANUFACTURE, SALE, IMPORTATION
OR USE OF THE LICENSED PRODUCT(S) WILL NOT INFRINGE ANY PATENT, COPYRIGHT,
TRADEMARK, OR OTHER RIGHTS, OR ANY OTHER EXPRESS OR IMPLIED WARRANTIES.

     7.4 Liability. NOTWITHSTANDING ANYTHING ELSE IN THIS AGREEMENT OR
         ---------
OTHERWISE, NEITHER PARTY WILL BE LIABLE WITH RESPECT TO ANY SUBJECT MATTER OF
THIS AGREEMENT UNDER ANY CONTRACT, NEGLIGENCE, STRICT LIABILITY OR OTHER LEGAL
OR EQUITABLE THEORY FOR (I) ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL OR PUNITIVE
DAMAGES OR LOST 

                                      28
<PAGE>
 
PROFITS OR (II) COST OF PROCUREMENT OF SUBSTITUTE GOODS, TECHNOLOGY OR SERVICES

     7.5 Notices. Any notices, requests, deliveries, approvals or consents
         -------
required or permitted to be given under this Agreement to BIOGEN or CURAGEN
shall be in writing and shall be personally delivered or sent by telecopy (with
written confirmation to follow via United States first class mail), overnight
courier providing evidence of receipt or certified mail, return receipt
requested, postage prepaid, in each case to the respective address specified
below (or to such address as may be specified in writing to the other Party
hereto):



        CURAGEN:          555 Long Wharf, 11th Floor
                          New Haven, CT   06511
                          Attn: Executive Vice President
                          Telecopy: (203) 401-3333

        BIOGEN:           14 Cambridge Center
                          Cambridge, MA 02142
                          Attn: Director, Marketing and Business Development 
                          Telecopy: (617) 679-2804

        with copies to:   Vice President - General Counsel
                          Telecopy: (617) 679-2838



     Such notices shall be deemed to have been sufficiently given on: (a) the
date sent if delivered in person or transmitted by telecopy, (b) the next
business day after dispatch in the case of overnight courier or (c) five (5)
business days after deposit in the U.S. mail in the case of certified mail.

     7.6 Governing Law. This Agreement will be construed, interpreted and
         -------------
applied in accordance with the laws of the State of Connecticut (excluding its
body of law controlling conflicts of law).
 
     7.7 Limitations. Except as set forth elsewhere in this Agreement, neither
         -----------
Party grants to the other Party any right or license to any of its intellectual
property.

                                      29
<PAGE>
 
     7.8 Entire Agreement. This is the entire Agreement between the Parties with
         ----------------
respect to the subject matter herein. No modification shall be effective unless
in writing and signed by the Parties.
 
     7.9 Waiver. The terms or conditions of this Agreement may be waived only by
         ------
a written instrument executed by the Party waiving compliance. The failure of
either Party at any time or times to require performance of any provision hereof
shall in no manner affect its rights at a later time to enforce the same. No
waiver by either Party of any condition or term shall be deemed as a continuing
waiver of such condition or term or of another condition or term.
 
     7.10 Headings. Section and subsection headings are inserted for convenience
          --------
of reference only and do not form part of this Agreement.

     7.11 Assignment. This Agreement may not be assigned by either Party without
          ----------
the consent of the other, except that each Party may, without such consent,
assign this Agreement and the rights, obligations and interests of such Party,
in whole or in part, to any of its Affiliates, to any purchaser of all or
substantially all of its assets in the line of business to which this Agreement
pertains or to any successor corporation resulting from any merger or
consolidation of such Party with or into such corporations.

     7.12 Force Majeure. Neither Party shall be liable for failure of or delay
          ------------- 
in performing obligations set forth in this Agreement, and neither shall be
deemed in breach of its obligations, if such failure or delay is due to natural
disasters or any causes beyond the reasonable control of such Party. In event of
such force majeure, the Party affected thereby shall use reasonable efforts to
cure or overcome the same and resume performance of its obligations hereunder.
 
     7.13 Construction. The Parties hereto acknowledge and agree that: (i) each
          ------------
Party and its counsel reviewed and negotiated the terms and provisions of this
Agreement and have contributed to its revision; (ii) the rule of construction to
the effect that any ambiguities are resolved against the drafting Party shall
not be employed in the interpretation of this Agreement; and (iii) the terms and
provisions of this Agreement shall be construed fairly as to all Parties 

                                      30
<PAGE>
 
hereto and not in a favor of or against any Party, regardless of which Party was
generally responsible for the preparation of this Agreement.
 
     7.14 Severability. If any provision(s) of this Agreement are or become
          ------------
invalid, are ruled illegal by any court of competent jurisdiction or are deemed
unenforceable under then current applicable law from time to time in effect
during the term hereof, it is the intention of the Parties that the remainder of
this Agreement shall not be affected thereby provided that a Party's rights
under this Agreement are not materially affected. The Parties hereto covenant
and agree to renegotiate any such term, covenant or application thereof in good
faith in order to provide a reasonably acceptable alternative to the term,
covenant or condition of this Agreement or the application thereof that is
invalid, illegal or unenforceable, it being the intent of the Parties that the
basic purposes of this Agreement are to be effectuated.

     7.15 Status. Nothing in this Agreement is intended or shall be deemed to
          ------
constitute a partner, agency, employer-employee, or joint venture relationship
between the Parties.

     7.16 Indemnification.
          --------------- 

     (a) BIOGEN shall indemnify, defend and hold harmless CURAGEN, its
Affiliates and their respective directors, officers, employees, and agents and
their respective successors, heirs and assigns (the "CURAGEN Indemnitees"),
against any liability, damage, loss or expense (including reasonable attorneys'
fees and expenses of litigation) incurred by or imposed upon the CURAGEN
Indemnitees, or any of them, in connection with any claims, suits, actions,
demands or judgments of third parties, including without limitation personal
injury and product liability matters (except to the extent that such claims,
suits, actions, demands or judgments result from a material breach of this
Agreement, or the negligence or willful misconduct on the part of CURAGEN or are
the subject matter of CURAGEN'S indemnification of BIOGEN as set forth in
Section 7.16(b)) arising out of or relating to any actions of BIOGEN or any
Affiliate, licensee, sublicensee, distributor or agent of BIOGEN in the
development, testing, production, manufacture, promotion, import, sale or use by
any person of any Licensed Product manufactured or sold by BIOGEN or by an
Affiliate, licensee, sublicensee, distributor or agent of BIOGEN.

                                      31
<PAGE>
 
     (b) CURAGEN shall indemnify, defend and hold harmless BIOGEN, its
Affiliates and their respective directors, officers, employees, and agents and
their respective successors, heirs and assigns (the "BIOGEN Indemnitees"),
against any liability, damage, loss or expense (including reasonable attorneys'
fees and expenses of litigation) incurred by or imposed upon the BIOGEN
Indemnitees, or any of them, in connection with any claims, suits, actions,
demands or judgments of third parties, including without limitation personal
injury matters (except to the extent that such claims, suits, actions, demands
or judgments result from a material breach of this Agreement, or the negligence
or willful misconduct on the part of BIOGEN) arising directly out of the use by
BIOGEN or CURAGEN of CURAGEN'S technology under the Research Agreement, except
to the extent such claims, suits, actions, demands or judgments are based on the
use of the samples or information provided to CURAGEN by BIOGEN under the
Research Agreement.

                                      32
<PAGE>
 
     IN WITNESS WHEREOF, the Parties have caused this Agreement to be executed
by their duly authorized representative in two (2) originals.


BIOGEN, INC.                            CURAGEN CORPORATION



By:                                     By: 
    ------------------------------          ------------------------------

Title:                                  Title: 
       -----------------------------           -----------------------------

                                      33
<PAGE>
 
                                   SCHEDULE I
                    (To be completed for each Licensed Clone)


Licensed Clone:
- ---------------

Type of License:
- ----------------

Project Data Set
- ----------------
or
- --
CURAGEN Data Set
- ----------------
Pertaining to Licensed Clone:
- -----------------------------

CURAGEN Proprietary
- -------------------
Material Pertaining to
- ----------------------
Licensed Clone:
- ---------------

CURAGEN Patent Rights
- ---------------------
Pertaining to Licensed Clone:
- -----------------------------

Rights under
- ------------
Extended License:
- -----------------

                                 Signed this        day of  
                                             ------        -------------, -----
                                 CURAGEN CORPORATION

                                 By: 
                                     --------------------------------------
                                          Name:
                                          Title:

                                 BIOGEN, INC.

                                 By: 
                                     --------------------------------------
                                          Name:
                                          Title:



                                      34
<PAGE>
 
                                  APPENDIX D
                                  ----------
 
                        Terms of Subscription Agreements



QEA/Gene Calling
- ----------------

Subscriber will receive secure access to CuraGen's QEA/GeneCalling subscription
database through the GeneScape( data base and software. Access will be provided
for up to [XXX] users on equipment to be provided by Subscriber.

CURAGEN will support and maintain the software provided for such access and will
use commercially reasonable efforts to update and maintain the database and to
keep it reasonably available for use.

Options and Licenses to clones identified using the database shall be provided
on terms substantially similar to those contained in this Agreement and the
License Agreement.

MIM/Path Calling
- ----------------

Subscriber will receive access to the MIM/PathCalling database through the
GeneScape(R) data base and software. Access will be provided for up to [XXX]
users on equipment to be provided by Subscriber.

CURAGEN will support and maintain the software provided for such access and will
use commercially reasonable efforts to update and maintain the database and to
keep it reasonably available for use.

Options and Licenses to clones identified using the database shall be provided
on terms substantially similar to those contained in this Agreement and the
License Agreement.

GeneTools
- ---------

Pursuant to any subscription agreement as described above Subscriber will also
receive secure access to the GeneTools database through the GeneScape(R)
software. Access will be provided for up to [XXX] users on equipment to be
provided by Subscriber.

                                      35

                      [Confidential Treatment Requested]




<PAGE>
 
                                                                   EXHIBIT 10.15

CuraGen Corporation has omitted from this Exhibit 10.15 portions of the 
Agreement for which CuraGen Corporation has requested confidential treatment 
from the Securities and Exchange commission. The portions of the Agreement for 
which confidential treatment has been requested are marked with X's in brackets 
and such confidential portions have been filed separately with the Securities 
and Exchange Commission.

                                                                  Execution Copy
                         RESEARCH AND OPTION AGREEMENT

     This Research and Option Agreement ("Agreement") is made effective as of
November 20, 1997 ("Effective Date") by and between GENENTECH, INC., a Delaware
corporation having its principal business office at 1 DNA Way, South San
Francisco, CA 94080 ("GENENTECH"), and CURAGEN CORPORATION, a Delaware
corporation with its principal place of business at 555 Long Wharf Drive, 11th
Floor, New Haven, Connecticut 06511 ("CURAGEN"). GENENTECH and CURAGEN are each
hereafter referred to individually as a "Party" and together as the "Parties".

     WHEREAS, GENENTECH desires to have access to CURAGEN's genomics
technologies (including GeneScape(R), QEA/GeneCalling, MIM/PathCalling and all
additional services provided by CURAGEN) and to have CURAGEN apply such
technologies to certain GENENTECH Proprietary Material in order to expedite the
discovery of information which may lead to the development of novel
pharmaceutical products;

     WHEREAS, GENENTECH and CURAGEN have previously collaborated on genomics
projects pursuant to the terms of that certain Research Services and Evaluation
Agreement dated June 12, 1996 and that certain Research and License Agreement
dated December 27, 1996 (together, the "Collaboration Agreements");

     WHEREAS, GENENTECH and CURAGEN wish to initiate the performance of certain
additional research by GENENTECH and CURAGEN;

     WHEREAS, GENENTECH wishes to obtain an option to evaluate and license the
inventions obtained or made by GENENTECH and/or CURAGEN in the performance of
the previous Collaboration Agreements and the performance of the research
pursuant to this Agreement, as well as an option to evaluate and license certain
other inventions of CURAGEN;

                      [Confidential Treatment Requested]
<PAGE>
 
     WHEREAS, CURAGEN wishes to retain rights to data and inventions made by
GENENTECH and CURAGEN hereunder and not licensed by GENENTECH;

     WHEREAS, GENENTECH wishes to make an equity investment in CURAGEN Common
Stock in the amount of Five Million Dollars ($5,000,000), such investment to be
made in a private placement contemporaneously with the initial public offering
of CURAGEN's Common Stock;

     WHEREAS, GENENTECH will also agree to loan CURAGEN up to Twenty-Six Million
Dollars ($26,000,000) on the terms and conditions as set forth herein; and

     WHEREAS, GENENTECH and CURAGEN therefore agree to undertake the foregoing,
all under the terms and conditions set forth in this Agreement.

     NOW, THEREFORE, in consideration of the mutual covenants contained herein,
and for other good and valuable consideration, the receipt and adequacy of which
is hereby acknowledged, the Parties hereby agrees as follows:

                                1.  DEFINITIONS
                                        
     Whenever used in the Agreement with an initial capital letter, the terms
defined in this Section 1 shall have the meanings specified.

     1.1   "AFFILIATE" shall mean any corporation, firm, limited liability
company, partnership or other entity which directly or indirectly controls or is
controlled by or is under common control with a Party to this Agreement.
"Control" means ownership, directly or through one or more Affiliates, of fifty
percent (50%) or more of the shares of stock entitled to vote for the election
of directors, in the case of a corporation, or fifty percent (50%) or more of
the equity interests in the case of any other type of legal entity, status as a
general partner in any partnership, or any other arrangement whereby a party
controls or has the right to control the Board of Directors or equivalent
governing body of a corporation or other entity.

                                       2
<PAGE>
 
     1.2   "CLONE" shall mean a segment of DNA representing a whole or partial
gene whose sequence or utility is determined from the analysis of one or more
Data Sets or from the Extended Research during the term of this Agreement.

     1.3   "CURAGEN BACKGROUND INVENTIONS" shall mean all patent rights and 
know-how of CURAGEN, other than those relating primarily to Inventions, which
CURAGEN has the right to license and which would be infringed by the activities
of GENENTECH permitted by this Agreement or by the development, manufacture,
use, sale or importation of a Licensed Product by GENENTECH; provided, however,
that CURAGEN Background Inventions shall expressly exclude (i) any patent rights
or know-how relating to Clones not licensed by GENENTECH pursuant to an executed
License Agreement and (ii) any patent rights or know-how arising from any
CURAGEN collaboration with a third party, except to the extent permitted
thereby.

     1.4   "CURAGEN DATA" shall mean all information obtained by CURAGEN from
the processing of specified CURAGEN samples, including QC data, QEA/GeneCalling
data, MIM/PathCalling data, sequence data and any other information obtained or
generated by CURAGEN in the performance of a discrete CURAGEN Project outside
the performance of the Research Program.

     1.5   "CURAGEN DATA SET" shall mean all CURAGEN Data resulting from a
discrete CURAGEN Project that CURAGEN can make exclusively available to
GENENTECH.

     1.6   "CURAGEN PROJECT" shall mean a particular project undertaken by
CURAGEN on its own outside the Research Program to process and analyze a
specified set of samples which do not contain GENENTECH Proprietary Material,
and as to which CURAGEN is free to grant rights to GENENTECH hereunder.

     1.7   "CURAGEN PROJECT INVENTION" shall mean any discovery, invention, 
know-how or trade secret conceived or made by employees of CURAGEN in the
performance of a CURAGEN Project that results in CURAGEN Data that becomes part
of an Exclusive Data Set, that is based on, incorporates or makes material use
of the corresponding CURAGEN Data.

     1.8   "CURAGEN PROJECT PATENT RIGHTS" shall mean Patent Rights containing a
claim or claims covering CURAGEN Project Inventions.  CURAGEN Project Patent
Rights shall 

                                       3
<PAGE>
 
also include Patent Rights containing a claim or claims covering CURAGEN Project
Inventions exclusively licensed in by CURAGEN, with the right to sublicense, now
or in the future.

     1.9  "CURAGEN PROJECT PROPRIETARY MATERIAL"   shall mean all substances
made by CURAGEN in the performance of CURAGEN Projects, including mRNA pools.
CURAGEN Project Proprietary Material shall include, without limitation, QEA
fragments, MIM constructs and materials derived or constructed from QEA
fragments and MIM constructs, including, without limitation, fragment and full
length cDNA clones made by CURAGEN in the performance of a CURAGEN Project.

     1.10  "CURAGEN ROYALTY PRODUCT" shall have the meaning set forth in Section
7.7.

     1.11  "DATA SET," which may be either a Project Data Set or a CURAGEN Data
Set, shall mean all Project Data resulting from a discrete Research Project or
all CURAGEN Data resulting from a discrete CURAGEN Project, respectively.

     1.12  "EXCLUSIVE DATA SET" shall mean any Project Data Set during the
corresponding Exclusive Evaluation Period as provided in Section 2.4.1 or any
CURAGEN Data Set during the corresponding Exclusive Evaluation Period as
provided in Section 2.5.2.

     1.13  "EXCLUSIVE EVALUATION PERIOD" shall have the meaning set forth in
Section 2.4.1 or 2.5.2.

     1.14  "EXTENDED RESEARCH" shall mean the research undertaken by CURAGEN
pursuant to Sections 2.4.1, 2.5.2 and/or 7.1.3 hereof.

     1.15  "EXTENDED RESEARCH DATA" shall mean all information and results
obtained by CURAGEN from its performance of Extended Research.

     1.16  "EXTENDED RESEARCH INVENTIONS" shall mean any discovery, invention,
know-how or trade secret conceived or made by employees of CURAGEN in the
performance of Extended Research, other than such discoveries, inventions, know-
how or trade secrets that are deemed to be defined as Research Project
Inventions pursuant to the terms of this Agreement or an executed License
Agreement.

     1.17  "EXTENDED RESEARCH PATENT RIGHTS" shall mean all rights and interests
in and to issued patents and pending patent applications in any country,
including, but not limited to, all provisional applications, substitutions,
continuations, continuations-in-part (solely to the extent that the claims of
such continuations-in-part cover Extended Research Inventions), divisions, and

                                       4
<PAGE>
 
renewals thereof, all letters patent granted thereon, and all reissues,
reexaminations and extensions thereof, whether owned now or hereafter, solely or
jointly by CURAGEN, and wherein at least one claim of such patent right covers
an Extended Research Invention.

     1.18  "FTE" shall mean the equivalent of a full year of effort on a full
time basis of a researcher possessing skills and experience necessary to carry
out applicable tasks under the Research Program.

     1.19  "GENENTECH PROPRIETARY MATERIAL" shall mean substances made by
GENENTECH or provided by GENENTECH to CURAGEN in the performance of the Research
Program, including without limitation (a) tissue samples provided by GENENTECH
to CURAGEN and (b) the nucleic acids and other substances actually contained in
such tissue samples, and (c) full length genes cloned by GENENTECH.

     1.20  "GENESCAPE(R)" shall mean the web-based software and database product
for accessing and storing Data Sets generated through the application of
CURAGEN's QEA/GeneCalling and MIM/PathCalling technologies.

     1.21  "INVENTION" shall mean either a CURAGEN Project Invention or a
Research Project Invention.

     1.22  "KNOW-HOW INFORMATION" shall have the meaning set forth in Section
2.1.4(c).

     1.23  "KNOW-HOW INFORMATION PRODUCT" shall have the meaning set forth in
Section 2.1.4(c).

     1.24  "LICENSED CLONE" shall mean any Clone licensed by GENENTECH pursuant
to an executed License Agreement.

     1.25  "LICENSED PRODUCT", as to each Clone, shall mean:

     [XXXXX]

     [XXXXX]

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[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

     1.26  "LICENSE AGREEMENT" shall mean a license agreement in the form of
Appendix C attached hereto executed by the Parties upon exercise of any Option
- ----------                                                                    
pursuant to Section 7.

     1.27  "MIM/PATHCALLING" shall mean the technology employed by CURAGEN for
identifying protein-protein interactions from libraries of cDNAs.

     1.28  "NET SALES" shall mean [XXXXX]

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[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

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[XXXXX]

     1.29 "OPTIONED CLONE" shall have the meaning set forth in Section 7.1.

     1.30 "OPTION PERIOD" shall have the meaning set forth in Section 7.3.

     1.31 "PATENT COORDINATORS" shall mean a patent attorney or patent agent
representing CURAGEN and a patent attorney or patent agent representing
GENENTECH, as further described in Section 6.2.

     1.32 "PATENT RIGHTS" means the rights and interests in and to issued
patents and pending patent applications in any country, including, but not
limited to, all provisional applications, substitutions, continuations,
continuations-in-part (solely to the extent claims of such continuations-in-part
cover Inventions) , divisions, and renewals, all letters patent granted thereon,
and all reissues, reexaminations and extensions thereof, whether owned now or
hereafter, solely or jointly by a Party, wherein at least one claim of such
patent right covers an Invention.

     1.33 "PREVIOUSLY COMMITTED CLONE" shall mean any Clone which, at the
relevant time under Section 7.1.1, (a) is subject to a license or an option
previously granted by CURAGEN to any third party, or (b) a third party
collaborator of CURAGEN or subscriber to CURAGEN's GeneCalling or PathCalling
database has requested CURAGEN to full-length clone such Clone or has itself
commenced full-length cloning of such Clone and notified

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CURAGEN thereof, and provided that such third party still retains evaluation,
option or license rights to such Clone pursuant to the terms of a written
agreement with CURAGEN.

     1.34 "PRIME RATE" shall mean the prime rate of interest as reported by
Citibank, N.A.  In the event that Citibank, N.A. ceases to report such a rate,
the term "Prime Rate" shall mean the generally prevailing base corporate lending
rate of Fleet National Bank.

     1.35 "PROJECT DATA" shall mean all information obtained by CURAGEN from the
processing of GENENTECH Proprietary Material in a particular Research Project,
including QC data, QEA/GeneCalling data, MIM/PathCalling data, sequence data and
any other information obtained or generated by CURAGEN in the performance of
each Research Project in the Research Program.

     1.36 "PROJECT DATA SET" shall mean all Project Data resulting from a
discrete Research Project.

     1.37 "QEA/GENECALLING" shall mean the software, database and other
technologies employed by CURAGEN for tagging and identifying the expression
level of specific gene fragments within a cDNA pool.

     1.38 "RESEARCH COMMITTEE" or "RC" shall have the meaning set forth in
Section 2.2.1.

     1.39 "RESEARCH PLAN" shall mean the written description of the Research
Program to be performed by CURAGEN and GENENTECH under this Agreement, as
further described in Section 2.1.3.  The Research Plan may specify one or more
independent Research Projects.

     1.40 "RESEARCH PROJECT" shall mean a particular project to process and
analyze a specified set of samples approved pursuant to Section 2.1.3.  Each
individual Research Project shall involve the analysis of [XXXXX] samples,
unless otherwise agreed by the Parties.

     1.41 "RESEARCH PROJECT INVENTION" shall mean any discovery, invention,
know-how or trade secret conceived or made (a) by employees of CURAGEN or
GENENTECH or jointly by employees of both in the performance of the Research
Program, (b) by GENENTECH employees in performing the specific following
activities utilizing any Data Set:  (i) QEA and MIM data analysis, confirmation
of QEA or MIM data, fragment cloning and sequencing of a Clone, and (ii) full-
length cloning of a Clone, or (c) any discovery, invention, know-how or trade
secret deemed to be a Research Project Invention pursuant to the terms of this
Agreement or an

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executed License Agreement. Research Project Inventions shall not include
inventions conceived or made solely by GENENTECH outside of the Research Program
except as specifically set forth in (b) above.

     1.42 "RESEARCH PROJECT PATENT RIGHTS" shall mean Patent Rights containing a
claim or claims covering Research Project Inventions.

     1.43 "RESEARCH PROJECT PROPRIETARY MATERIAL" shall mean all substances made
by CURAGEN in the performance of the Research Program other than mRNA pools
extracted from GENENTECH Proprietary Material.  Research Project Proprietary
Material shall include, without limitation, QEA fragments, MIM constructs and
materials derived or constructed from QEA fragments and MIM constructs,
including, without limitation, fragment and full length cDNA clones made by
CURAGEN in the performance of a Research Project.

     1.44 "RESEARCH PROGRAM" shall mean the Research Projects to be performed by
CURAGEN and GENENTECH under this Agreement as described in the Research Plan and
amendments thereto.

     1.45 "RESEARCH TERM" shall have the meaning set forth in Section 2.3.1.

     1.46 "RETAINED GENE" shall have the meaning set forth in Section 7.7.

     1.47 "TERM" shall have the meaning set forth in Section 8.1.

     1.48 "TERRITORY" shall mean the world.

     1.49 "VALID CLAIM(S)" shall mean an unexpired claim of any issued patent
within Patent Rights which has not been finally declared invalid or
unenforceable by a patent office or by a court or other body of competent
jurisdiction in any unappealed or unappealable decision and which has not been
lost through an interference or opposition proceeding.

                              2. RESEARCH PROGRAM


     2.1    IMPLEMENTATION OF RESEARCH PROGRAM.
            ---------------------------------- 

     2.1.1  Basic Provisions of Program.
            --------------------------- 

     (a)    The objective of the Research Program will be to generate Project
            Data Sets by performing Research Projects utilizing GENENTECH
            Proprietary Material. CURAGEN and GENENTECH shall each use
            commercially reasonable efforts to
 
                                       10
<PAGE>
 
          perform such tasks as are set forth in the Research Plan, including
          the provision of such facilities, samples and materials (including
          GENENTECH Proprietary Material), equipment and consultants as each
          deems necessary to the achievement of such Research Plan. In carrying
          out the Research Program, CURAGEN shall devote an average of at least
          [XXXXX] FTEs per year to the Research Program over its five year
          duration (the "Staffing Level") unless GENENTECH and CURAGEN have
          agreed on an increase in the Staffing Level as provided in (b) below.

     (b)  GENENTECH may request an increase in the Staffing Level of up to 
          [XXXXX] additional FTEs per year to be devoted to the Research
          Program, subject to the agreement of CURAGEN. CURAGEN will use
          commercially reasonable efforts to increase the staffing level if
          mutually agreed as promptly as practical. Once the Staffing Level is
          increased, it may not be decreased [XXXXX] without the consent of
          CURAGEN, which consent may be withheld at CURAGEN's sole discretion.

     2.1.2  Collaborative Efforts and Reports.
            --------------------------------- 

     (a)  The Parties agree that the successful execution of the Research
          Program will require the collaborative use of both Parties' areas of
          expertise.  Each Party shall keep the RC fully informed about the
          status of the portions of the Research Program they respectively
          perform including, without limitation, summaries of their direct uses
          of the Project Data itself for so long as GENENTECH shall have an
          option to license such Project Data hereunder.  CURAGEN shall promptly
          provide GENENTECH with a description of Project Data Sets from
          completed Research Projects.  All information provided hereunder will
          be treated as Confidential Information of the disclosing Party
          pursuant to the provisions of Article 4.

     (b)  Scientists at CURAGEN and GENENTECH shall cooperate in the performance
          of the Research Program and, subject to any confidentiality
          obligations to third parties, shall exchange information and materials
          as necessary to carry out the Research Program, subject to the
          provisions of Section 4.  Each Party will attempt 

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          to accommodate any reasonable request of the other Party to send or
          receive personnel for purposes of collaborating or exchanging
          information under the Research Program. Such visits and/or access will
          have defined purposes and be scheduled in advance.

     (c)  CURAGEN will give written notice to GENENTECH and the RC promptly upon
          completion of the Project Data Set from each Research Project.
          "Completion" of a Project Data Set shall occur upon generation of all
          completed QEA/GeneCalling data or MIM/PathCalling data from a Research
          Project as contemplated by the Research Plan. Provision of access to
          such data shall be promptly provided to GENENTECH through the
          GeneScape(R) database.

     (d)  CURAGEN shall set up and maintain, throughout the Research Term, a
          secure partition of its GeneScape(R) database and software for the
          exclusive use of GENENTECH and CURAGEN solely for the purpose of
          identifying genes from Exclusive Data Sets, and shall provide online
          E-mail and telephone help during normal business hours in the use
          thereof to GENENTECH.  CURAGEN and GENENTECH shall jointly set up and
          maintain a secure connection to said partition of the GeneScape(R)
          database and software in order to give GENENTECH on-line access
          thereto.

     (e)  GENENTECH will also receive, at its request, access to CURAGEN's
          QEA/GeneCalling and MIM/PathCalling subscription databases and to
          GeneTools pursuant to one or more subscription agreements to be
          executed by the Parties with terms substantially as described in
          Appendix E hereto.  [XXXXX]  Such subscription 
          ----------                                                     

                                       12

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          agreements may be terminated by GENENTECH at any time, without
          affecting the Research Program, either in their entirety or with
          respect to any database at GENENTECH's sole discretion upon three (3)
          months prior written notice. GENENTECH shall have no rights to use the
          GeneScape(R) database and software except as expressly set forth
          herein or in an executed database subscription agreement.

     (f)  If, after receiving access to any Data Set under the terms of this
          Agreement, GENENTECH becomes aware that analysis of such Data Set has
          led GENENTECH to file a patent application on, or to full-length
          sequence, any Clone whose sequence or utility was identified from such
          Data Set, GENENTECH shall promptly notify the RC of such patent filing
          or sequencing.  Any full-length Clone sequenced by GENENTECH after the
          identification of such Clone from a Data Set shall be a Research
          Project Invention, unless at the time of such sequencing, such full-
          length sequence:  (i) is in the public domain, (ii) is in the
          possession of GENENTECH (as can be documented by written or computer
          records), or (iii) is independently developed by GENENTECH (as can be
          documented by written or computer records).  If CURAGEN becomes aware
          that analysis of a Data Set during GENENTECH's Exclusive Evaluation
          Period pertaining to such Data Set has led CURAGEN to file a patent
          application on, or to full-length sequence, any Clone whose sequence
          or utility was identified from such Data Set, CURAGEN shall promptly
          notify the RC of such patent filing or sequencing, and any full-length
          Clone sequenced by CURAGEN after the identification of such Clone from
          a Data Set shall be deemed a Research Project Invention, unless at the
          time of such sequencing, such full-length sequence:  (i) is in the
          public domain, (ii) is in the possession of CURAGEN (as can be
          documented by written or computer records), or (iii) is independently
          developed by CURAGEN (as can be documented by written or computer
          records).

     2.1.3  Research Plans.
            -------------- 

     The Research Plan for the first twelve months of the Research Program shall
be agreed upon by the Parties within thirty (30) days of the Effective Date and
shall include the initial

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Research Projects and plans to implement the installation of access to the
GeneScape(R) database and software for GENENTECH. Every six (6) months during
the Research Term or at any time on request of either GENENTECH or CURAGEN, the
Research Plan shall be updated by CURAGEN and GENENTECH to cover the next twelve
months and shall be approved by the RC no later than thirty (30) days before the
end of each semi-annual period. The Research Plan shall set forth specific
Research Projects for the period covered by the Research Plan. For each Research
Project, the Research Plan will be deemed to include the following activities:
[XXXXX] GENENTECH shall not perform the activities specified in (i)-(iii) above
except as part of the Research Program, or as permitted in Section 2.4.3, in an
executed License Agreement, or in a subscription agreement. During any Exclusive
Evaluation Period for a Data Set, CURAGEN shall not utilize such Data Set in
performing the activities specified in (i)-(iii) except as part of the Research
Program. The RC will consider adjustments in the Research Plan at any time upon
the request of GENENTECH or CURAGEN. Notwithstanding the foregoing, no project
shall become a Research Project without the express consent of both GENENTECH
and CURAGEN; provided, however, that CURAGEN shall consent to any reasonable
proposed Research Project which is not substantially similar to a project that
is ongoing, planned internally solely by CURAGEN, the subject of active
negotiation with a third party or subject to a prior commitment to a third
party, all the above as evidenced by written or computer records, and which
would not violate a prior restriction under an agreement with a third party.
During the Research Term, once a Research Project becomes part of the Research
Plan, such Research Project will not be discontinued (unless such
discontinuation is approved by the RC) regardless of any other negotiations or
commitments with third parties.

     2.1.4  Exclusivity.
            ----------- 

     (a)  CURAGEN agrees that, commencing upon inclusion of a Research Project
          in the Research Plan, and continuing through the duration of any
          subsequent Exclusive Evaluation Period, CURAGEN shall not undertake to
          perform a substantially similar research project with any third party.

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     (b)  CURAGEN agrees that during any Exclusive Evaluation Period, CURAGEN
          will not grant access to any Exclusive Data Set to any other party and
          that during any Option Period, CURAGEN shall not grant to any third
          party rights to any Optioned Clone or to any Licensed Products related
          to such Optioned Clone. In addition, CURAGEN shall not, during any
          Exclusive Evaluation Period, grant a third party any rights to option
          or to license a Clone contained in the corresponding Exclusive Data
          Set (i) which GENENTECH has requested CURAGEN to full-length clone or
          (ii) for which GENENTECH has commenced full-length cloning and
          notified CURAGEN thereof, or to option or license Licensed Products
          relating to such a Clone. Notwithstanding the provisions of Article 4,
          upon the expiration of any Exclusive Evaluation Period for any
          Exclusive Data Set, CURAGEN shall have the right, at its sole option,
          to make such Data Set and, subject to the provisions of Section 2.4.4,
          reasonable descriptions of the data contained therein available to
          third parties or to put the Data Set and such descriptions in the
          subscription portion of the GeneScape(R) database. CURAGEN may perform
          research or collaborate with third parties and grant to third parties
          the right to exploit the results of any such research or
          collaborations without restriction other than as expressly provided in
          this Agreement or in an executed License Agreement.

     (c)  CURAGEN acknowledges that during the Research Program GENENTECH may
          obtain useful proprietary information from Research Projects, Project
          Data, CURAGEN Projects, CURAGEN Data and CURAGEN's databases and other
          information which is not covered by a Valid Claim of a Research
          Project Patent Right or a CURAGEN Project Patent Right (collectively,
          "Know-How Information").  Without limitation, Know-How Information may
          include identification of pathways involved in diseases or protein-
          protein interactions involved in diseases, which involvement was not
          previously  known by GENENTECH.  GENENTECH shall have a right to use
          Know-How Information for all purposes and CURAGEN hereby grants
          GENENTECH a nonexclusive, worldwide, sublicensable license to use
          Know-How Information for such 

                                       15
<PAGE>
 
          purposes. In the event that GENENTECH or a Sublicensee develops a
          product which is not covered by a Valid Claim of a Research Project
          Patent Right, a Valid Claim of a CURAGEN Project Patent Right or a
          Valid Claim of an Extended Research Patent Right and is not licensed
          to GENENTECH under a License Agreement or an executed subscription
          agreement, and which was discovered by GENENTECH or a Sublicensee
          based directly and materially on its use of such Know-How Information
          (a "Know-How Information Product"), GENENTECH shall pay to CURAGEN a
          [XXXXX] on Net Sales of such Know-How Information Product. Without
          limitation, GENENTECH's development of a product which has the
          intended biological activity of modifying the outcome of a pathway by
          binding to a protein or inhibiting protein function and such pathway
          was directly identified in a Research Project, such product would be a
          Know-How Information Product subject to the [XXXXX] set forth
          above, provided that such pathway identification makes a direct and
          material contribution to the development of such product.
          Notwithstanding the above, the obligation above to pay a [XXXXX] to
          CURAGEN on Net Sales of Know-How Information Products shall not apply
          to GENENTECH if, at the time of receipt by GENENTECH from CURAGEN and
          first use by GENENTECH in the discovery of such Know-How Information
          Product, such Know-How Information: (i) was in the public domain; (ii)
          was known to, or in the possession or control of, GENENTECH (as
          demonstrated by its written or computer records); (iii) had already
          been obtained by GENENTECH from sources independent of CURAGEN; or
          (iv) was developed by GENENTECH independently of such Know-How
          Information (as can be demonstrated by written or computer records).
          The right contained in this paragraph does not include any license
          under any patent claims owned or controlled in whole or in part by
          CURAGEN.

     (d)  GENENTECH agrees that, until any such information is in the public
          domain other than as a result of a disclosure by GENENTECH in
          violation of this Agreement, an executed subscription agreement or an
          executed License 

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          Agreement, or until GENENTECH discovers or obtains such information
          independently of CURAGEN without use of CURAGEN Data Sets or
          Inventions or knowledge thereof, GENENTECH will only utilize Project
          Data, CURAGEN Data, CURAGEN Project Proprietary Material, Research
          Project Proprietary Material, Inventions or Patent Rights as expressly
          provided herein or in an executed License Agreement or executed
          subscription agreement. CURAGEN agrees that CURAGEN will not utilize
          any GENENTECH Proprietary Material, Project Data, Research Project
          Proprietary Material, Research Project Inventions or Research Project
          Patent Rights other than as expressly provided herein.

     (e)  Royalty payments due pursuant to subsection (c) above shall be made to
          CURAGEN in United States Dollars quarterly within sixty (60) days
          following the end of each calendar quarter for which royalties are
          due.  Each royalty payment shall be accompanied by a report
          summarizing the total Net Sales for each Know-How Information Product
          during the relevant three-month period and the calculation of
          royalties, if any, due thereon pursuant to this Section 2.1.4.  All
          royalties shall be payable in full in the United States in United
          States Dollars, regardless of the countries in which sales are made.
          For the purpose of computing Net Sales for Know-How Information
          Products sold in a currency other than United States dollars, such
          currency shall be converted into United States dollars at the exchange
          rate for buying U.S. dollars set forth in The Wall Street Journal for
                                                    -----------------------    
          the last business day of the calendar quarter.

     (f)  GENENTECH shall pay royalties with respect to each Know-How
          Information Product on a country by country basis for a period of
          ten (10) years from the first commercial sale of such Know-How
          Information Product in such country. Following such period, GENENTECH
          shall have a fully paid-up, irrevocable license in such country to
          make, have made, use, have used, sell, have sold, offer for sale,
          import and have imported such Know-How Information Product in such
          country.

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     (g)  OVERDUE ROYALTIES.  Royalties not paid within the time period set
          -----------------                                                
          forth in this Section 2.1.4 shall bear interest at [XXXXX] accruing
          monthly, from the due date until paid in full.

     (h)  RECORDS RETENTION.  AUDITS.  GENENTECH shall keep for [XXXXX] from the
          date of each payment of royalties complete and accurate records of
          sales by GENENTECH of each Know-How Information Product in sufficient
          detail to allow the accruing royalties to be determined accurately.
          CURAGEN shall have the right for a period of [XXXXX] after receiving
          any report or statement with respect to royalties due and payable to
          appoint an independent certified public accountant reasonably
          acceptable to GENENTECH to inspect the relevant records of GENENTECH
          to verify such report or statement. GENENTECH shall make its records
          available for inspection by such independent certified public
          accountant during regular business hours at such place or places where
          such records are customarily kept, upon reasonable notice from
          CURAGEN, solely to verify the accuracy of the reports and payments.
          Such inspection right shall not be exercised more than once in any
          calendar year nor more than once with respect to sales of any Know-How
          Information Product in any given payment period. CURAGEN agrees to
          hold in strict confidence all information concerning royalty payments
          and reports, and all information learned in the course of any audit or
          inspection, except to the extent necessary for CURAGEN to reveal such
          information in order to enforce its rights under this Agreement or if
          disclosure is required by law, regulation or judicial order. The
          results of each inspection, if any, shall be binding on both Parties.
          CURAGEN shall pay for such inspections, except that in the event there
          is any upward adjustment in aggregate royalties payable for any year
          shown by such inspection of more than [XXXXX] of the amount paid,
          GENENTECH shall pay for such inspection.

     2.1.5  Research License.  CURAGEN hereby grants to GENENTECH a non-
            ----------------                                           
exclusive license under CURAGEN Background Inventions and CURAGEN's interest in
any Inventions solely during the Term hereof and to the extent necessary to
allow GENENTECH to perform its

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obligations under the Research Program and to exercise the rights granted
herein, including without limitation, the evaluation hereunder of Research
Project Data, CURAGEN Data and Clones.

     2.1.6  Software License.  Any access granted to the GeneScape(R) database
            ----------------                                                  
and software hereunder, or any components thereof, is granted according to the
following terms:

     The GeneScape(R) database, software and display screens are protected by
copyright, patent, trade secret and other intellectual property laws.  CURAGEN
hereby grants to GENENTECH and its employees a non-exclusive non-transferable
license to access the GeneScape(R) database and software solely for the purposes
of and during the Term of this Agreement.  GENENTECH shall access Project Data
Sets and CURAGEN Data Sets only through the GeneScape(R) database and software
provided by CURAGEN.  GENENTECH shall not copy the GeneScape(R) database,
software or display screens except as occurs during the normal course of
CURAGEN-provided access.  In particular, GENENTECH will not retain such normal
copies for a time not reasonably related to CURAGEN-provided access.  GENENTECH
shall not reverse engineer, decompile, or disassemble the GeneScape(R) software
or display screens.  The GeneScape(R) database and software embody trade secrets
of CURAGEN that are considered Confidential Information of CURAGEN and subject
to the provisions of Article 6 hereof.

     2.2  RESEARCH COMMITTEE.
          ------------------ 

     2.2.1  Establishment and Functions of the RC.
            ------------------------------------- 

     (a)  CURAGEN and GENENTECH shall establish a "Research Committee" (the
          "RC").  The RC will act on behalf of the two companies and will be
          responsible for the planning and monitoring of the Research Program.
          In particular, the activities of the RC shall include reviewing
          progress in the Research Program and recommending necessary
          adjustments to the Research Program, including any Research Project
          substitutions deemed desirable based on results and on GENENTECH's
          commercial interest, as the research and development progresses.

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<PAGE>
 
     (b)  In planning and monitoring the Research Program, the RC shall assign
          tasks and responsibilities taking into account each Party's respective
          specific capabilities and expertise in order in particular to avoid
          duplication and enhance efficiency and synergies. The RC shall also
          monitor the assignment of CURAGEN employees to the Research Program
          and the allocation of such CURAGEN employees to specific Research
          Projects.

     2.2.2  RC Membership.
            ------------- 

     CURAGEN and GENENTECH each shall appoint, in their sole discretion, three
(3) members to the RC, which shall include a Co-Chair to be designated by
GENENTECH and a Co-Chair to be designated by CURAGEN.  Substitutes or alternates
for the Co-Chairs or other RC members may be appointed at any time by notice in
writing to the other Party.  The Parties may mutually agree to change the size
of the RC as long as there shall be an equal number of representatives of each
party on the RC.  The initial Co-Chairs and other RC members shall be designated
by the parties upon execution of this Agreement.  CURAGEN shall appoint a
Project Coordinator, who shall be reasonably satisfactory to GENENTECH, to serve
as the principal CURAGEN liaison with GENENTECH for the Research Program.  Such
Project Coordinator will be one of CURAGEN's members of the RC.

     2.2.3  Meetings.
            -------- 

     The RC shall meet once a year in New Haven, Connecticut, and once a year in
South San Francisco, California unless the Parties agree otherwise.  Any
additional meetings shall be held at places and on dates selected by the Co-
Chairs of the RC.  The RC shall also conduct two meetings a year by conference
call, or as otherwise agreed by the RC members.  In addition, the RC may act
without a formal meeting by a written memorandum signed by the Co-Chairs of the
RC.  Whenever any action by the RC is called for hereunder during a time period
in which the RC is not scheduled to meet, the Co-Chairs of the RC shall cause
the RC to take the action in the requested time period by calling a special
meeting, conference call or by action without a meeting.  Subject to the
obligations set forth in Section 4, representatives of each Party, in addition
to the members of the RC, may attend RC meetings at the invitation of either
Party with the prior approval of the other Party, which shall not be
unreasonably withheld.

     2.2.4  Minutes.
            ------- 

                                       20
<PAGE>
 
     The RC shall keep accurate minutes of its deliberations which record all
proposed decisions and all actions recommended or taken.  Drafts of the minutes
shall be delivered to the Co-Chairs of the RC within twenty (20) days after the
meeting. The Party hosting the meeting shall be responsible for the preparation
and circulation of the draft minutes.  Draft minutes shall be edited by the Co-
Chairs and shall be issued in final form only with their approval and agreement
as evidenced by their signatures on the minutes.

     2.2.5  Quorum; Voting; Decisions.
            ------------------------- 

     At each RC meeting, at least two (2) member(s) appointed by each Party
present in person or by telephone shall constitute a quorum and decisions shall
be made by majority vote.  Each RC member shall have one vote on all matters
before the RC, provided that the member or members of each Party present at an
RC meeting shall have the authority to cast the votes of any of such Party's
members on the RC who are absent from the meeting.  Notwithstanding the
foregoing, the objective of the Parties to this Agreement is that decisions of
the RC shall be made by consensus.  However, except as otherwise set forth
herein, in the event that the RC is unable to resolve any matter before it as
set forth above, such matter shall be resolved by GENENTECH, taking into
reasonable consideration the best interests of both GENENTECH and CURAGEN.
Notwithstanding the foregoing, no project shall become a Research Project
without the express consent of both GENENTECH and CURAGEN; provided, however,
that CURAGEN shall consent to any reasonable proposed Research Project which is
not substantially similar to a project that is ongoing, planned internally
solely by CURAGEN, the subject of active negotiation with a third party or
subject to a prior commitment to a third party, all the above as evidenced by
written or computer records, and which would not violate a prior restriction
under an agreement with a third party.

     2.2.6  Expenses.
            -------- 

     CURAGEN and GENENTECH shall each bear all expenses of their respective RC
members related to their participation on the RC and attendance at RC meetings.

     2.2.7  Record Keeping.
            -------------- 

     Throughout the Term of this Agreement the Parties will maintain a list of
Research Projects and start dates and completion dates thereof, Exclusive Data
Sets, Exclusive Evaluation

                                       21
<PAGE>
 
Periods and extensions thereof, Option Periods and extensions thereof and
Optioned Clones.  Such task shall be performed by the RC unless otherwise
mutually agreed by the Parties.

     2.3    RESEARCH TERM.
            ------------- 

     2.3.1  Term of the Research Program.
            ---------------------------- 

     The Research Program shall expire five (5) years after the Effective Date
unless extended as provided below or unless earlier terminated by either Party
by virtue of termination of the Research Program or this Agreement pursuant to
the provisions of Sections 2.3.3 or 2.3.4 and/or Article 8 (the "Research
Term").

     2.3.2  Extension of the Research Program.
            --------------------------------- 

     The Research Term may be extended upon six (6) months prior written notice
by mutual agreement of the Parties on terms to be agreed upon between the
Parties.

     2.3.3  Termination of the Research Program.
            ----------------------------------- 

     (a)    GENENTECH may terminate the Research Program at its sole discretion
            effective upon the 18 month anniversary of the Effective Date by
            giving written notice to CURAGEN within one (1) month prior to such
            date and by: (i) paying CURAGEN up to Three Million Seven Hundred
            and Fifty Thousand Dollars ($3,750,000) in cash within thirty (30)
            days of giving CURAGEN such written notice of termination and/or
            (ii) forgiving up to Three Million Seven Hundred and Fifty Thousand
            Dollars ($3,750,000) of any outstanding balance under the Loan
            pursuant to a written instrument delivered to CURAGEN within thirty
            (30) days of giving CURAGEN such written notice of termination, in
            any combination of (i) and (ii) such that the combined payment and
            forgiveness amounts total Three Million Seven Hundred and Fifty
            Thousand Dollars ($3,750,000). In the event that, as of one month
            following such termination date (the "Section 2.3.3(a) Balance
            Date"), the outstanding balance under the Loan is less than
            $3,750,000, GENENTECH will forgive the amount of such outstanding
            balance and may, in lieu of or in addition to paying cash as
            specified in (i) above, elect to pay the balance of the $3,750,000
            by transferring back to CURAGEN within ten (10) days of the Section
            2.3.3(a) Balance Date, shares of CURAGEN stock received by GENENTECH
            pursuant to the terms of the Note at the value (as determined

                                       22

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            pursuant to the terms of the Note) as of the Section 2.3.3(a)
            Balance Date in an amount necessary to bring the combined
            forgiveness, cash payment and payment in stock amounts to a total of
            $3,750,000. Any such early termination of the Research Program shall
            automatically terminate any ongoing Exclusive Evaluation Periods
            hereunder. In addition, all but [XXXXX] existing on the effective
            date of such termination shall be terminated and GENENTECH may elect
            which [XXXXX] shall survive upon notice given to CURAGEN prior to
            termination. All of GENENTECH's rights under this Agreement with
            respect to such [XXXXX] shall be unaffected by any such termination
            and any License Agreement executed prior to any such termination
            shall survive such termination.

     (b)    Provided that GENENTECH has elected to proceed under Section
            2.3.4(a)(iii) on the third anniversary of the Effective Date,
            GENENTECH may terminate the Research Program at its sole discretion
            at any time after the third anniversary of the Effective Date upon
            three (3) months prior written notice to CURAGEN. Any such early
            termination of the Research Program shall not affect GENENTECH's
            rights under any Exclusive Evaluation Periods or any Option Periods
            then ongoing, any License Agreement executed between the Parties
            prior to such termination or any Options that have been exercised
            prior to such termination for which the License Agreement has not
            yet been executed; provided, however, that any surviving Exclusive
            Evaluation Periods shall not be extendible pursuant to Section
            2.4.2.

     2.3.4  Rights at Third and Fifth Anniversary
            -------------------------------------

     (a)    Upon the third anniversary of the Effective Date, unless previously
            terminated, GENENTECH shall have three choices for how to proceed
            with respect to continuation or termination of the Research Program
            and/or this Agreement:

            (i)  GENENTECH may, by written notice given within thirty (30) days
                 prior to such third anniversary date, terminate the Research
                 Program and this Agreement and all licenses granted pursuant to
                 any executed License

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                 Agreement and all Exclusive Evaluation Periods and Options
                 granted pursuant to this Agreement. No payment will be due
                 CURAGEN.

            (ii) GENENTECH may terminate the Research Program by written notice
                 given within thirty (30) days prior to such third anniversary
                 date, but if GENENTECH: (x) pays CURAGEN up to $7,500,000 in
                 cash within 30 days of the third anniversary date and/or (y)
                 forgives up to $7,500,000 of any outstanding balance under the
                 Loan (as defined in Section 3.2 below) pursuant to a written
                 instrument delivered to CURAGEN within 30 days of such third
                 anniversary date, in any combination of (x) and (y) such that
                 the combined payment and forgiveness amounts total $7,500,000,
                 then GENENTECH's termination of the Research Program shall not
                 affect GENENTECH's rights under any Exclusive Evaluation
                 Periods or any Option Periods then ongoing, any License
                 Agreement executed between the Parties prior to such
                 termination, or any Options that have been exercised by
                 GENENTECH prior to such termination for which the License
                 Agreement has not yet been executed; provided, however, that
                 any such Exclusive Evaluation Periods shall not be extendible
                 pursuant to Section 2.4.2. In the event that, as of one month
                 following such termination date (the "Section 2.3.4(a)(ii)
                 Balance Date"), the outstanding balance under the Loan is less
                 than $7,500,000, GENENTECH will forgive the amount of such
                 outstanding balance and may, in lieu of or in addition to
                 paying cash as specified in (x) above, elect to pay the balance
                 of the $7,500,000 by transferring back to CURAGEN within ten
                 (10) days of the Section 2.3.4(a)(ii) Balance Date, shares of
                 CURAGEN stock received by GENENTECH pursuant to the terms of
                 the Note at the value (as determined pursuant to the terms of
                 the Note) as of the Section 2.3.4(a)(ii) Balance Date in an
                 amount necessary to bring the combined forgiveness, cash
                 payment and payment in stock amounts to a total of $7,500,000.
                 All provisions of this Agreement governing such Exclusive
                 Evaluation
                                       24

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                  Periods, Option Periods, Options and related license rights
                  shall continue in full force and effect.

            (iii) GENENTECH may continue with the Research Program and this
                  Agreement in their entirety and retain its rights in any
                  Exclusive Evaluation Periods and any Option Periods then
                  ongoing, any License Agreement executed between the parties
                  prior to such termination and any Options that have been
                  exercised by GENENTECH prior to such early termination for
                  which the License Agreement has not yet been executed. Under
                  this choice, GENENTECH shall: (x) pay CURAGEN up to $7,500,000
                  in cash within 30 days of the third anniversary date and/or
                  (y) forgive up to  $7,500,000 of any outstanding balance under
                  the Loan pursuant to a written instrument delivered to CURAGEN
                  within 30 days of such third anniversary date, in any
                  combination of (x) and (y) such that the combined payment and
                  forgiveness amounts total $7,500,000. In the event that, as of
                  one month following such termination date (the "Section
                  2.3.4(a)(iii) Balance Date"), the outstanding balance under
                  the Loan is less than $7,500,000, GENENTECH will forgive the
                  amount of such outstanding balance and may, in lieu of or in
                  addition to paying cash as specified in (x) above, elect to
                  pay the balance of the $7,500,000 by transferring back to
                  CURAGEN within ten (10) days of the Section 2.3.4(a)(iii)
                  Balance Date, shares of CURAGEN stock received by GENENTECH
                  pursuant to the terms of the Note at the value (as determined
                  pursuant to the terms of the Note) as of the Section
                  2.3.4(a)(iii) Balance Date in an amount necessary to bring the
                  combined forgiveness, cash payment and payment in stock
                  amounts to a total of $7,500,000. Under this Section
                  2.3.4(a)(iii) only, the maximum principal amount on the Loan
                  shall increase to Twenty-Six Million Dollars as described in
                  Section 3.2(a).

     (b)    In the event that the Research Program does not terminate as set
            forth in Section 2.3.3 or Section 2.3.4(a)(i) or (ii), upon the
            fifth anniversary of the Effective Date,

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            the Research Program, this Agreement and all licenses to any
            Licensed Clones optioned pursuant to Section 7.1 from an Exclusive
            Data Set which was completed after the third anniversary of the
            Effective Date and all licenses to any Licensed Clones licensed to
            GENENTECH without an Option from any such Exclusive Data Set
            completed after the third anniversary of the Effective Date, shall
            terminate as of such fifth anniversary date unless GENENTECH: (i)
            pays CURAGEN up to an additional Seven Million Five Hundred Thousand
            Dollars ($7,500,000) in cash within thirty (30) days of such fifth
            anniversary date and/or (ii) forgives up to an additional Seven
            Million Five Hundred Thousand Dollars ($7,500,000) of any
            outstanding balance under the Loan pursuant to a written instrument
            delivered to CURAGEN within thirty (30) days of such fifth
            anniversary date, in any combination of (i) and (ii) such that the
            combined payment and forgiveness amounts total an additional Seven
            Million Five Hundred Thousand Dollars ($7,500,000). In the event
            that, as of such termination date, the outstanding balance under the
            Loan is less than $7,500,000, GENENTECH will forgive the amount of
            such outstanding balance and may, in lieu of or in addition to
            paying cash as specified in (i) above, elect to pay the balance of
            the $7,500,000 by transferring back to CURAGEN within ten (10) days
            of such termination date, shares of CURAGEN stock received by
            GENENTECH pursuant to the terms of the Note at the value (as
            determined pursuant to the terms of the Note) as of such termination
            date in an amount necessary to bring the combined forgiveness, cash
            payment and payment in stock amounts to a total of $7,500,000. Such
            termination shall not affect GENENTECH's rights under any Exclusive
            Evaluation Period, Option Period or License Agreement then ongoing
            which relates to a Data Set completed prior to the third anniversary
            of the Effective Date, and all provisions of this Agreement
            governing such Exclusive Evaluation Periods, Option Periods, Options
            and related license rights shall continue in full force and effect.

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     2.3.5  Effect of Termination.
            --------------------- 

     (a)    Upon any termination of the Research Program pursuant to Section
            2.3.3 or 2.3.4, GENENTECH shall grant to CURAGEN a license as set
            forth in Section 7.5 under GENENTECH's rights in Research Project
            Patent Rights and Research Project Inventions to the extent not
            previously granted to CURAGEN or not expressly retained by GENENTECH
            pursuant to the terms of Sections 2.3.3 or 2.3.4 of this Agreement.
            CURAGEN shall pay royalties to GENENTECH for such license rights as 
            provided in Section 7.7; provided, however, that CURAGEN's license
            shall be royalty-free for all purposes if this Agreement is
            terminated pursuant to Section 2.3.4(a)(i) and royalty-free with
            respect to all Patent Rights covering Inventions discovered
            utilizing Data Sets completed after the third anniversary of the
            Effective Date if this Agreement is terminated pursuant to Section
            2.3.4(b).

     (b)    Any termination of the Research Program under Section 2.3.3 or
            Section 2.3.4 shall be without prejudice to the rights of either
            Party against the other, then accruing or otherwise accrued under
            this Agreement and upon any such termination, all remaining
            GENENTECH Proprietary Material provided to CURAGEN under this
            Agreement shall be returned to GENENTECH or destroyed, except as
            provided in Section 7.5, and all remaining CURAGEN Project
            Proprietary Material and Research Project Proprietary Material
            provided to GENENTECH under this Agreement shall be returned to
            CURAGEN or destroyed, except for any CURAGEN Project Proprietary
            Material or Research Project Proprietary Material licensed pursuant
            to an executed License Agreement or which is the subject of a
            surviving Evaluation Period or Option.

     2.4    PROJECT DATA EVALUATIONS.
            ------------------------ 

     2.4.1  Exclusive Access.  From the time at which a Research Project is
            ----------------                                               
begun and continuing through a one-year period which shall commence at the
beginning of the calendar quarter following the calendar quarter in which
delivery of a proper notice of a complete Project Data Set is made pursuant to
Section 2.1.2(c) and access to such complete Project Data Set is given to
GENENTECH (the "Exclusive Evaluation Period"), GENENTECH shall have the right

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to use all Project Data, Research Project Inventions and Research Project
Material related to such Research Project to evaluate Clones and the proteins
encoded thereby and derived therefrom for potential licensing. During each
Exclusive Evaluation Period, CURAGEN (a) shall not use such Project Data Set
(which, during such Exclusive Evaluation Period shall be an Exclusive Data Set)
and related Research Project Proprietary Material for any purpose other than
conducting the Research Program hereunder and (b) shall keep such Project Data
Set and related Research Project Inventions and Research Project Proprietary
Material confidential and will not disclose or transfer the Project Data Set, or
related Research Project Inventions and Research Project Proprietary Material to
third parties by publication or otherwise, without the prior written consent of
GENENTECH. Notwithstanding the foregoing, CURAGEN shall have the right during
such Exclusive Evaluation Period to use, but not to transfer to third parties
(except pursuant to an agreement with a third party who has identified such
Clone independently of the Project Data), all Clones or the proteins derived
therefrom, outside of the Research Program as part of CURAGEN's libraries for
internal, general, non-directed research purposes (including, without
limitation, full length cloning, expression analysis, protein-protein
interactions and drug screening). For example, but without limitation, inclusion
of the Clone together with other clones in research to determine multiple
protein-protein interactions, or inclusion of the Clone together with other
clones in a screen against one or more molecules to determine inhibition would
be "non-directed" research, whereas activities associated with choosing a
specific Clone and conducting research to elucidate the biological activity of
such Clone (e.g., generating antibodies to the Clone, testing the Clone or
protein encoded thereby in preclinical models, enriching libraries with such
Clone to purposefully look for proteins which bind to such Clone) would be
considered "directed" research and CURAGEN shall not be permitted to perform
such activities under this Section 2.4.1. CURAGEN shall keep GENENTECH
reasonably informed of the results of any such research and patent applications
and patents relating to such research on a confidential and timely basis in
order to allow GENENTECH to make informed decisions regarding the exercise of
its option and license rights hereunder. All inventions conceived or made during
such research which relate to the Clone, the proteins derived therefrom
(including antibodies), homologs or mutants with substantially the same
biological activity as such Clone, or uses thereof, shall be deemed Research
Project Inventions subject to GENENTECH's option 

                                       28
<PAGE>
 
rights for such Clone under Article 7. All other inventions from such research
shall be Extended Research Inventions and GENENTECH will have rights to such
Extended Research Inventions and Extended Research Patent Rights resulting
therefrom as provided in Article 7 hereof and in Section 2.3 of the License
Agreement attached hereto as Appendix C.

     2.4.2  Extensions.  GENENTECH may elect to extend the Exclusive Evaluation
            ----------      
Period for any Project Data Set that has become an Exclusive Data Set, and all
rights thereunder, for an additional twelve (12) months by giving written notice
to CURAGEN and making a payment of [XXXXX] to CURAGEN prior to expiration of the
initial Exclusive Evaluation Period for such Project Data Set. An Exclusive
Evaluation Period will be automatically extended for up to three months in order
to allow the completion of any reasonable requests for confirmation of data made
by GENENTECH during the primary twelve-month period of such Exclusive Evaluation
Period.

            2.4.3  Non-exclusive Access.  Following the expiration of the
                   --------------------                                  
Exclusive Evaluation Period for a Project Data Set, GENENTECH shall continue to
have non-exclusive access to such Project Data Set solely through the
GeneScape(R) database and solely for the purpose of identifying Clones of
interest to GENENTECH in such Data Set, or to the extent otherwise set forth in
an executed subscription agreement.  However, the preceding restriction shall
not apply to any information which becomes part of the public domain other than
as a result of a disclosure by GENENTECH in violation of this Agreement, an
executed License Agreement or an executed subscription agreement.

     2.4.4. Data Annotations.  Upon the expiration of the Exclusive Evaluation
            ----------------                                                  
Period for each Project Data Set, CURAGEN shall furnish to GENENTECH reasonable
descriptions of the Project Data Set to be included as annotations in the
GeneScape(R) database with the Project Data Set.  GENENTECH shall have a period
of [XXXXX] to review such descriptions and advise CURAGEN of reasonable
objections. CURAGEN shall not include in the GeneScape(R) database any
descriptions, or portions thereof, to which GENENTECH reasonably objects.
CURAGEN shall not include any Confidential Information of GENENTECH (as defined
in Section 4.1 below) in any annotation.

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     2.5    CURAGEN PROJECTS.
            ---------------- 

     2.5.1  Access.  GENENTECH shall have the option, for such reasonable period
            ------                                                              
or periods as CURAGEN may specify, to review specified proprietary CURAGEN Data
Sets and related CURAGEN Project Inventions, which are offered by CURAGEN in its
sole discretion to GENENTECH for review and to request exclusive access thereto.
Such option shall be exercisable as set forth in Section 2.5.2 below.

     2.5.2  Exclusive Evaluation Option.  Subject to any rights which CURAGEN
            ---------------------------                                      
may grant or have granted to third parties, GENENTECH may request at any time
during the time period specified by CURAGEN (as described in Section 2.5.1) that
it receive exclusive access to any CURAGEN Data Set offered to GENENTECH
pursuant to Section 2.5.1.  Such exclusive access to such CURAGEN Data Set shall
be granted to GENENTECH for an Exclusive Evaluation Period of [XXXXX] commencing
upon CURAGEN's receipt of written notice from GENENTECH and payment of an
exclusive evaluation fee of [XXXXX], unless GENENTECH is notified by CURAGEN at
any time prior to CURAGEN's receipt of GENENTECH's written notice that exclusive
access to such CURAGEN Data Set is no longer available as a result of CURAGEN's
agreements with third parties existing at the time of the request. During each
Exclusive Evaluation Period, CURAGEN (a) shall not use such CURAGEN Data Set
(which, during such Exclusive Evaluation Period shall be an Exclusive Data Set)
and related CURAGEN Project Proprietary Material for any purpose other than
conducting the Research Program hereunder and (b) shall keep such CURAGEN Data
Set and related CURAGEN Project Inventions and CURAGEN Project Proprietary
Material confidential and will not disclose or transfer the CURAGEN Data Set, or
related CURAGEN Project Inventions and CURAGEN Project Proprietary Material to
third parties by publication or otherwise, without the prior written consent of
GENENTECH. Notwithstanding the foregoing, CURAGEN shall have the right during
such Exclusive Evaluation Period to use, but not transfer to third parties
(except pursuant to an agreement with a third party who has identified such
Clone independently of the CURAGEN Data) all Clones or the proteins derived
therefrom, outside of the Research Program as part of CURAGEN's libraries for
internal, general, non-directed research purposes (including, without
limitation, full length cloning, protein-protein interactions and drug
screening). For example, but without limitation, inclusion of the Clone together
with other clones in research to

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determine multiple protein-protein interactions, or inclusion of the Clone
together with other clones in a screen against one or more molecules to
determine inhibition would be "non-directed" research, whereas activities
associated with choosing a specific Clone and conducting research to elucidate
the biological activity of such Clone (e.g., generating antibodies to the Clone,
testing the Clone or protein encoded thereby in preclinical models, enriching
libraries with such Clone to purposefully look for proteins which bind to such
Clone) would be considered "directed" research and CURAGEN shall not be
permitted to perform such activities under this Section 2.5.2. Such research
shall be Extended Research, and GENENTECH shall have rights to such Extended
Research and Extended Research Inventions and Extended Research Patent Rights
resulting therefrom as provided in Article 7 hereof and in Section 2.3 of the
License Agreement attached hereto as Appendix C. CURAGEN shall keep GENENTECH
                                     ---------- 
reasonably informed of the results of any such Extended Research and Extended
Research Patent Rights on a confidential and timely basis in order to allow
GENENTECH to make informed decisions regarding the exercise of its option and
license rights hereunder.

     2.5.3  Extensions.  GENENTECH may elect to extend the Exclusive Evaluation
            ----------                                                         
Period for any CURAGEN Data Set for an additional [XXXXX] by giving written
notice to CURAGEN and making a second payment of [XXXXX] to CURAGEN prior to
expiration of the initial Exclusive Evaluation Period for such CURAGEN Data Set.
An Exclusive Evaluation Period will be automatically extended for up to [XXXXX]
in order to allow the completion of any reasonable requests for confirmation of
data made by GENENTECH during the primary [XXXXX] period of such Exclusive
Evaluation Period. Following the expiration of the Exclusive Evaluation Period
for a CURAGEN Data Set, GENENTECH shall have no access to or right to use such
CURAGEN Data Set, other than as expressly permitted in an executed License
Agreement.

     2.6    DATA FROM PREVIOUS PROJECTS.  Pursuant to the Collaboration
            ---------------------------                                
Agreements, CURAGEN has generated the data sets listed on Appendix D hereto and
                                                          ----------           
has provided such data sets to GENENTECH.  Notwithstanding any other provision
of the Collaboration Agreements between the Parties, such data sets shall be
deemed Project Data Sets for all purposes hereunder and shall be deemed
completed as of the date indicated for each data set on Appendix D.  GENENTECH
                                                        ----------            
shall have exclusive access to all such Project Data Sets for Exclusive
Evaluation 

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Periods commencing on such indicated completion dates and continuing as provided
in Section 2.4, and shall have evaluation and option rights as otherwise
provided for Project Data Sets herein.

                              3.  FINANCIAL TERMS

     3.1  EQUITY INVESTMENT.  GENENTECH agrees to make an equity investment in
          -----------------                                                   
CURAGEN in the amount of Five Million Dollars ($5,000,000), such investment to
be made in a transaction exempt from registration under the Securities Act of
1933 pursuant to the terms of a stock purchase agreement in substantially the
form of Appendix F hereto.

     3.2  LOAN COMMITMENT.  As partial consideration for rights granted
          ---------------                                              
hereunder, GENENTECH hereby commits to the following:

     (a)  GENENTECH shall, subject to the terms set forth below, make funds
          available to CURAGEN for general corporate purposes in the form of a
          loan or loans to CURAGEN in an amount up to Twenty-One Million Dollars
          ($21,000,000.00) (the "Loan"). Unless this Agreement or the Research
          Program has been terminated for any reason (except that in the event
          of termination pursuant to Section 2.3.3(a) or 2.3.4(a), CURAGEN shall
          be permitted to continue to draw down the Loan for a period of thirty
          (30) days following any such notice of termination under Section
          2.3.3(a) or Section 2.3.4(a)), and subject to the drawdown limits
          discussed below, CURAGEN may, in such amounts and at such times as
          CURAGEN, in its sole discretion, may determine, draw down the balance
          of the Loan over a period of five (5) Loan Years (as defined below)
          following the Effective Date.  For the purposes of this section, a
          "Loan Year" commences on the Effective Date or an anniversary thereof
          and terminates twelve months later.  GENENTECH shall not be obligated
          to advance more than Nine Million Dollars ($9,000,000) in the first
          Loan Year, or more than a total Sixteen Million Dollars ($16,000,000)
          in the first two Loan Years or to advance any funds under the Loan at
          any time during which an Event of Default (as defined in the Note) has
          occurred and is continuing under the Note (defined below).
          Additionally, in the event that a temporary restraining order or
          preliminary injunction is entered against CURAGEN by a court of
          competent jurisdiction, the effect of which is to enjoin CURAGEN from
          utilizing its 

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          proprietary genomics technologies such that it is substantially unable
          to perform the Research Program, for as long as such temporary
          restraining order or preliminary injunction remains outstanding
          GENENTECH shall not be obligated to advance any funds under the Loan.
          GENENTECH's obligation to advance any funds under the Loan shall
          terminate upon the earlier to occur of (i) the last day of the fifth
          Loan Year, (ii) CURAGEN's receipt of notice of termination or the
          expiration of the Research Program or this Agreement, or (iii)
          termination or the expiration of the Research Program or this
          Agreement, except that in the event of termination pursuant to Section
          2.3.3(a) or 2.3.4(a), CURAGEN shall be permitted to continue to draw
          down the Loan for a period of thirty (30) days following notice of
          such termination under Section 2.3.3(a) or Section 2.3.4(a).
          Notwithstanding the foregoing, if GENENTECH has elected to continue
          this Agreement pursuant to Section 2.3.4(a)(iii), the maximum
          principal amount of the Loan will be increased to a total of Twenty-
          Six Million Dollars ($26,000,000.00), and CURAGEN may thereafter draw
          down the balance of such principal amount subject to the conditions
          described above.

     (b)  On the Effective Date, CURAGEN shall execute and deliver to GENENTECH
          an unsecured note, substantially in the form set forth in Appendix B
                                                                    ----------
          attached hereto and made a part hereof (the "Note"), evidencing the
          Loan.  The schedule attached to the Note shall be revised each time
          any amount is drawn down under the Loan and each time any amount is
          repaid.

     (c)  In the event that CURAGEN makes any repayment hereunder in CURAGEN
          Convertible Non-Voting Common Stock and CURAGEN is eligible to file a
          registration statement on Form S-3 (or successor short form) at the
          time of repayment, then within 20 days of the repayment date, CURAGEN
          shall file a registration statement on Form S-3 covering the resale by
          GENENTECH of the shares issuable upon conversion of any shares of
          Convertible Non-Voting Common Stock so delivered to GENENTECH.

                                       33

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     3.3  ADDITIONAL RESEARCH FUNDING.
          --------------------------- 

     In partial consideration of the work to be done by CURAGEN in the Research
Program, GENENTECH will pay CURAGEN non-refundable research payments of [XXXXX]
[XXXXX] in the Staffing Level above [XXXXX] FTEs. Such payments will be made
quarterly in advance, commencing on the first day of any calendar quarter in
which the Staffing Level is to increase above [XXXXX], and on or before the
first day of each calendar quarter thereafter. [XXXXX] In the event that the
Staffing Level is to change during any calendar quarter, such payment shall be
pro-rated accordingly, if necessary, based on the above-specified level of
funding per FTE. GENENTECH will fund its own activities under the Research
Program.

     3.4  ADDITIONAL ADVANCE.
          ------------------ 

     Notwithstanding the provisions of Section 3.2(a), in the event that, during
the term of the Loan, CURAGEN completes a public offering of shares of CURAGEN
Common Stock after any portion of the Note has been converted to CURAGEN Series
F Preferred Stock (the "Conversion Shares") pursuant to Section 6 of the Note,
GENENTECH shall, upon the written request of CURAGEN received within thirty (30)
days of such event (the "Redemption Notice"), advance to CURAGEN, under the
terms of the Note and Section 3.2(a) hereof, the aggregate Redemption Price (as
defined in the Certificate of Designation for the Series F Preferred Stock) of
the Conversion Shares (the "Redemption Amount").  CURAGEN shall use the
Redemption Amount received from GENENTECH solely for the purpose of repurchasing
the Conversion Shares from GENENTECH.  CURAGEN shall repurchase the Conversion
Shares, and GENENTECH shall sell and deliver the Conversion Shares to CURAGEN,
for a price equal to the Redemption Amount contemporaneously with the advance of
the Redemption Amount.

                                       34

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                   4.  TREATMENT OF CONFIDENTIAL INFORMATION

     4.1  CONFIDENTIAL INFORMATION.  During the course of the Research Program,
          ------------------------
or in discussions concerning Exclusive Data Sets, each Party may disclose to the
other proprietary technical, research and business information, including but
not limited to information contained in Data Sets (which Data Set information
shall be deemed Confidential Information of CURAGEN), (collectively,
"Confidential Information"). For a period of [XXXXX] after the receipt of any
such Confidential Information, except as expressly permitted hereunder, the
receiving Party shall keep confidential all such Confidential Information of the
other Party and will not disclose such Confidential Information of the other
Party to third parties by publication or otherwise. Each Party further agrees
not to use Confidential Information of the other Party for any purpose other
than conducting or evaluating research hereunder, evaluating and analyzing Data
Sets or exercising any rights granted to it or reserved by it under this
Agreement. Notwithstanding the foregoing, it is understood and agreed that the
receiving Party's obligations of confidentiality and nonuse herein shall not
apply to any information which:

     (a)  is, at the time of disclosure by the disclosing Party hereunder, or
          thereafter becomes, a part of the public domain or publicly known or
          available through no fault or negligence of the receiving Party or any
          of its Affiliates; or

     (b)  was otherwise in the receiving Party's lawful possession prior to
          disclosure by the disclosing Party, as demonstrated by the receiving
          Party's written records; or

     (c)  is lawfully disclosed to the receiving Party on a non-confidential
          basis by a third party who is not in violation of an obligation of
          confidentiality to the disclosing Party relative to such information.

Each Party may disclose the other Party's Confidential Information to the extent
reasonably necessary to comply with applicable government law or regulations,
provided that prompt notice of any such disclosure shall be given to the other
Party.  Information disclosed other than in written or electronic form shall be
subject to the terms of this Section 4.1 only if confirmed in

                                       35

                       Confidential Treatment Requested
<PAGE>
 
writing to other Party within thirty (30) days of initial disclosure and
specifying with particularity that Confidential Information disclosed other than
in written form which is subject to the provisions of this Section 4.1.

     4.2  PUBLICATIONS.  It is expected that each Party may wish to publish the
          -------------                                                        
results of the research under this Agreement. In order to safeguard intellectual
property rights, the Party wishing to publish or otherwise publicly disclose the
results of its research hereunder shall first submit a draft of the proposed
manuscripts to the RC for each Party's review, comment and consideration of
appropriate patent action at least [XXXXX] prior to any submission for
publication or other public disclosure. Within [XXXXX] of receipt of the
prepublication materials, the RC will advise the Party seeking publication as to
whether a patent application will be prepared and filed or whether trade secret
protection should be pursued and, if so, the RC will, in cooperation with both
parties, determine the appropriate timing and content of any such publications.
CURAGEN shall have the right to reasonably withhold consent for publications
based primarily upon CURAGEN Projects. CURAGEN shall also have the right to
reasonably withhold consent for publication of QEA/GeneCalling or
MIM/PathCalling data. Each Party shall have the right to reasonably withhold
consent for publication of its own Confidential Information provided to the
other Party hereunder. Consent to all other publications regarding Clones shall
be governed by the RC as indicated above in this Section.

     4.3  PRESS RELEASE AND REGULATORY FILINGS.  The Parties shall mutually
          -------------------------------------                            
agree on a press release announcing the execution of this Agreement and on any
confidential treatment request to be filed with the Securities and Exchange
Commission with respect to this Agreement. Once any such written statement is
approved for disclosure by both Parties, either Party may make subsequent public
disclosures of the contents of such statement without the further approval of
the other Party. Neither Party shall make any disclosure of the terms of this
Agreement except as required by applicable law or as set forth above without the
prior written consent of the other Party.

                                       36

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                       5.  INTELLECTUAL PROPERTY RIGHTS

     5.1  GENENTECH PROPRIETARY MATERIAL.  mRNA pools extracted by CURAGEN from
          ------------------------------                                       
a GENENTECH Proprietary Material in the performance of the Research Program and
full-length genes cloned by GENENTECH using any Clone shall be GENENTECH
Proprietary Material.  All other substances made by CURAGEN in the performance
of the Research Program shall be Research Project Proprietary Material and all
other substances made by GENENTECH shall be GENENTECH Proprietary Material.
Except as provided in Section 7.5 or in an executed License Agreement, GENENTECH
Proprietary Material shall remain the property of GENENTECH, and CURAGEN shall
use such GENENTECH Proprietary Material only for the purpose of conducting the
Research Program hereunder or as otherwise permitted herein, and shall not
transfer GENENTECH Proprietary Material to any other person or entity.

     5.2  CURAGEN PROJECT PROPRIETARY MATERIAL AND RESEARCH PROJECT PROPRIETARY
          ---------------------------------------------------------------------
MATERIAL.
- -------- 

     (a)  CURAGEN Project Proprietary Material shall remain the property of
          CURAGEN and GENENTECH shall use such CURAGEN Project Proprietary
          Material only for purposes relating to performance of the Research
          Program, evaluation of the CURAGEN Data, the exercise of the option
          provided in Section 7.1, or pursuant to the terms of an executed
          License Agreement.  GENENTECH shall not transfer CURAGEN Project
          Proprietary Material to any other person or entity except in
          connection with rights granted to GENENTECH pursuant to an executed
          License Agreement.  CURAGEN shall not transfer to any third party or
          otherwise use CURAGEN Project Proprietary Material during an Exclusive
          Evaluation Period or Option Period except as otherwise permitted
          herein.

     (b)  Research Project Proprietary Material shall remain the property of
          CURAGEN and GENENTECH shall use such Research Project Proprietary
          Material only for purposes relating to performance of the Research
          Program, evaluation of the Project Data, the exercise of the option
          provided in Section 7.1, or pursuant to the terms of an executed
          License Agreement.  GENENTECH shall not transfer

                                       37
<PAGE>
 
          Research Project Proprietary Material to any other person or entity
          except in connection with rights granted to GENENTECH pursuant to an
          executed License Agreement.  CURAGEN shall not transfer to any third
          party or otherwise use Research Project Proprietary Material during an
          Exclusive Evaluation Period or Option Period except as otherwise
          permitted herein.

     5.3  INVENTIONS.  Each Party shall promptly disclose to the other Party all
          -----------                                                           
Inventions. During the term of any Exclusive Evaluation Period or relevant
Option Period, CURAGEN shall not use Research Project Inventions, Project Data,
CURAGEN Project Inventions or CURAGEN Data to support patent filings made by
CURAGEN outside the Research Program without GENENTECH's express prior written
consent.  GENENTECH shall not at any time use Research Project Inventions,
Project Data, CURAGEN Project Inventions or CURAGEN Data to support patent
filings made by GENENTECH outside the Research Program except to the extent that
such filings relate to Licensed Clones or corresponding Licensed Products.
Except as set forth in Sections 5.1 and 5.2, (i) all Research Project
Inventions, and Research Project Patent Rights shall be owned jointly by CURAGEN
and GENENTECH; and (ii) all CURAGEN Project Inventions and CURAGEN Project
Patent Rights shall be owned by CURAGEN.  Inventorship of Patent Rights shall be
agreed upon in good faith by the Parties prior to the filing of each new patent
application in accordance with applicable law.  The rights and interests of
CURAGEN and GENENTECH in Inventions shall be subject to the provisions of
Article 7.

             6.  PROVISIONS CONCERNING THE FILING, PROSECUTION AND
                         MAINTENANCE OF PATENT RIGHTS

     6.1  APPLICABILITY.  The provisions of this Section 6 shall be applicable
          -------------                                                       
to all Inventions and Patent Rights unless and until (i) they become subject to
a License Agreement, whereupon the License Agreement will govern the rights of
the parties with respect to the subject matter thereof, or (ii) the relevant
Research Project is completed and the relevant Exclusive Evaluation Period
expires and the relevant Option Period, if any, expires, whereupon this Section
6 shall cease to apply with respect to Inventions and Patent Rights relating to
such Research Project or License Agreement.

                                       38
<PAGE>
 
     6.2  PATENT FILING.
          ------------- 

     (a)  CURAGEN shall have the responsibility to prepare, file, prosecute,
          obtain and maintain U.S. and foreign patent applications and patents
          on Inventions at its sole expense.  Initial patent filings shall be
          made in the form of a regular CFR Rule 1.51 U.S. Priority patent
          application or a provisional application, as determined by the Patent
          Coordinators.  The Patent Coordinators for each Party will be
          designated by such Party from time to time.  Patent applications will
          be perfected by making, as soon as available, an ATCC deposit of at
          least such Clone(s) as reasonably agreed by the Patent Coordinators,
          and by making any subsequent application filings necessary to perfect
          U.S. or foreign priority patent rights in the countries of Europe that
          are members of the European Patent Organization, Japan, Canada, Mexico
          and at least such other countries as mutually agreed by the Parties.
          GENENTECH agrees to provide reasonable and timely assistance and
          cooperation to CURAGEN to facilitate such filing, prosecution and
          maintenance, including without limitation, the execution of
          appropriate powers of attorney.  CURAGEN agrees that any such
          preparation, filing, prosecution and maintenance shall be conducted
          diligently and in a timely fashion.  GENENTECH shall be kept fully
          informed by CURAGEN of the progress of all patent filings and
          prosecution hereunder and shall be provided with copies of all
          material documents pertaining thereto including, without limitation,
          information regarding inventorship, sequences and sequence listings,
          serial numbers, filing dates, foreign filing licenses and copies of
          patent applications, until the end of the Exclusive Evaluation Period,
          and for any Invention which becomes subject to an Option, until the
          end of the Option Period.  GENENTECH shall be given the opportunity,
          whenever practical, to review and comment in advance on any patent
          filings or other correspondence with the patent office during such
          periods and CURAGEN shall use reasonable efforts to incorporate any
          comments provided by GENENTECH.  CURAGEN shall pursue its priority to
          claims on Inventions by filing all necessary interferences and
          opposition papers, motions and the like.  

                                       39
<PAGE>
 
          Any proposed interference settlement agreement relating to Inventions
          subject to potential Option by GENENTECH hereunder will be reviewed by
          the RC.

     (b)  If CURAGEN is unable to file patent applications as set forth in
          Section 6.2(a) on a timely basis despite diligent efforts concerning
          Inventions made regarding Clones where the majority of the sequencing
          of such Clones has taken place at GENENTECH, GENENTECH shall have the
          option to prepare, file, prosecute, obtain and maintain patent
          applications and patents on Inventions in the same manner as described
          in Section 6.2(a) above at any time for any such Inventions by giving
          written notice thereof to GENENTECH.  Following the receipt of such
          notice and the election of such option by GENENTECH, GENENTECH shall
          have the right to prepare, file, prosecute, obtain and maintain the
          patent application(s) and patent(s) identified in the notice, at its
          sole expense, on behalf of the owner of the Invention, subject to the
          rights granted herein, until the end of the Exclusive Evaluation
          Period, and for any Invention which becomes subject to an Option,
          until the end of the Option Period.  CURAGEN shall be given the
          opportunity to review and comment in advance on any patent filings or
          other correspondence with the patent office during such periods and
          GENENTECH shall use reasonable efforts to incorporate any comments
          provided by CURAGEN.

     (c)  The Parties shall mutually agree before permitting any patent
          application or patent within Patent Rights to lapse as well as before
          authorizing any amendment to any patent application or patent within
          Patent Rights that would irrevocably limit the lawful scope of the
          Patent Rights, until the end of the Exclusive Evaluation Period, and
          for any Invention which becomes subject to an option, until the end of
          the Option Period.

     (d)  No Party shall have any obligation under this Agreement to pay any
          fees or costs: (i) for bringing a lawsuit or other action to enforce
          any of the Patent Rights against an actual or suspected infringement
          or (ii) for any other Party to obtain for its own benefit independent
          business or legal advice concerning any of the Patent Rights.

                                       40
<PAGE>
 
     6.3   NOTICE OF INFRINGEMENT.  If either Party learns of any infringement
           ----------------------
or threatened infringement by a third party of the patents within Patent Rights,
such Party shall promptly notify the other Party and shall provide such other
Party with available evidence of such infringement.

     6.4   INFRINGEMENT.  CURAGEN shall have all rights, at its own expense, to
           ------------                                                        
bring suit (or other appropriate legal action) against any actual or suspected
infringement of the Patent Rights except as may be provided in a License
Agreement executed by the Parties.

     6.5   COOPERATION.  Each Party shall execute all papers and perform such
           -----------                                                       
other acts as may be reasonably required to file and prosecute any patent
applications as provided in Section 6.2 and to maintain any infringement suit
brought in accordance with Section 6.4 above (including giving legal consent for
bringing such suit, and agreeing to be named as a plaintiff or otherwise joined
in such suit), and at its option and expense, may be represented in such suit by
counsel of its choice.

                            7.  OPTION TO GENENTECH
                                        
     7.1   OPTION GRANT.
           ------------ 

     7.1.1 Option.  Subject to rights third parties have obtained by virtue of
           ------                                                             
access to other CURAGEN Data Sets, data sets resulting from written agreements
between CURAGEN and third parties, or the subscription portion of the
GeneScape(R) database prior to GENENTECH's election, CURAGEN hereby grants to
GENENTECH the right to elect an exclusive option (the "Option") to license all
Inventions and know-how relating to any Clone whose sequence or utility is
determined in whole or in part by GENENTECH or CURAGEN from the use of an
Exclusive Data Set or which is identified by GENENTECH pursuant to the rights
granted in Section 2.4.3, and which is not a Previously Committed Clone.  Such
Option shall give GENENTECH the right to obtain, at GENENTECH's sole discretion
and as further described in the License Agreement, either (a) subject to the
rights reserved by CURAGEN in Section 7.1.3 hereof, an exclusive license to the
Clone specified in GENENTECH's notice of exercise (the "Optioned Clone") and to
all Research Project Patent Rights, CURAGEN Project Patent Rights, Inventions,
Extended Research Inventions, Extended Research Patent Rights and know-how to
the extent that they relate to such Optioned Clone or Licensed Products related
to such Optioned 

                                       41
<PAGE>
 
Clone, to develop, make, have made, use, have used, sell, offer for sale, have
sold, import and have imported any and all products, in the Territory, for any
and all human uses; (b) a non-exclusive license to the Optioned Clone under all
Research Project Patent Rights, CURAGEN Project Patent Rights, Inventions and
know-how, to the extent that they relate to such Optioned Clone, solely for use
of the Optioned Clone or the protein encoded thereby as a reagent for
discovering or developing Licensed Products and to develop, make, have made,
use, have used, sell, offer for sale, have sold, import and have imported
Licensed Products; or (c) subject to the rights reserved by CURAGEN in Section
7.1.3 hereof, an exclusive license to all Research Project Patent Rights,
CURAGEN Project Patent Rights, Inventions, Extended Research Inventions,
Extended Research Patent Rights and know-how to the extent that they relate to a
"known" Optioned Clone or Licensed Products related to such Optioned Clone, to
develop, make, have made, use, have used, sell, offer for sale, have sold,
import and have imported any and all products, in the Territory, for any and all
human uses. Such Option shall be exercisable at any time during the Option
Period specified in Section 7.3. If any Previously Committed Clone is or becomes
available for licensing by GENENTECH on an exclusive or non-exclusive basis,
CURAGEN shall so notify GENENTECH and GENENTECH shall have the right to obtain
an option to license any available rights on the terms set forth in the form of
License Agreement attached hereto as Appendix C.

     7.1.2 Option Election.
           --------------- 

     Such Option shall be elected by GENENTECH by giving written notice to
CURAGEN within the Exclusive Evaluation Period for such Exclusive Data Set,
which shall specify in detail the Optioned Clone to be included within the terms
of any such Option and which shall be accompanied by the payment of any Option
Fee as specified in Section 7.2.  Each Optioned Clone, and the term of the
corresponding Option Period, shall be listed on Appendix A hereto from time to
                                                ----------                    
time.  Notwithstanding the foregoing, GENENTECH may request such an Option from
Project Data Sets after expiration of the Exclusive Evaluation Period, which
Option shall be granted by CURAGEN upon payment of the Option Fee specified in
Section 7.2, unless prohibited by written agreements with third parties.

     7.1.3 Reservation of Rights.  Notwithstanding the foregoing, during any
           ---------------------                                            
Option Period, CURAGEN shall retain for itself the right to use, but not to
transfer to third parties (except 

                                       42
<PAGE>
 
pursuant to an agreement with a third party who has identified such Optioned
Clone independently of the related Data Set) the Optioned Clone or the protein
derived therefrom outside of the Research Program as part of CURAGEN's libraries
for internal, general, non-directed research purposes (including, without
limitation, full length cloning, expression analysis, protein-protein
interactions and drug screening). For example, but without limitation, inclusion
of the Clone together with other clones in research to determine multiple
protein-protein interactions, or inclusion of the Clone together with other
clones in a screen against one or more molecules to determine inhibition would
be "non-directed" research, whereas activities associated with choosing a
specific Clone and conducting research to elucidate the biological activity of
such Clone (e.g., generating antibodies to the Clone, testing the Clone or
protein encoded thereby in preclinical models, enriching libraries with such
Clone to purposefully look for proteins which bind to such Clone) would be
considered "directed" research and CURAGEN shall not be permitted to perform
such activities under this Section 7.1.3. All inventions conceived or made
during such research which relate to any Clone whose sequence or utility is
determined from the analysis of a Project Data Set, the proteins derived
therefrom (including antibodies), homologs or mutants with substantially the
same biological activity as such Clone, or uses thereof, shall be deemed
Research Project Inventions if licensed by GENENTECH. All other inventions from
such research shall be Extended Research Inventions and GENENTECH will have
rights to such Extended Research Inventions and Extended Research Patent Rights
resulting therefrom as provided in this Article 7 and in Section 2.3 of the
License Agreement attached hereto as Appendix C. CURAGEN shall keep GENENTECH
reasonably informed of the results of any such research using an Optioned Clone
and patent applications and patents relating to such research on a timely basis
in order to allow GENENTECH to make informed decisions regarding the exercise of
its option and license rights hereunder.

     7.2  OPTION FEE.  An Option Fee of [XXXXX] per Optioned Clone shall be due
          ----------                                                            
upon the election of an Option with respect to any Clone from any Exclusive Data
Set; provided, however, that [XXXXX]

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     7.3  OPTION PERIOD.  Each Option shall remain in effect for a period of
          -------------                                                     
[XXXXX] from receipt by CURAGEN of GENENTECH's written notice of its election of
such Option and payment of any required Option Fee (the "Option Period");
provided, however, that any Option Period may be extended for one additional
[XXXXX] period upon payment by GENENTECH of an additional [XXXXX] per Optioned
Clone.

     7.4  OPTION EXERCISE.  During each Option Period, upon notice to CURAGEN
          ---------------                                                    
and upon payment of the corresponding license fee, GENENTECH shall have the
right to receive a license to the Optioned Clone under the terms and conditions
set forth in an executed License Agreement and CURAGEN shall grant such license
to GENENTECH.  The license fee for a license described in Section 7.1.1, clause
(a) shall be [XXXXX] and the license fee for a license described in Section
7.1.1, clause (b) or (c), shall be [XXXXX].  The License Agreement shall be
executed in substantially the form attached hereto upon exercise of the first
Option and shall be amended from time to time in accordance with the terms
hereof and thereof as additional Options are exercised.

     7.5  REVERSION OF RIGHTS.  CURAGEN shall retain all rights to all Project
          -------------------                                                 
Data, CURAGEN Data, Extended Research Data, CURAGEN Project Proprietary
Material, Research Project Proprietary Material, Inventions, Extended Research
Inventions, Patent Rights and Extended Research Patent Rights not expressly
granted to GENENTECH hereunder.  Upon expiration of any Exclusive Evaluation
Period for any Research Project or CURAGEN Project CURAGEN shall recover and
retain, with respect to Clones whose sequence or utility was determined from
such project and that are not optioned by GENENTECH, all of CURAGEN's rights to
the corresponding Exclusive Data Set, Extended Research Data, CURAGEN Project
Proprietary Material or Research Project Proprietary Material and corresponding
Inventions, Extended Research Inventions, Patent Rights and Extended Research
Patent rights thereon, other than such rights granted to GENENTECH as provided
in Sections 2.1.4(c), 2.4.3 or 7.1.2 or, with respect to Optioned Clones,
Section 2.1.5.  In the event that upon the expiration of any Option Period any
corresponding Option has not been exercised by GENENTECH, all of CURAGEN's
rights in the corresponding Optioned Clone and related Project Data, CURAGEN
Data, Extended Research Data, CURAGEN Project Proprietary Material, Research
Project Proprietary Material, Inventions, Extended Research Inventions, Patent
Rights and Extended Research Patent Rights 

                                       44

                       Confidential Treatment Requested
<PAGE>
 
thereon shall revert to CURAGEN, other than such rights granted to GENENTECH as
provided in Sections 2.1.4(c), 2.4.3 or 7.1.2, or with respect to Optioned
Clones, Section 2.1.5. Notwithstanding the foregoing, nothing contained in this
Section 7.5 shall be deemed to limit any rights of GENENTECH expressly provided
in an executed License Agreement. In addition, GENENTECH shall (a) upon the
expiration of each Exclusive Evaluation Period, without any further action on
its part, be deemed to have granted to CURAGEN an exclusive (except for uses by
GENENTECH permitted in Sections 2.1.4(c), 2.4.3 and 7.1.2) license, with the
right to sublicense, for all purposes under GENENTECH's rights in Research
Project Inventions and Research Project Patent Rights relating to any Clone
whose sequence or utility was determined in whole or in part from the use of the
corresponding Data Set and which is not the subject of any Option or License
Agreement and (b) upon the expiration of each Option Period, without any further
action on its part, be deemed to have granted to CURAGEN a license as set forth
in (a) above with respect to each Optioned Clone for which an Option has not
been exercised. Such licenses from GENENTECH to CURAGEN shall be [XXXX]. Upon
the request of CURAGEN, GENENTECH shall provide to CURAGEN available GENENTECH
Proprietary Material which is a full-length gene cloned by GENENTECH using any
Clone described in (a) above and which is not contained in a proprietary vector.
For the avoidance of doubt, CURAGEN shall have no rights to any patents or
patent applications of GENENTECH which relate to inventions (including
inventions related to Clones) made outside the Research Program and CURAGEN
shall only have exclusive rights to Research Project Inventions and Research
Project Patent Rights as expressly provided herein.

     7.6  NO OTHER RIGHTS.  No rights to Data Sets or Clones under Patent
          ---------------                                                
Rights, Inventions, Extended Research Patent Rights or Extended Research
Inventions are granted to GENENTECH hereunder except as expressly set forth
herein or in an executed License Agreement.  CURAGEN shall receive no rights to
Data Sets or Clones under GENENTECH's interests in Research Project Patent
Rights or Research Project Inventions except as expressly set forth herein or in
an executed License Agreement.

     7.7  ROYALTIES TO GENENTECH.
          ----------------------

      (a) Solely with respect to any novel, full-length gene cloned as part of a
          Research Project and not licensed by GENENTECH pursuant to an executed
          License 

                                       45

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<PAGE>
 
          Agreement, which gene (a "Retained Gene") is covered by Research
          Project Patent Rights, CURAGEN shall pay royalties to GENENTECH with
          respect to each Licensed Product developed and commercialized by
          CURAGEN and its Affiliates and sublicensees from any Clone which is a
          Retained Gene (a "CURAGEN Royalty Product") on a country-by-country
          basis as follows:

          (i)   If the CURAGEN Royalty Product is as described in Subsections 
                (a)-(c) of the definition of Licensed Product, the royalty rate
                on Net Sales of such CURAGEN Royalty Product shall be as
                follows:

                [XXX]   if the manufacture, use, importation or sale in such 
                        country of such CURAGEN Royalty Product by a third party
                        would infringe a Valid Claim of a Research Project
                        Patent Right.

          (ii)  If the CURAGEN Royalty Product is as described in Subsections 
                (d)-(i) of the definition of Licensed Product, the royalty rate
                on Net Sales of such CURAGEN Royalty Product shall be:

                [XXX]   if the manufacture, use, importation or sale in such 
                        country of such CURAGEN Royalty Product by a third party
                        would infringe a Valid Claim of a Research Project
                        Patent Right.

          (iii) Royalties due to GENENTECH pursuant to subsections (i) and (ii) 
                above for a given CURAGEN Royalty Product may be reduced by
                [XXX] of any royalties paid to third parties by CURAGEN on net
                sales of such CURAGEN Royalty Product under patent licenses that
                are required in order to allow CURAGEN to manufacture, use and
                sell such CURAGEN Royalty Product; provided, however, that such
                reductions shall in no event reduce the royalty for such CURAGEN
                Royalty Product payable pursuant to such subsection by more
                than [XXX].


                                      46

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<PAGE>
 
      (b) Notwithstanding the foregoing, in the event that the Retained Gene was
          at any time during the Term of this Agreement an Optioned Clone, or
          was ever a Licensed Clone, the royalty due to GENENTECH pursuant to
          Section 7.7(a) shall be [XXX].

      (c) Notwithstanding the foregoing, in the event that CURAGEN Royalty 
          Products are sold by sublicensees of CURAGEN, and the royalty received
          by CURAGEN under such sublicense is less than two times the applicable
          royalty due to GENENTECH pursuant to Section 7.7(a) and (b) hereof,
          the amount payable to GENENTECH under this Section 7.7 shall be [XXX]
          of (i) royalties, (ii) licenses fees and (iii) product development
          milestone payments based on the sublicensee's performance, received by
          CURAGEN or its Affiliates. For the avoidance of doubt (x) equity
          payments, (y) research funds and (z) milestone payments based on
          CURAGEN'S research performance, received by CURAGEN or its Affiliates
          from a sublicensee shall not be included in such calculation. CURAGEN
          shall not intentionally structure any sublicense agreement in order to
          shift payments from categories (i), (ii) or (iii) to categories (x),
          (y) or (z), so as to reduce amounts payable to GENENTECH hereunder.
          Copies of all executed sublicenses of CURAGEN's rights hereunder shall
          be provided to GENENTECH.

      (d) Only one royalty, calculated at the highest applicable royalty rate 
          hereunder, shall be payable to GENENTECH hereunder for each sale of
          a CURAGEN Royalty Product, regardless of the number of patents, patent
          applications or Valid Claims directed to or covering such CURAGEN
          Royalty Product.

      (e) Royalty payments shall be made to GENENTECH in United States Dollars 
          quarterly within sixty (60) days following the end of each calendar
          quarter for which royalties are due. Each royalty payment shall be
          accompanied by a report summarizing the total Net Sales for each
          CURAGEN Royalty Product during 


                                       47

                      [Confidential Treatment Requested]
<PAGE>         


          the relevant three-month period and the calculation of royalties, if
          any, due thereon pursuant to this Section 7.7. All royalties shall be
          payable in full in the United States in United States Dollars,
          regardless of the countries in which sales are made. For the purpose
          of computing Net Sales for CURAGEN Royalty Products sold in a currency
          other than United States dollars, such currency shall be converted
          into United States dollars at the exchange rate for buying U.S.
          dollars set forth in The Wall Street Journal for the last business day
                               -----------------------
          of the calendar quarter.
          
      (f) CURAGEN shall pay royalties with respect to each CURAGEN Royalty 
          Product on a country by country basis until (i) the expiration or
          revocation or complete rejection of the last to expire or to be
          revoked or to be completely rejected of any Valid Claim of a GENENTECH
          Patent Right covering such CURAGEN Royalty Product in such country, or
          (ii) ten (10) years from the first commercial sale of such CURAGEN
          Royalty Product in such country, whichever is later. Following such
          period, CURAGEN shall have a fully paid-up, irrevocable license in
          such country under the relevant GENENTECH Patent Rights to make, have
          made, use, have used, sell, have sold, offer for sale, import and have
          imported such CURAGEN Royalty Product in such country.

      (g) OVERDUE ROYALTIES. Royalties not paid within the time period set forth
          -----------------
          in this Section 7.7 shall bear interest at [XXX] accruing monthly,
          from the due date until paid in full.

      (h) RECORDS RETENTION. AUDITS. CURAGEN shall keep for [XXX] from the date 
          -------------------------
          of each payment of royalties complete and accurate records of sales by
          CURAGEN of each CURAGEN Royalty Product in sufficient detail to allow
          the accruing royalties to be determined accurately. GENENTECH shall
          have the right for a period of [XXX] after receiving any report or
          statement with respect to royalties due an payable to appoint an
          independent certified public accountant reasonably acceptable to
          CURAGEN to inspect the relevant records of


                                      48

                      [Confidential Treatment Requested]
<PAGE>
 
          CURAGEN to verify such report or statement. CURAGEN shall make its
          records available for inspection by such independent certified public
          accountant during regular business hours at such place or places where
          such records are customarily kept, upon reasonable notice from
          GENENTECH, solely to verify the accuracy of the reports and payments.
          Such inspection right shall not be exercised more than once in any
          calendar year nor more than once with respect to sales of any CURAGEN
          Royalty Product in any given payment period. GENENTECH agrees to hold
          in strict confidence all information concerning royalty payments and
          reports, and all information learned in the course of any audit or
          inspection, except to the extent necessary for GENENTECH to reveal
          such information in order to enforce its rights under this Agreement
          or if disclosure is required by law, regulation or judicial order. The
          results of each inspection, if any, shall be binding on both Parties.
          GENENTECH shall pay for such inspections, except that in the event
          there is any upward adjustment in aggregate royalties payable for any
          year shown buy such inspection of more than [XXX] of the amount paid,
          CURAGEN shall pay for such inspection.

                           8.  TERM AND TERMINATION

     8.1  TERM.  The term of this Agreement shall be for the duration of the
          ----                                                              
Research Term plus the length of all surviving Exclusive Evaluation Periods and
any permitted extensions thereof and the length of all surviving Option Periods
and any permitted extensions thereof or until the date on which GENENTECH no
longer has access to Project Data Sets hereunder, whichever is later (the
"Term").

     8.2  TERMINATION.
          ----------- 

     (a)  This Agreement, the Research Program, and the rights granted herein
          may be terminated by either Party upon any breach by the other Party
          of any material obligation or condition, effective fifteen (15) days
          after giving written notice to the other Party of such termination in
          the case of a payment breach and sixty (60) days after giving  written
          notice to the other Party of such termination in the case 

                                       49

                       Confidential Treatment Requested
<PAGE>
 
          of any other breach, which notice shall describe such breach in
          reasonable detail. The foregoing notwithstanding, if the default or
          breach is cured or shown to be non-existent within the aforesaid
          fifteen (15) or sixty (60) day period, the notice shall be deemed
          automatically withdrawn and of no effect.

     (b)  If either Party files for protection under bankruptcy laws, makes an
          assignment for the benefit of creditors, appoints or suffers
          appointment of a receiver or trustee over its property, files a
          petition under any bankruptcy or insolvency act or has any such
          petition filed against it which is not discharged within sixty (60)
          days of the filing thereof, then the other party may terminate the
          Research Program and this Agreement effective upon giving written
          notice to such Party.

     8.3  TERMINATION AFTER INJUNCTION.  In addition to the rights set forth in
          ----------------------------                                         
Section 8.2, GENENTECH may terminate the Research Program effective thirty (30)
days after giving written notice to CURAGEN in the event that a final non-
appealable injunction is entered against CURAGEN by a court of competent
jurisdiction the effect of which is to enjoin CURAGEN from utilizing its
proprietary genomics technologies such that it is substantially unable to
perform the Research Program.  Any such termination shall not affect GENENTECH's
rights hereunder with respect to any Exclusive Evaluation Period or Option
Period then ongoing, or any License Agreement executed by the Parties prior to
such termination.  Upon any such termination the Note shall become due in
accordance with its terms.

     8.4  ADDITIONAL EFFECTS OF TERMINATION.
          --------------------------------- 

     (a)  Upon termination of this Agreement by a Party pursuant to Section
          8.2(a) due to a payment breach by the other Party with respect to
          payments due on a specific product pursuant to Section 2.1.4(c) and
          (e) or Section 7.7. hereof (but not any other breach), all relevant
          rights and licenses granted by such terminating Party to the breaching
          Party under such Section regarding the specific product shall
          immediately and automatically terminate and revert to the terminating
          Party, subject to the breaching Party's right to sell any remaining
          quantities of product remaining in its inventories as of the date of
          termination.

     (b)  Upon termination of this Agreement by a Party pursuant to Section
          8.2(a) due to a breach other than a payment breach covered by Section
          8.4(a), the Research 

                                       50
<PAGE>
 
          Program shall end. If CURAGEN is the terminating Party, all Exclusive
          Evaluation Periods and all Option Periods shall terminate, but all
          License Agreements previously executed shall continue. If GENENTECH is
          the terminating Party, all of GENENTECH's rights under Exclusive
          Evaluation Periods, Option Periods and License Agreements then ongoing
          shall continue in accordance with their terms, and the Note shall
          become due in accordance with its terms.

     (c)  Documentation.  At the request of the terminating Party, the breaching
          -------------                                                         
          Party shall execute and deliver such bills of sale, assignments and
          licenses and other documents as may be necessary to fully vest in the
          non-breaching Party all right, title and interest to which it is
          entitled as aforesaid pursuant to this Section 8.4.

     (d)  Payment Obligations.  The breaching Party shall have no obligation to
          -------------------                                                  
          make any payment to the terminating Party that has not accrued prior
          to the effective date of such termination except for royalties on
          remaining inventory, but shall remain liable for all obligations
          accruing prior to termination.

     8.5  REMEDIES.  If either Party shall fail to perform or observe or
          --------                                                      
otherwise breaches any of its material obligations under this Agreement, in
addition to any right to terminate this Agreement, the non-defaulting Party may
elect to obtain other relief and remedies available under law.

     8.6  SURVIVING PROVISIONS.  Notwithstanding any provision herein to the
          --------------------                                              
contrary, the rights and obligations set forth in Sections 2.1.6, 2.3.5, 3.2,
3.4, Articles 4, 5, and 6, and Sections 7.5, 8.4 and 8.6, and Article 9 hereof,
as well as any rights and obligations otherwise accrued, shall survive the
expiration of the Term or any termination of this Agreement.  In addition, the
rights and obligations set forth in Sections 2.1.4 (c)-(h) and Section 7.7 shall
survive the expiration or termination of this Agreement, unless otherwise
terminated as specified in Section 8.4 above, and the rights and obligations
with respect to ongoing Exclusive Evaluation Periods and Option Periods shall
survive as described elsewhere in this Agreement.

                                       51
<PAGE>
 
                               9.  MISCELLANEOUS

     9.1  CURAGEN REPRESENTATIONS AND COVENANTS.  CURAGEN represents and
          -------------------------------------                         
warrants that:  (a) the execution and delivery of this Agreement and the
performance of the transactions contemplated hereby have been duly authorized by
all appropriate CURAGEN corporate action; (b) CURAGEN is under no obligation
which is inconsistent with this Agreement; (c) CURAGEN employees are
contractually bound to assign all rights in inventions and know-how arising from
their employment to CURAGEN; (d) there are no adverse proceedings claims or
actions pending, or to the best of CURAGEN's knowledge, threatened relating to
CURAGEN's genomics technologies, including without limitation, GeneScape,
QEA/GeneCalling, MIM/PathCalling and all additional services to be provided by
CURAGEN to GENENTECH hereunder, and at the time of disclosure and access thereof
to GENENTECH, to the best of CURAGEN's knowledge, CURAGEN shall have the full
right and legal capacity to disclose and provide access to such CURAGEN genomics
technologies to GENENTECH and to itself use such technologies to perform its
obligations under this Agreement without violating the rights of third parties;
and (e) CURAGEN has the full right and legal capacity to grant the rights to
GENENTECH pursuant to Article 7 without violating the rights of any third party.
CURAGEN covenants that it will not enter into any agreement with any third party
that is inconsistent with the terms of this Agreement. Subject to CURAGEN's
obligation not to enter into any agreement that is inconsistent with the terms
of this Agreement, CURAGEN shall use commercially reasonable efforts to obtain,
at its sole cost, any rights, licenses, approvals or permissions related to its
genomics technology and know-how that are required, now or in the future, to
carry out its obligations to conduct the Research Projects hereunder and to
provide its services and genomics technologies to GENENTECH hereunder and to
grant GENENTECH the intellectual property rights under Article 7 above. Nothing
in this Agreement shall be interpreted as obligating either Party to
commercialize technology made hereunder or to perform any additional work beyond
that set forth in the Research Plan.

     9.2  GENENTECH REPRESENTATIONS.  GENENTECH represents and warrants that:
          -------------------------                                           
(a) the execution and delivery of this Agreement and the performance of the
transactions contemplated hereby have been duly authorized by all appropriate
GENENTECH corporate 

                                       52
<PAGE>
 
action; (b) GENENTECH is under no obligation which is inconsistent with this
Agreement, and (c) GENENTECH has the full right and legal capacity to grant the
rights to CURAGEN pursuant to Article 7 without violating the rights of any
third party. Nothing in this Agreement shall be interpreted as obligating either
Party to commercialize technology made hereunder or to perform any additional
work beyond that set forth in the Research Plan.

     9.3  NO WARRANTIES.
          ------------- 

     (a) Nothing in this Agreement is or shall be construed as:

               (i)  a warranty or representation by CURAGEN or GENENTECH as to
                    the validity or scope of any application or patent within
                    the Patent Rights;

               (ii) a warranty or representation that anything made, used, sold
                    or otherwise disposed of under any license granted pursuant
                    to this Agreement is or will be free from infringement of
                    patents, copyrights, and other rights of third parties.

     (b)  Except as expressly set forth in this Agreement, NEITHER PARTY MAKES
          ANY REPRESENTATIONS OR EXTENDS ANY WARRANTIES OF ANY KIND, EITHER
          EXPRESS OR IMPLIED.  THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF
          MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR OF NON-
          INFRINGEMENT OF ANY PATENT, COPYRIGHT, TRADEMARK, OR OTHER RIGHTS, OR
          ANY OTHER EXPRESS OR IMPLIED WARRANTIES.

     9.4  LIABILITY.  NOTWITHSTANDING ANYTHING ELSE IN THIS AGREEMENT OR
          ---------                                                     
OTHERWISE, NEITHER PARTY WILL BE LIABLE WITH RESPECT TO ANY SUBJECT MATTER OF
THIS AGREEMENT UNDER ANY CONTRACT, NEGLIGENCE, STRICT LIABILITY OR OTHER LEGAL
OR EQUITABLE THEORY FOR (I) ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL OR PUNITIVE
DAMAGES OR LOST PROFITS OR (II) COST OF PROCUREMENT OF SUBSTITUTE GOODS,
TECHNOLOGY OR SERVICES.

     9.5  NOTICES.  Any notices, requests, deliveries, approvals or consents
          -------                                                           
required or permitted to be given under this Agreement to GENENTECH or CURAGEN
shall be in writing 

                                       53
<PAGE>
 
and shall be personally delivered or sent by telecopy (with written confirmation
to follow via United States first class mail), overnight courier providing
evidence of receipt or certified mail, return receipt requested, postage
prepaid, in each case to the respective address specified below (or to such
address as may be specified in writing to the other Party hereto):

          CURAGEN:       555 Long Wharf, 11th Floor
                         New Haven, CT   06511
                         Attn: Vice President, Business Development
                         Telecopy: (203) 401-3333

          GENENTECH:     1 DNA Way
                         South San Francisco, CA  94080
                         Attn:  Corporate Secretary
                         Telecopy: (650) 952-9881

     Such notices shall be deemed to have been sufficiently given on:  (a) the
date sent if delivered in person or transmitted by telecopy, (b) the next
business day after dispatch in the case of overnight courier or (c) five (5)
business days after deposit in the U.S. mail in the case of certified mail.

     9.6  GOVERNING LAW.  This Agreement will be construed, interpreted and
          -------------                                                    
applied in accordance with the laws of the State of New York (excluding its body
of law controlling conflicts of law).

     9.7  LIMITATIONS.  Except as set forth elsewhere in this Agreement, neither
          -----------                                                           
Party grants to the other Party any right or license to any of its intellectual
property.

     9.8  ENTIRE AGREEMENT.  This is the entire Agreement between the Parties
          ----------------                                                   
with respect to the subject matter hereof and supersedes all prior agreements
between the Parties with respect to the subject matter hereof.  No modification
shall be effective unless in writing with specific reference to this Agreement
and signed by the Parties.

     9.9  WAIVER.  The terms or conditions of this Agreement may be waived only
          ------                                                               
by a written instrument executed by the Party waiving compliance.  The failure
of either Party at any time or times to require performance of any provision
hereof shall in no manner affect its rights at a later time to enforce the same.
No waiver by either Party of any condition or term shall be deemed as a
continuing waiver of such condition or term or of another condition or term.

                                       54
<PAGE>
 
     9.10 HEADINGS.  Section and subsection headings are inserted for
          --------                                                   
convenience of reference only and do not form part of this Agreement.

     9.11 ASSIGNMENT.  This Agreement may not be assigned by either Party
          ----------                                                     
without the consent of the other, except that each Party may, without such
consent, assign this Agreement and the rights, obligations and interests of such
Party, in whole or in part, to any of its wholly-owned subsidiaries, to any
purchaser of all or substantially all of its assets in the line of business to
which this Agreement pertains, or of all of its capital stock, or to any
successor corporation resulting from any merger or consolidation of such Party
with or into such corporation.

     9.12 FORCE MAJEURE.  Neither Party shall be liable for failure of or delay
          -------------                                                        
in performing obligations set forth in this Agreement, and neither shall be
deemed in breach of its obligations, if such failure or delay is due to natural
disasters or any causes beyond the reasonable control of such Party.  In event
of such force majeure, the Party affected thereby shall use reasonable efforts
to cure or overcome the same and resume performance of its obligations
hereunder.

     9.13 CONSTRUCTION.  The Parties hereto acknowledge and agree that:  (i)
          ------------                                                      
each  Party and its counsel reviewed and negotiated the terms and provisions of
this Agreement and have contributed to its revision; (ii) the rule of
construction to the effect that any ambiguities are resolved against the
drafting Party shall not be employed in the interpretation of this Agreement;
and (iii) the terms and provisions of this Agreement shall be construed fairly
as to all Parties hereto and not in a favor of or against any Party, regardless
of which Party was generally responsible for the preparation of this Agreement.

     9.14 SEVERABILITY.  If any provision(s) of this Agreement are or become
          ------------                                                      
invalid, are ruled illegal by any court of competent jurisdiction or are deemed
unenforceable under then current applicable law from time to time in effect
during the Term hereof, it is the intention of the Parties that the remainder of
this Agreement shall not be affected thereby provided that a Party's rights
under this Agreement are not materially affected.  The Parties hereto covenant
and agree to renegotiate any such term, covenant or application thereof in good
faith in order to provide a reasonably acceptable alternative to the term,
covenant or condition of this Agreement or the application thereof that is
invalid, illegal or unenforceable, it being the intent of the Parties that the
basic purposes of this Agreement are to be effectuated.

                                       55
<PAGE>
 
     9.15 STATUS.  Nothing in this Agreement is intended or shall be deemed to
          ------                                                              
constitute a partner, agency, employer-employee, or joint venture relationship
between the Parties.

     9.16 INDEMNIFICATION.
          --------------- 

     (a)  GENENTECH shall indemnify, defend and hold harmless CURAGEN, its
          Affiliates and their respective directors, officers, employees, and
          agents and their respective successors, heirs and assigns (the
          "CURAGEN Indemnitees"), against any liability, damage, loss or expense
          (including reasonable attorneys' fees and expenses of litigation)
          incurred by or imposed upon the CURAGEN Indemnitees, or any of them,
          in connection with any claims, suits, actions, demands or judgments
          ("Claims") of third parties, for personal injury and product liability
          matters (except in cases where such Claims result from a willful
          material breach of this Agreement or the gross negligence or willful
          misconduct on the part of a CURAGEN Indemnitee or are the subject
          matter of CURAGEN's indemnification of GENENTECH as set forth in
          Section 9.16(b)) arising out of the performance of the Research
          Program by GENENTECH or arising out of or relating to any actions of
          GENENTECH or any Affiliate, licensee, sublicensee, distributor agent
          of GENENTECH in the development, testing, production, manufacture,
          promotion, import, sale or use by any person of any Know-How
          Information Product manufactured or sold by GENENTECH or by an
          Affiliate, licensee, sublicensee, distributor or agent of GENENTECH.

     (b)  CURAGEN shall indemnify, defend and hold harmless GENENTECH, its
          Affiliates and their respective directors, officers, employees, and
          agents and their respective successors, heirs and assigns (the
          "GENENTECH Indemnitees"), against any liability, damage, loss or
          expense (including reasonable attorneys' fees and expenses of
          litigation) incurred by or imposed upon the GENENTECH Indemnitees, or
          any of them, in connection with any Claims of third parties, for
          personal injury matters and product liability matters (except to the
          extent such Claims result from a material breach of this Agreement or
          the gross negligence or willful misconduct on the part of GENENTECH or
          are the subject matter of GENENTECH's indemnification of CURAGEN as
          set forth in Section 9.16(a)) 

                                       56
<PAGE>
 
          arising out of the performance of the Research Program by CURAGEN or
          arising out of or relating to any actions of CURAGEN or any Affiliate,
          licensee, sublicensee, distributor agent of CURAGEN in the
          development, testing, production, manufacture, promotion, import, sale
          or use by any person of any product manufactured or sold by CURAGEN or
          by an Affiliate, licensee, sublicensee, distributor or agent of
          CURAGEN.

     (c)  GENENTECH's obligation to indemnify, defend and hold the CURAGEN
          Indemnitees harmless pursuant to Section 9.16(a), and CURAGEN's
          obligation to indemnify, defend and hold the GENENTECH Indemnitees
          harmless pursuant to Section 9.16(b), are conditioned on the
          indemnified Party:  (i) providing written notice to the indemnifying
          Party of any Claim arising out of the indemnified activities promptly
          after the indemnified Party has knowledge of such Claim, (ii)
          permitting the indemnifying Party to assume, at its discretion, sole
          and full control of the investigation, preparation, defense, trial and
          settlement in connection with such Claim, (iii) assisting and
          cooperating with the indemnifying Party, at the indemnifying Party's
          reasonable expense, in the investigation of, preparation for and
          defense of any such Claim, and (iv) not compromising, negotiating or
          settling such Claim without the indemnifying Party's prior written
          consent.

     9.17 COUNTERPARTS.
          ------------ 

     This Agreement may be executed in any number of counterparts, each of which
counterparts, when so executed and delivered, shall be deemed to be an original,
and all of which counterparts, taken together, shall constitute one and the same
instrument.

                                       57
<PAGE>
 
IN WITNESS WHEREOF, the Parties have this Agreement to be by their duly
authorized representation in two (2) originals.


GENENTECH, INC.                    CURAGEN CORPORATION

By: /s/                            By: /s/
   ---------------------------        ---------------------------------
Title: _______________________     Title: EXECUTIVE VICE PRESIDENT
                                         ------------------------------

                                       58
<PAGE>
 
                                  APPENDIX A
                                  ----------
                                        
                                OPTIONED CLONES

                                       59
<PAGE>
 
                                  APPENDIX B
                                  ----------
                                        
                                     NOTE

                                       60
<PAGE>
 
NEITHER THIS SECURITY NOR THE SECURITIES INTO WHICH IT IS CONVERTIBLE HAVE BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE "ACT"), OR
APPLICABLE STATE SECURITIES LAWS AND NEITHER MAY BE TRANSFERRED OR OTHERWISE
DISPOSED OF UNLESS SUCH SECURITIES HAVE BEEN REGISTERED UNDER THE ACT AND SUCH
LAWS OR REGISTRATION UNDER APPLICABLE STATE SECURITIES LAWS IS NOT REQUIRED AND
AN OPINION OF COUNSEL SATISFACTORY TO THE BORROWER IS FURNISHED TO THE BORROWER
TO THE EFFECT THAT REGISTRATION UNDER THE ACT IS NOT REQUIRED.


                                PROMISSORY NOTE
                                        

UP TO $26,000,000.00                                            __________, 1997


     FOR VALUE RECEIVED, the undersigned, CURAGEN CORPORATION (the "Borrower"),
having an address of 555 Long Wharf Drive, 11th Floor, New Haven, Connecticut
06511, hereby promises to pay to GENENTECH, INC. (the "Lender"), having an
address at 1 DNA Way, South San Francisco, CA  94080 , the principal sum of up
to

                    TWENTY SIX MILLION DOLLARS ($26,000,000)

or such lesser sum which may from time to time be advanced pursuant to the terms
of the section of the Research and Option Agreement dated November 20, 1997
between the Borrower and the Lender (the "Agreement") entitled "Section 3.2-Loan
Commitment", together with interest thereon in accordance with the terms hereof.
Capitalized terms used herein and not defined herein have the meanings assigned
to them in the Agreement.
<PAGE>
 
     1.   Payments
          --------

          (a)  The Borrower shall pay the accrued interest and principal balance
               of this Note, which represents the Loan, in full within fifteen 
               (15) days of the last day of the fifth Loan Year (the "Maturity
               Date"), subject to the extension of the Maturity Date pursuant to
               Section 1(c) below.

          (b)  This Note may be prepaid by the Borrower at any time, subject to
               Section 1(c) below, without premium or penalty.

          (c)  Payments made pursuant to paragraph (a) or (b) shall be paid in
               cash, or, at any time after the last day of the first Loan Year,
               at the option of Borrower, subject to Section 7 of this Note, in
               shares of Convertible Non-Voting Common Stock, $.01 par value per
               share (the "Non-Voting Common Stock"), of the Borrower, valued at
               the then Fair Market Value of CuraGen Common Stock (as defined
               below) having the rights, preferences and privileges set forth in
               the form of the Restated Certificate of Incorporation attached
               hereto as Exhibit 1. The Borrower may prepay any amounts due
                         ---------                              
               under this Note, upon written notice to the Lender specifying the
               prepayment date, in shares of Non-Voting Common Stock at any time
               after the last day of the first Loan Year as long as the Lender's
               Beneficial Ownership (as defined below) is less than 10% prior to
               such prepayment. In the event that the Borrower proposes a
               prepayment by issuing shares of Non-Voting Common Stock under
               this Note at a time when the Lender's Beneficial Ownership is
               equal to or exceeds 10%, the Lender may request in writing that
               the Borrower refrain from issuing

                                      -2-

                       Confidential Treatment Requested
<PAGE>
 
               additional shares of Non-Voting Common Stock until the earliest
               to occur of (i) two (2) years from the date of the issuance which
               caused the Lender's Beneficial Ownership to be equal to or exceed
               10% (the "Additional Issuance Date"), (ii) the date which is
               thirty (30) days from the date on which Lender's Beneficial
               Ownership falls below 10% and (iii) the Maturity Date; provided,
               that, in the event that the Additional Issuance Date occurs after
               the last day of the third Loan Year and prior to the Maturity
               Date, then the Lender may, at its option, extend the Maturity
               Date to a date two (2) years from the Additional Issuance Date.
               As used in this Note (i) the term "Beneficial Ownership" shall
               have the meaning set forth in Section 16 of the Securities
               Exchange Act of 1934, as amended, and the rules and regulations
               promulgated thereunder (the "1934 Act") and (ii) the term "Fair
               Market Value of CuraGen Common Stock" shall mean the average of
               the closing prices of the Borrower's Common Stock as reported by
               the Nasdaq Stock Market or, if not traded on the Nasdaq Stock
               Market, by such other principal securities exchange on which the
               Borrower's shares of Common Stock are traded, as applicable, over
               the 20 trading days preceding the date on which a payment is made
               by issuance of Non-Voting Common Stock. Notwithstanding the
               foregoing, at any time prior to the date on which CuraGen Common
               Stock is first registered under the 1934 Act, any payments made
               pursuant to paragraph (a) or (b) above shall be paid in cash, or
               at the option of the Borrower, in shares of a new series of
               Preferred Stock, $.01 par value per share (the "Preferred
               Stock"), of the Borrower having substantially the same rights,
               preferences and privileges as the Borrower's Series A Preferred
               Stock (other than with respect to (i) the applicable conversion
               rate, (ii) those certain adjustments to the

                                      -3-
<PAGE>
 
               applicable conversion rate set forth in Section 5(c)(ii) of
               Exhibit A of the Restated Certificate of Incorporation of the
               Borrower dated June 24, 1997 and (iii) voting rights), valued at
               the price at which the Borrower sold shares of Preferred Stock in
               the round of equity financing immediately preceding such
               prepayment date raising in excess of $3,000,000 from investors
               not involved in a collaborative relationship with the Borrower
               (the "Preferred Stock Value"). Delivery of any shares of Non-
               Voting Common Stock or Preferred Stock shall take place no later
               than five (5) days after the repayment date and shall be subject
               to execution by the parties of an agreement containing customary
               representations and provisions to comply with Federal and state
               securities laws, as mutually agreed by the parties.

     2.   Interest
          --------

     Interest shall accrue on the outstanding principal balance hereunder at a
rate per annum equal to the Prime Rate plus one percent (1%). As used herein,
the term "Prime Rate" shall mean the prime rate of interest as reported by 
Citibank, N.A. or, if Citibank, N.A. ceases to report such a rate, the generally
prevailing base corporate lending rate of Fleet National Bank. The applicable
rate of interest for this Note shall be adjusted quarterly according to the
Prime Rate as announced for each calendar quarter. Interest shall accrue and be
compounded quarterly commencing on the three-month anniversary of the date of
the first advance under the Loan and shall continue to accrue and be compounded
every calendar quarter thereafter until all amounts due hereunder have been paid
in full.

                                      -4-

                       Confidential Treatment Requested
<PAGE>
 
     3.   Recording of Advances, Repayments and Conversions
          -------------------------------------------------

     The advances described in the Agreement and made by the Lender to the
Borrower, and all repayments made on the account of principal hereof and all
conversions of the principal hereof and accrued interest hereon into shares of
the Borrower's capital stock shall be recorded by the Lender on the Schedule
attached hereto which is a part of this Note; provided, however, that the
failure of the Lender so to record on this Note (or any error in recording on
this Note) shall not affect the Borrower's obligations hereunder.

     4.  Subordination
         -------------

     This Note shall be subordinated to (i) all secured debt and liabilities of 
the Borrower existing as of the date hereof or incurred hereafter and (ii) all 
liabilities of the Borrower to institutional or commercial lenders and equipment
lessors existing as of the date hereof or incurred hereafter (including, without
limitation any lease obligations).

     5.   Acceleration and Conversion if Borrower is Public
          -------------------------------------------------

     If at any time after the date that CuraGen Common Stock is first registered
under the 1934 Act, the Market Capitalization of the Borrower is, for a period 
of ten (10) consecutive Trading Days, less than two (2) times the aggregate 
unpaid principal amount and accrued unpaid interest under this Note, the
Borrower shall promptly give written notice (to be delivered by hand or
facsimile transmission) of such occurrence to the Lender. The Lender may, at its
option exercisable at any time within fifteen (15) business days of the receipt
of such notice from the

                                      -5-


                       Confidential Treatment Requested
<PAGE>
 
Borrower (the "Acceleration Option"), declare all amounts owed hereunder
immediately due and payable by giving the Borrower written notice of such
declaration. Within fifteen (15) days of the Borrower's receipt of the Lender's
notice of exercise of the Acceleration Option, the Borrower shall make repayment
in full of the outstanding principal balance and accrued interest of this Note
in cash, or, at the option of the Borrower and subject to Section 7 of this
Note, in shares of Non-Voting Common Stock valued at the then Fair Market Value
of CuraGen Common Stock. For purposes hereof, (i) the Borrower's "Market
Capitalization" shall be equal to an amount determined by multiplying the number
of shares of the Borrower's Common Stock and Non-Voting Common Stock outstanding
on any Trading Day by the average of the closing prices of the Borrower's Common
Stock as reported by the Nasdaq Stock Market or, if not traded on the Nasdaq
Stock Market, by such other principal securities exchange on which shares are
traded, as applicable, over the twenty (20) trading days preceding such date;
and (ii) "Trading Days" shall mean days when trading is available on the Nasdaq
Stock Market or on the principal securities exchange on which the Borrower's
Common Stock may be traded.

     If the Borrower does not repay this Note in full upon exercise by the
Lender of the Acceleration Option in accordance with the preceding paragraph,
the entire unpaid principal amount of the Note and all unpaid accrued interest
hereon shall automatically be converted into shares of Non-Voting Common Stock
on the sixteenth day after Borrower's receipt of notice of the exercise by the
Lender of the Acceleration Option (such date, the "Automatic Conversion Date"),
subject to Section 7 of this Note. Notwithstanding the foregoing limitation,
Lender reserves the right to convert the remaining loan balance into shares of
Non-Voting Common Stock in excess of the 19.8% limitation provided in Section 7
of this Note. The number of shares of Non-Voting Common Stock into which this
Note shall be converted shall be determined by dividing the sum of the aggregate
unpaid principal amount of this Note and the unpaid accrued

                                      -6-
<PAGE>
 
interest hereon on the Automatic Conversion Date by the Fair Market Value of
CuraGen Common Stock on the Automatic Conversion Date.

     If this Note is automatically converted as provided above, written notice
thereof shall be delivered by the Borrower to the Lender, which notice shall
specify the Automatic Conversion Date, the Fair Market Value of CuraGen Common
Stock on the Automatic Conversion Date, the unpaid principal amount of and
unpaid accrued interest on the Note converted and, if such conversion is of the
Note in full, calling upon such Lender to surrender to the Borrower, in the
manner and at the place designated, the originally-executed Note.  Upon any such
conversion of this Note in full, the Lender shall surrender this Note, duly
endorsed, at the principal executive office of the Borrower. At its expense, the
Borrower shall, as soon as practicable thereafter, issue and deliver to the
Lender at such principal office a certificate or certificates for the number of
shares of Non-Voting Common Stock to which the Lender shall be entitled upon
such conversion.  Any conversion of this Note hereunder shall be deemed to have
been made at the close of business, California time, on the applicable
Conversion Date, and at and after such time the Lender shall be treated for all
purposes as the record holder of such shares of Non-Voting Common Stock.

     Upon payment of this Note in full, the Borrower shall be forever released
from all its obligations and liabilities under this Note.

     The Borrower shall at all times reserve and keep available for issuance out
of its authorized but unissued shares of Non-Voting Common Stock such number of
shares as shall from time to time be sufficient to effect the conversion of the
Note into shares of Non-Voting Common Stock, and if such reserve shall not be
sufficient to effect the conversion of the entire outstanding principal amount
of and accrued interest on this Note, without limitation of such other remedies
as shall be available to the Lender, the Borrower will use commercially
reasonable efforts to take such corporate actions as may, in the opinion of its
counsel, be

                                      -7-
<PAGE>
 
necessary to increase its authorized but unissued shares of Non-Voting Common
Stock. In addition, the Borrower shall at all times reserve and keep available
for issuance out of its authorized but unissued shares of Common Stock, such
number of its shares of Common Stock as shall from time to time be sufficient to
effect the conversion of the shares of Non-Voting Common Stock into Common
Stock, and if such reserve shall not be sufficient to effect the conversion of
the shares of Non-Voting Common Stock, without limitation of such other remedies
as shall be available to the Lender, the Borrower will use its commercially
reasonable efforts to take such corporate actions as may, in the opinion of
counsel, be necessary to increase its authorized but not outstanding shares of
Common Stock to such number of shares as shall be sufficient for such purposes.

     6.   Conversion to Preferred Stock if Borrower is not Public
          -------------------------------------------------------

     If at any time prior to the date on which CuraGen's Common Stock is first
registered under the 1934 Act, the ratio (the "Ratio") of (a)(i) the Borrower's 
cash plus marketable securities, minus (ii) Borrower's secured debt and
liabilities plus all liabilities of the Borrower to institutional or commercial
lenders plus any other long-term debt or liabilities of the Borrower senior or
equal in right of payment to this Note, all as shown on the Borrower's most
recent quarterly or annual balance sheet, to (b) the outstanding principal of,
and accrued interest on, this Note is less than 1.5, then (A) the Borrower shall
promptly provide written notice thereof to the Lender and (B) subject to Section
7 of this Note, the Lender may, by written notice to the Borrower (the "Series F
Conversion Notice"), convert that portion of the indebtedness represented by
this Note into shares of Series F Non-Voting Convertible Preferred Stock, $.01
par value per share (the "Series F Preferred Stock"), of the Borrower as may be
necessary to increase the Ratio to 1.5 at a conversion price equal to one (1)
share of Series F Preferred Stock


                                      -8-


                       Confidential Treatment Requested



<PAGE>
 
for each $100 of outstanding principal and accrued interest surrendered for
conversion. The Series F Preferred Stock shall have the rights, preferences and
privileges as set forth in the form of Certificate of Designation attached
hereto as Exhibit 2.
          --------- 

     Upon any such conversion of this Note in full, the Lender shall surrender
this Note, duly endorsed, at the principal executive office of the Borrower. At
its expense, the Borrower shall, as soon as practicable thereafter, issue and
deliver to the Lender at such principal office a certificate or certificates for
the number of shares of Series F Preferred Stock to which the Lender shall be
entitled upon such full or partial conversion. Any conversion of this Note under
this Section 6 shall be deemed to have been made at the close of business,
California time, on the Series F Conversion Date (as defined below), and at and
after such times the Lender shall be treated for all purposes as the record
holder of such shares of Series F Preferred Stock. As used herein, the term
"Series F Conversion Date" shall mean the date on which the Certificate of
Designation establishing the Series F Preferred Stock has been accepted for
filing by the Delaware Secretary of State.

     The Borrower shall at all times after the Series F Conversion Date reserve
and keep available for issuance out of its authorized but unissued shares of
Series F Preferred Stock such number of shares of Series F Preferred Stock as
shall be sufficient to effect the conversion of the Note into shares of Series F
Preferred Stock, and if at any time such reserve shall not be sufficient to
effect the conversion of the entire outstanding principal amount of, and accrued
interest on, this Note, without limitation of such other remedies as shall be
available to the Lender, the Borrower will use commercially reasonable efforts
to take such corporate actions as may, in the opinion of counsel, be necessary
to increase its authorized but unissued shares of Series F Preferred Stock. The
Borrower shall at all times after the Series F Conversion Date reserve and keep
available for issuance out of its authorized but unissued shares of Common Stock
such number of shares as shall from time to time be sufficient to effect the
conversion of 

                                      -9-
<PAGE>
 
the outstanding shares of Series F Preferred Stock into shares of Common Stock,
and if such reserve shall not be sufficient to effect the conversion of the
aggregate number of shares of Series F Preferred Stock then outstanding plus
accrued dividends thereon, without limitation of such other remedies as shall be
available to the Lender, the Borrower will use commercially reasonable efforts
to take such corporate actions as may, in the opinion of its counsel, be
necessary to increase its authorized but unissued shares of Common Stock.

     7.  Limitation on Conversion of Principal and Interest
         --------------------------------------------------

     If the payment or conversion of any indebtedness represented by this Note
into shares of Non-Voting Common Stock, Preferred Stock or Series F Preferred
Stock would cause the Lender's Percentage Interest (as defined below) to exceed
19.8%, the Lender may, by written notice to the Borrower, require the Borrower
to make that portion of such conversion or payment in cash as is necessary to
reduce the Lender's Percentage Interest to less than 19.8%. If, at any time
during the term of this Note, the Lender's Percentage Interest (as defined
below) exceeds 19.8%, the Lender may, upon written notice to the Borrower,
require the Borrower to repurchase that number of shares of Non-Voting Common
Stock, Preferred Stock or Series F Preferred Stock, at the Borrower's option, as
is necessary to maintain the Lender's Percentage Interest at less than 19.8%.
The price of such repurchase shall be equal to (i) the Fair Market Value of
CuraGen Common Stock, with respect to a repurchase of Non-Voting Common Stock,
(ii) the Preferred Stock Value with respect to a repurchase of Preferred Stock
or (iii) $100 per share with respect to a repurchase of Series F Preferred
Stock. As used herein the term "Lender's Percentage Interest" shall mean the
result obtained by dividing (i) the aggregate amount of shares
of the capital stock of the Borrower held by the Lender with present voting
privileges plus the aggregate amount of shares of Non-Voting Common Stock held
by the Lender by (ii) the 

                                     -10-
<PAGE>
 
aggregate amount of then outstanding shares of the capital stock of the Borrower
whose holders have present voting privileges plus the aggregate amount of then
outstanding shares of Non-Voting Common Stock held by holders other than the
Lender.

     8.   Adjustments in Event of Reclassification or Reorganization
          ----------------------------------------------------------

     In the event the Borrower reclassifies its Common Stock or consolidates
with or merges into another person or otherwise reorganizes its capital
structure or conveys or transfers all or substantially all of its assets (each,
a "Reorganization Event"), then and in each such event, the shares of Non-Voting
Common Stock, Preferred Stock or Series F Preferred Stock issued under this Note
shall be convertible into the kind and amount of shares of stock and other
securities and property that were receivable by a holder of Common Stock upon
such Reorganization Event.

     9.   Events of Default
          -----------------

     Subject to Section 4 hereof, the Lender may declare the entire unpaid
principal amount of, and all accrued but unpaid interest on, this Note,
immediately due and payable, effective upon written notice to the Borrower, if
any of the following events shall occur (individually an "Event of Default"):

          (i)  Payment of Note.  Default in the payment of this Note when due.
               ---------------                                                

          (ii) Bankruptcy, Insolvency, etc. Commenced by the Borrower.  If the
               ------------------------------------------------------         
               Borrower:

                                     -11-
<PAGE>
 
                 (a)  shall commence any proceeding in bankruptcy or seek
          reorganization, arrangement, readjustment of its debts, dissolution,
          liquidation, winding-up, composition or any other relief under the
          United States Bankruptcy Act, as amended, or under any other
          insolvency, reorganization, liquidation, dissolution, arrangement,
          composition, readjustment of debt or any other similar act or law, of
          any jurisdiction, domestic or foreign, now or hereafter existing;

                 (b)  shall admit its inability to pay its debts as they mature
          in any petition or pleading in connection with any such proceeding;

                 (c)  shall apply for, or, in writing, consent to or acquiesce
          in, an appointment of a receiver, conservator, trustee or similar
          officer for it or for all or substantially all of its assets;

                 (d)  shall make a general assignment for the benefit of
          creditors; or

                 (e)  shall admit in writing its inability to pay its debts as
          they mature.

          (iii)  Bankruptcy, Insolvency, etc. Commenced Against the Borrower. 
                 -----------------------------------------------------------  
                 If any proceedings are commenced or any other action is taken
                 against the Borrower in bankruptcy or seeking reorganization,
                 arrangement, readjustment of its debts, dissolution,
                 liquidation, winding-up, composition or any other relief under
                 the United States Bankruptcy Act, as amended, or under any
                 other insolvency, reorganization, liquidation, dissolution,
                 arrangement, composition, readjustment of debt or any other

                                     -12-
<PAGE>
 
                 similar act or law, of any jurisdiction, domestic or foreign,
                 now or hereafter existing, or a receiver, conservator, trustee
                 or similar officer for the Borrower or for all or substantially
                 all of its assets is appointed; and in each such case, such
                 event continues for sixty (60) days undismissed, unbounded and
                 undischarged.

          (iv)   Certain Terminations of the Agreement.  Termination of the
                 -------------------------------------                     
                 Agreement by the Lender in accordance with Section 8.2(a) or
                 Section 8.3 of the Agreement.

     10.  Any notice required or permitted under this Note shall be given in
writing and in accordance with Section 9.5 of the Agreement.

     11.  If any action at law or in equity is necessary to enforce or interpret
the terms of this Note, the prevailing party shall be entitled to reasonable
attorneys' fees, costs and necessary disbursements to any other relief to which
such party may be entitled.

     12.  The Borrower hereby waives presentment, demand, protest or notice of
any kind in connection with this Note. No failure on the part of the Lender in
exercising any right or remedy hereunder, and no single, partial or delayed
exercise by the Lender of any right or remedy shall preclude the full and timely
exercise by the Lender at any time of any right or remedy of the Lender
hereunder without notice. No course of dealing or other conduct, no oral
agreement or representation made by the Lender or usage of trade shall operate
as a waiver of any right or remedy of the Lender. This Note and the Agreement
contain the entire agreement between the parties with respect to the subject
matter hereof, and supersedes every course of

                                     -13-
<PAGE>
 
dealing, other conduct, oral agreement or representation previously made by the
Lender. In the event that any court of competent jurisdiction shall determine
that any provision, or portion thereof, contained in this Note shall be
unenforceable in any respect, then such provision shall be deemed limited to the
extent that such court deems it enforceable, and the remaining provisions of
this Note shall nevertheless remain in full force and effect.

     13.  None of the terms or provisions of this Note may be excluded,
modified, or amended except by a written instrument duly executed on behalf of
both the Borrower and the Lender expressly referring hereto and setting forth
the provision so excluded, modified or amended. No waiver or forbearance of any
of the rights and remedies of the Lender hereunder shall be effective unless
made specifically in a writing signed by the Lender, and any such waiver or
forbearance shall be effective only in the specific instance and for the
specific purpose for which given.

     14.  This Note is the "Note" referred to in the Agreement and is entitled
to all of the rights and benefits referred to therein.

     15.  This Note is delivered to the Lender at its principal office in South
San Francisco, California, shall be governed by, and construed and enforced in
accordance with, the laws of the state of California, without regard to its
principles of conflicts of laws.

                                     -14-
<PAGE>
 
     IN WITNESS WHEREOF, the Borrower has caused this Note to be executed by its
duly authorized officer as of the date first above written.

Witness:                           CURAGEN CORPORATION


_________________________________       by:________________________________
                                        (Signature)
 
                                        ___________________________________
                                        (Print or type name)

                                        its:_______________________________
                                        (Title or Capacity)

                                     -15-
<PAGE>
 
                          SCHEDULE TO PROMISSORY NOTE

                            DATED ___________, 1997

                            FROM CURAGEN CORPORATION

                               TO GENENTECH, INC.

                       IN THE AMOUNT OF UP TO $26,000,000

       Amount     Amount    Amount        CuraGen         Genentech
Date   Drawn      Repaid   Converted  Acknowledgement  Acknowledgement
- ----   -----      ------   ---------  ---------------  ---------------

                                     -16-
<PAGE>
 
                                                                       EXHIBIT 1
                                                                       ---------
                                        
                                    RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                              CURAGEN CORPORATION
                                        
                         Adopted in accordance with the
                       provisions of Sections 242 and 245
            of the General Corporation Law of the State of Delaware
            -------------------------------------------------------

  CuraGen Corporation, a Delaware corporation, hereby certifies as follows:

     1.  The name of the corporation is CuraGen Corporation. The date of the
filing of its original Certificate of Incorporation with the Secretary of State
of the State of Delaware was November 22, 1991.

     2.  This Restated Certificate of Incorporation amends and restates the
provisions of the Certificate of Incorporation of said corporation and was duly
adopted pursuant to resolutions adopted by the Board of Directors and
Stockholders of the corporation in accordance with the provisions of Sections
242 and 245 of the General Corporation Law of the State of Delaware (the
"Delaware General Corporation Law"). In lieu of a meeting and vote of the
Stockholders, the holders of the necessary number of shares of the corporation's
capital stock have given written consent to said amendment and restatement in
accordance with the provisions of Section 228 of the Delaware General
Corporation Law, and said written consent was filed with the corporation and
notice thereof has been given to those Stockholders who have not consented in
writing.

     3.  The text of the Certificate of Incorporation is hereby amended and
restated to read in its entirety as follows:

     FIRST:  The name of the corporation is CuraGen Corporation (the
"Corporation").

     SECOND:  The address of the registered office of the Corporation in the
State of Delaware is 1013 Centre Road, City of Wilmington, County of New Castle;
and the name of the registered agent of the Corporation in the State of Delaware
is The Prentice-Hall Corporation System, Inc.

     THIRD:  The purpose of the Corporation is to engage in any lawful act or
activity or carry on any business for which corporations may be organized under
the Delaware General Corporation Law or any successor statue.

     FOURTH:

     A.  Designation and Number of Shares.
         -------------------------------- 

     The total number of shares of all classes of stock which the Corporation
shall have the authority to issue is 58,000,000 shares, consisting of 50,000,000
shares of common stock, par value $.01 per share (the "Common Stock"), 3,000,000
shares of non-voting common stock, par value $.01 per share (the "Non-Voting
Common Stock"), and 5,000,000 shares of Preferred Stock, par value $.01 per
share (the "Preferred Stock").
<PAGE>
 
     Each share of common stock, par value $.01 per share, of the Corporation
issued and outstanding at the time and date that this Restated Certificate of
Incorporation becomes effective (the "Effective Time") is hereby reclassified
and changed, without any action on the part of the holders of any such common
stock or on the part of the Corporation, into one share of fully paid and
nonassessable Common Stock, and each person holding of record any shares of such
common stock issued and outstanding at the Effective Time shall be entitled to
receive, upon the surrender of certificates evidencing such shares to the
Corporation, one or more certificates to evidence the number of shares of Common
Stock into which such shares of common stock have been reclassified.

     A statement of the designations of the different classes of stock of the
Corporation and of the powers, preferences and rights, and the qualifications,
limitations or restrictions thereof, and of the authority conferred upon the
Board of Directors to fix by resolution or resolutions any of the foregoing in
connection with the creation of one or more series of Preferred Stock and the
limitation of variations between or among such series, is set forth below in
this Article FOURTH.

     B.   Preferred Stock
          ---------------

          1.  Shares of Preferred Stock may be issued in one or more series at
such time or times and for such consideration as the Board of Directors may
determine. All shares of any one series shall be of equal rank and identical in
all respects.

          2.  Authority is hereby expressly granted to the Board of Directors to
fix from time to time, by resolution or resolutions providing for the
establishment and/or issuance of any series of Preferred Stock, the designation
of such series and the powers, preferences and rights of the shares of such
series, and the qualifications, limitations or restrictions thereof, including,
without limitation, the following:

          (a)  The distinctive designation and number of shares comprising such
     series, which number may (except where otherwise provided by the Board of
     Directors in creating such series) be increased or decreased (but not below
     the number of shares then outstanding) from time to time by action of the
     Board of Directors;

          (b)  The rate of dividends, if any, on the shares of that series,
     whether dividends shall be (i) non-cumulative, (ii) cumulative to the
     extent earned or (iii) cumulative (and, if cumulative, from which date or
     dates), whether dividends shall be payable in cash, property or rights, or
     in shares of the Corporation's capital stock, and the relative rights of
     priority, if any, of payment of dividends on shares of that series over
     shares of any other series or class;

          (c)  Whether the shares of that series shall be redeemable and, if so,
     the terms and conditions of such redemption, including the date or dates
     upon or after which they shall be redeemable, and the amount per share
     payable in case of redemption (which amount may vary under different
     conditions and at different redemption dates) or the property or rights,
     including securities of any other corporation, payable in case of
     redemption;

          (d)  Whether the series shall have a sinking fund for the redemption
     or purchase of shares of that series and, if so, the terms and amounts
     payable into such sinking fund;

          (e)  The rights to which the holders of the shares of that series
     shall be entitled in the event of the voluntary or involuntary liquidation,
     dissolution or winding-up of the

                                       2
<PAGE>
 
     Corporation, and the relative rights of priority, if any, of payment of
     shares of that series in any such event;

          (f)  Whether the shares of that series shall be convertible into or
     exchangeable for shares of stock of any other class or any other series
     and, if so, the terms and conditions of such conversion or exchange,
     including the rate or rates of conversion or exchange, the date or dates
     upon or after which they shall be convertible or exchangeable, the period
     or periods during which they shall be convertible or exchangeable, the
     event or events upon or after which they shall be convertible or
     exchangeable or at whose option they shall be convertible or exchangeable,
     and the method (if any) of adjusting the rates of conversion or exchange in
     the event of a stock split, stock dividend, combination of shares or
     similar event;

          (g)  Whether the issuance of any additional shares of such series, or
     of any shares of any other series, shall be subject to restrictions as to
     issuance, or as to the powers, preferences or rights of any such additional
     shares of such series or shares of such other series;

          (h)  Whether or not the shares of that series shall have voting
     rights, the extent of such voting rights on specified matters or on all
     matters, the number of votes to which the holder of a share of such series
     shall be entitled in respect of such share, whether such series shall vote
     generally with the Common Stock on all matters or (either generally or upon
     the occurrence of specified circumstances) shall vote separately as a class
     or with other series of Preferred Stock; and

          (i)  Any other preferences, privileges and powers and relative,
     participating, optional or other special rights and qualifications,
     limitations or restrictions of such series, as the Board of Directors may
     deem advisable and as shall not be inconsistent with the provisions of this
     Restated Certificate of Incorporation and to the full extent now or
     hereafter permitted by the Delaware General Corporation Law.

     C.  Common Stock and Non-Voting Common Stock.
         ---------------------------------------- 

     The Common Stock and the Non-Voting Common Stock shall be identical in all
respects and shall have equal rights and privileges, except as otherwise
expressly provided herein.  The relative powers, preferences, rights,
qualifications, limitations and restrictions of the shares of the Common Stock
and the Non-Voting Common Stock are as follows:

     1.  Dividends.  The holders of record of Common Stock and the Non-Voting
         ---------                                                           
Common Stock shall be entitled to receive, when, if and as declared by the Board
of Directors, such dividends of cash, property or stock of the Corporation as
the Board of Directors shall from time to time declare, subject to the following
rights and restrictions and the rights and restrictions set forth in paragraph
(C)(2) of this Article FOURTH:

          (a)  No cash dividends shall be declared and paid on the Common Stock
     unless at the same time an equal cash dividend is declared and paid, per
     share, on the Non-Voting Common Stock. No cash dividends shall be declared
     and paid on the Non-Voting Common Stock unless at the same time an equal
     cash dividend is declared and paid, per share, on the Common Stock.

                                       3
<PAGE>
 
          (b)  No dividend of property (including capital stock of the
     Corporation) shall be declared and paid on the Common Stock unless a
     dividend of an equal amount of the same property has also been declared and
     paid, per share, on the Non-Voting Common Stock. No dividend of property
     (including capital stock of the Corporation) shall be declared and paid on
     the Non-Voting Common Stock unless a dividend of an equal amount of the
     same property has also been declared and paid, per share, on the Common
     Stock.

          2.  Stock Subdivisions and Combinations.  The Corporation shall not
              ----------------------------------- 
subdivide or combine shares Common Stock by stock split, stock dividend,
reclassification, reorganization or otherwise without at the same time making a
proportionate subdivision or combination of the Non-Voting Common Stock. The
Corporation shall not subdivide or combine shares of Non-Voting Common Stock by
stock split, stock dividend, reclassification, reorganization or otherwise
without at the same time making a proportionate subdivision or combination of
the Common Stock.

          3.  Liquidation.  In the event of any liquidation, dissolution or
              -----------
winding up of the Corporation, whether voluntary or involuntary, after payment
or provision for payment of the debts and other liabilities of the Corporation
and the amounts to which the holders of any Preferred Stock shall be entitled,
the holders of Common Stock and Non-Voting Common Stock shall be entitled
(together as one class) to share ratably in the remaining assets of the
Corporation.

          4.  Voting.  The holders of the Common Stock are entitled to one vote
              ------
for each share held. Except as provided under the Delaware General Corporation
Law, the holders of the Non-Voting Common Stock are not entitled to vote. There
shall be no cumulative voting.

          5.  Conversion of Non-Voting Common Stock.
              --------------------------------------

          (a)  Optional Conversion.  Each share of Non-Voting Common Stock shall
     be convertible, at the option of the holder thereof, at any time and from
     time to time, into shares of Common Stock at the rate of one share of
     Common Stock for each share of Non-Voting Common Stock by surrendering the
     certificate or certificates for such shares of Non-Voting Common Stock,
     together with written notice that such holder elects to convert all or any
     portion of the shares of Non-Voting Common Stock represented by such
     certificate or certificates, to the office of the transfer agent (which
     shall be the principal office of the Corporation if it serves as its own
     transfer agent). Such notice shall state the names of the nominees, if any,
     in which such holder wishes the certificate or certificates for the shares
     of Common Stock to be issued. The date of receipt of such certificates and
     notice by the transfer agent (or by the Corporation if it serves as its own
     transfer agent) shall be the conversion date. The Corporation shall, as
     soon as practicable after such conversion date, issue and deliver at such
     office to such holder of Non-Voting Common Stock, or to its nominees, a
     certificate or certificates for the number of shares of Common Stock to
     which such holder shall be entitled, together with cash in lieu of any
     fraction of a share.

          (b)  Automatic Conversion.  (i) Except as provided in paragraph
               --------------------   
     5(b)(ii), upon the transfer of beneficial ownership of any shares of Non-
     Voting Common Stock, such shares shall automatically, with no further
     action being required by any party to such transfer or otherwise, be
     converted into shares of Common Stock at the rate of one share of Common
     Stock for each share of Non-Voting Common Stock.

          (ii) The provisions of paragraph 5(b)(i) shall not apply, and Non-
     Voting Common Stock shall be issued to a transferee of Non-Voting Common
     Stock upon the transfer of 

                                       4
<PAGE>
 
     beneficial ownership of any shares thereof, if such transfer is made to (i)
     a majority- owned subsidiary of Genentech, Inc., a Delaware corporation
     ("Genentech"), (ii) a corporation ("Genentech Parent") of which Genentech
     is a wholly owned subsidiary or (iii) a wholly owned subsidiary of
     Genentech Parent (in any such case, a "qualifying transfer"); provided that
                                                                   --------   
     if such transfer is made to a wholly owned subsidiary of Genentech or of
     Genentech Parent, as the case may be, and such wholly owned subsidiary
     ceases to be a wholly owned subsidiary of Genentech or of Genentech Parent,
     as the case may be, then such shares shall automatically, with no further
     action being required by any party, be converted into shares of Common
     Stock at the rate of one share of Common Stock for each share of Non-Voting
     Common Stock. Upon any qualifying transfer, the transferor shall provide
     written certification to the transfer agent for the Common Stock and Non-
     Voting Common Stock of such facts which constitute such transfer as a
     "qualifying transfer" and, absent prima facie evidence that such
     certification is false, the Corporation or any transfer agent shall accept
     such certification as being correct and shall not be required to conduct
     any investigation with respect thereto.

          (c)  The Corporation shall reserve and keep available out of its
     authorized but unissued Common Stock such number of shares of Common Stock
     as shall from time to time be sufficient to effect the conversion of all
     outstanding shares of Non-Voting Common Stock.

     FIFTH:  The Corporation is to have perpetual existence.

     SIXTH: The following provisions are inserted for the management of the
business and the conduct of the affairs of the Corporation, and for further
definition, limitation and regulation of the powers of the Corporation and of
its directors and stockholders:

     A.  The business and affairs of the Corporation shall be managed by or
under the direction of the Board of Directors. In addition to the powers and
authority expressly conferred upon them by statute or by this Restated
Certificate of Incorporation or the By-Laws of the Corporation as in effect from
time to time, the directors are hereby empowered to exercise all such powers and
do all such acts and things as may be exercised or done by the Corporation.

     B.  The directors of the Corporation need not be elected by written ballot
unless the By-Laws so provide.

     C.  Any action required or permitted to be taken by the stockholders of the
Corporation may be effected only at a duly called annual or special meeting of
stockholders of the Corporation and not by written consent.

     SEVENTH:  A.  Subject to the rights of the holders of shares of any series
of Preferred Stock then outstanding to elect additional directors under
specified circumstances, the number of directors shall be fixed from time to
time exclusively by the Board of Directors pursuant to a resolution adopted by a
majority of the Board of Directors.

     B.  On or prior to the Effective Time, the Board of Directors of the
Corporation shall divide the directors into three classes, as nearly equal in
number as reasonably possible, with the term of office of the first class to
expire at the 1998 annual meeting of stockholders or any special meeting in lieu
thereof, the term of office of the second class to expire at the 1999 annual
meeting of stockholders or any special meeting in lieu thereof, and the term of
office of the third class to expire 

                                       5
<PAGE>
 
at the 2000 annual meeting of stockholders or any special meeting in lieu
thereof. At each annual meeting of stockholders or special meeting in lieu
thereof following such initial classification, directors elected to succeed
those directors whose terms expire shall be elected for a term of office to
expire at the third succeeding annual meeting of stockholders or special meeting
in lieu thereof after their election and until their successors are duly elected
and qualified.

     C.  Subject to the rights of the holders of any series of Preferred Stock
then outstanding, newly created directorships resulting from any increase in the
authorized number of directors or any vacancies in the Board of Directors
resulting from death, resignation, retirement, disqualification, removal from
office or other cause may be filled only by a majority vote of the directors
then in office even though less than a quorum, or by a sole remaining director.
In the event of any increase or decrease in the authorized number of directors,
(i) each director then serving as such shall nevertheless continue as a director
of the class of which he is a member until the expiration of his current term or
his prior death, retirement, removal or resignation and (ii) the newly created
or eliminated directorships resulting from such increase or decrease shall if
reasonably possible be apportioned by the Board of Directors among the three
classes of directors so as to ensure that no one class has more than one
director more than any other class. To the extent reasonably possible,
consistent with the foregoing rule, any newly created directorships shall be
added to those classes whose terms of office are to expire at the latest dates
following such allocation and newly eliminated directorships shall be subtracted
from those classes whose terms of office are to expire at the earliest dates
following such allocation, unless otherwise provided for from time to time by
resolution adopted by a majority of the directors then in office, although less
than a quorum. In the event of a vacancy in the Board of Directors, the
remaining directors, except as otherwise provided by law, may exercise the
powers of the full Board of Directors until the vacancy is filled.

     D.  Advance notice of stockholder nominations for the election of directors
and of business to be brought by stockholders before any meeting of the
stockholders of the Corporation shall be given in the manner provided in the By-
Laws of the Corporation.

     E.  Subject to the rights of the holders of any series of Preferred Stock
then outstanding, any director, or the entire Board of Directors, may be removed
from office at any time only for cause. A director may be removed for cause only
after a reasonable notice and opportunity to be heard before the body proposing
to remove him.

     EIGHTH:  The Board of Directors is expressly empowered to adopt, amend or
repeal By-Laws of the Corporation.  Any adoption, amendment or repeal of the By-
Laws of the Corporation by the Board of Directors shall require the approval of
a majority of the Board of Directors.  The stockholders shall also have power to
adopt, amend or repeal the By-Laws of the Corporation; provided, that, in
                                                       --------          
addition to any vote of the holders of any class or series of stock of the
Corporation required by law or by this Restated Certificate of Incorporation,
the affirmative vote of the holders of at least seventy percent (70%) of the
voting power of all of the then outstanding shares of the capital stock of the
Corporation entitled to vote generally in the election of directors, voting
together as a single class, shall be required for the stockholders to adopt,
amend or repeal any provision of the By-Laws of the Corporation.

     NINTH:  A.  To the fullest extent permitted by the Delaware General
Corporation Law as the same now exists or may hereafter be amended, the
Corporation shall indemnify, and advance expenses to, its directors, officers
and any person who is or was serving at the request of the Corporation as a
director, officer, trustee, employee or agent of another corporation, or of a
partnership, joint venture, trust or other enterprise, if such person was or is
made a party to or is 

                                       6
<PAGE>
 
threatened to be made a party to or is otherwise involved (including, without
limitation, as a witness) in any action, suit or proceeding, whether civil,
criminal, administrative or investigative, by reason of the fact that such
person is or was a director or officer of the Corporation or is or was serving
at the request of the Corporation as a director, officer, trustee, employee or
agent of another corporation, or of a partnership, joint venture, trust or other
enterprise, including service with respect to an employee benefit plan;
provided, that except with respect to proceedings to enforce rights to
- --------                                                              
indemnification or as is otherwise required by law, the By-Laws of the
Corporation may provide that the Corporation shall not be required to indemnify,
and advance expenses to, any director, officer or other person in connection
with a proceeding (or part thereof) initiated by such director, officer or other
person, unless such proceeding (or part thereof) was authorized by the Board of
Directors. The Corporation, by action of its Board of Directors, may provide
indemnification or advance expenses to employees and other agents of the
Corporation or other persons only on such terms and conditions and to the extent
determined by the Board of Directors in its sole and absolute discretion.

     B.  The indemnification and advancement of expenses provided by, or granted
pursuant to, this Article NINTH shall not be deemed exclusive of any other
rights to which a person seeking indemnification or advancement of expenses may
be entitled under any By-Law, agreement, vote of stockholders or disinterested
directors or otherwise, both as to action in such person's official capacity and
as to action in another capacity while holding such office.

     C.  The Corporation shall have the power to purchase and maintain insurance
on behalf of any person who is or was a director, officer, employee or agent of
the Corporation, or is or was serving at the request of the Corporation as a
director, officer, trustee, employee or agent of another corporation, or of a
partnership, joint venture, trust or other enterprise, against any liability
asserted against such person and incurred by such person in any such capacity,
or arising out of such person's status as such, whether or not the Corporation
would have the power to indemnify such person against such liability under this
Article NINTH.

     D.  The indemnification and advancement of expenses provided by, or granted
pursuant to, this Article NINTH shall, unless otherwise specified when
authorized or ratified, continue as to a person who has ceased to be a director,
officer, employee or agent and shall inure to the benefit of the heirs,
executors and administrators of such person.  The indemnification and rights to
advancement of expenses that may have been provided to an employee or agent of
the Corporation by action of the Board of Directors, pursuant to the last
sentence of paragraph 1 of this Article NINTH, shall, unless otherwise specified
when authorized or ratified, continue as to a person who has ceased to be an
employee or agent of the Corporation and shall inure to the benefit of the
heirs, executors and administrators of such person, after the time such person
has ceased to be an employee or agent of the Corporation, only on such terms and
conditions and to the extent determined by the Board of Directors in its sole
discretion.  No repeal or amendment of this Article NINTH shall adversely affect
any rights of any person pursuant to this Article NINTH which existed at the
time of such repeal or amendment with respect to acts or omissions occurring
prior to such repeal or amendment.

     TENTH:  No director shall be personally liable to the Corporation or its
stockholders for any monetary damages for breaches of fiduciary duty as a
director, notwithstanding any provision of law imposing such liability; provided
that this provision shall not eliminate or limit the liability of a director, to
the extent that such liability is imposed by applicable law, (i) for any breach
of the director's duty of loyalty to the Corporation or its stockholders; (ii)
for acts or omissions not in good faith or which involve intentional misconduct
or a knowing violation of law; (iii) under 

                                       7
<PAGE>
 
Section 174 or successor provisions of the Delaware General Corporation Law; or
(iv) for any transaction from which the director derived an improper personal
benefit. This provision shall not eliminate or limit the liability of a director
for any act or omission if such elimination or limitation is prohibited by the
Delaware General Corporation Law. No amendment to or repeal of this provision
shall apply to or have any effect on the liability or alleged liability of any
director for or with respect to any acts or omissions of such director occurring
prior to such amendment or repeal. If the Delaware General Corporation Law is
amended to authorize corporate action further eliminating or limiting the
personal liability of directors, then the liability of a director of the
Corporation shall be eliminated or limited to the fullest extent permitted by
the Delaware General Corporation Law, as so amended.

     ELEVENTH:  The Corporation reserves the right to amend or repeal any
provision contained in this Restated Certificate of Incorporation in the manner
prescribed by the Delaware General Corporation Law and all rights conferred upon
stockholders are granted subject to this reservation; provided that, in addition
                                                      --------                  
to the vote of the holders of any class or series of stock of the Corporation
required by law or by this Restated Certificate of Incorporation, the
affirmative vote of the holders of shares of voting stock of the Corporation
representing at least seventy percent (70%) of the voting power of all of the
then outstanding shares of the capital stock of the Corporation entitled to vote
generally in the election of directors, voting together as a single class, shall
be required to (i) reduce or eliminate the number of authorized shares of Common
Stock or Non-Voting Common Stock or the number of authorized shares of Preferred
Stock set forth in Article FOURTH or (ii) amend or repeal, or adopt any
provision inconsistent with, Articles SIXTH, SEVENTH, EIGHTH, NINTH, TENTH, and
this Article ELEVENTH of this Amended and Restated Certificate of Incorporation.

     TWELFTH:  Whenever a compromise or arrangement is proposed between this
Corporation and its creditors or any class of them and/or between this
Corporation and its stockholders or any class of them, any court of equitable
jurisdiction within the State of Delaware may, on the application in a summary
way of this Corporation or of any creditor or stockholder thereof or on the
application of any receiver or receivers appointed for this Corporation under
the provisions of Section 291 of the Delaware General Corporation Law or on the
application of trustees in dissolution or of any receiver or receivers appointed
for this Corporation under the provisions of Section 279 of the Delaware General
Corporation Law, order a meeting of the creditors or class of creditors, and/or
of the stockholders or class of stockholders of this Corporation, as the case
may be, to be summoned in such manner as the said court directs.  If a majority
in number representing three-fourths (3/4) in value of the creditors or class of
creditors, and/or of the stockholders or class of stockholders of this
Corporation, as the case may be, agree to any compromise or arrangement and to
any reorganization of this Corporation as consequence of such compromise or
arrangement, the said compromise or arrangement and the said reorganization
shall, if sanctioned by the court to which the said application has been made,
be binding on all the creditors or class of creditors, and/or on all the
stockholders or class of stockholders, of this Corporation, as the case may be,
and also on this Corporation.

                     [THIS SPACE INTENTIONALLY LEFT BLANK]

                                       8
<PAGE>
 
     IN WITNESS WHEREOF, the Corporation has caused this certificate to be
signed by its Chairman of the Board of Directors, President and Chief Executive
Officer this _______ day of __________ 1997.

                                   CURAGEN CORPORATION



                                   By:_________________________________________
                                      Jonathan M. Rothberg, Ph.D.
                                      Its Chairman of the Board, President 
                                        and Chief Executive Officer

                                       9
<PAGE>
 
                                                                       EXHIBIT 2
                                                                       ---------
                                                                                
                                                                                
            CERTIFICATE OF DESIGNATION, PREFERENCES, AND RIGHTS OF
                SERIES F NON-VOTING CONVERTIBLE PREFERRED STOCK

                                      OF

                              CURAGEN CORPORATION

     CURAGEN CORPORATION, a Delaware corporation (the "Company"), DOES HEREBY
CERTIFY:

     That, pursuant to authority conferred on the Board of Directors of the
Company by the Certificate of Incorporation of the Company and pursuant to the
provisions of Section 151 of Title 8 of the Delaware Code, said Board of
Directors, by the affirmative vote of at least a majority of its members,
adopted a resolution providing for the powers, designation, preferences and
relative, participating, optional or other rights, and qualifications,
limitations or restrictions thereof, of __________ (____________) shares of the
Company's Preferred Stock, par value $.01 per share, which resolution is as
follows:

     "RESOLVED: That pursuant to the authority granted to and vested in
      --------                                                               
                the Board of Directors of this Company in accordance with the
                provisions of its Restated Certificate of Incorporation, as
                amended, the Board of Directors hereby designates a series of
                Preferred Stock of the Company, par value $.01 per share (the
                "Preferred Stock"), consisting of _________ (______________)
                shares of the authorized, unissued Preferred Stock of the
                Company, as the Series F Non-Voting Convertible Preferred Stock
                (the "Series F Preferred"), and hereby fixes such designation
                and number of shares, and the powers, preferences and relative,
                participating, optional or other rights, and qualifications,
                limitations and restrictions thereof, as set forth below, and
                that the officers of the Company, and each acting singly, are
                hereby authorized, empowered and directed to execute and file
                with the Secretary of State of the State of Delaware a
                Certificate of Designation, Preferences and Rights of Series F
                Non-Voting Convertible Preferred Stock, as the officer or
                officers shall deem necessary and advisable to carry out the
                purposes of this resolution."

     Series F Preferred.  The powers, preferences, and relative, participating,
     ------------------                                                        
optional or other rights, and qualifications, limitations and restrictions
thereof, with respect to the Series F Preferred, par value $.01 per share, are
as follows:

     1.  Designation and Amount. The shares of such series shall be designated
         ----------------------
as "Series F Non-Voting Convertible Preferred Stock" (the "Series F Preferred"),
and the number of shares constituting the Series F Preferred shall be
__________________(____________). 
<PAGE>
 
     2.  Dividends.  Subject to the provisions of law and this Certificate of
         ---------                                                           
Incorporation, the holders of shares of Series F Preferred shall be entitled to
receive, out of funds legally available therefor, in preference to the holders
of Series A Convertible Preferred Stock (the "Series A Preferred"), Series B
Redeemable Preferred Stock (the "Series B Preferred"), Series C Convertible
Preferred Stock (the "Series C Preferred"), Series D Convertible Preferred Stock
(the "Series D Preferred") and Series E Preferred Stock (the "Series E
Preferred"), and any other class or series of the capital stock of the Company
ranking junior to the Series F Preferred Stock as to the payment of dividends,
quarterly dividends equal to the Series F Dividend Rate (as hereinafter
defined), payable when and as declared by the Board of Directors, and, whether
or not declared, with respect to liquidation under Section 4(a), conversion
under Section 5(a) or redemption under Section 6(a). Such dividends shall accrue
and be cumulative from the date of issuance of each share of Series F Preferred
Stock, whether or not declared.  As used herein, the term "Series F Dividend
Rate" shall mean that dividend rate as is equal to (i) the prime rate of
interest as reported from time to time by Citibank, N.A. (or, if Citibank, N.A.
ceases to report such rate, the generally prevailing base lending rate of Fleet
National Bank) (ii) plus one percent (1%).

     3.  Voting Rights.  Except as otherwise provided by the Delaware General
         -------------                                                       
Corporation Law, the holders of shares of Series F Preferred shall not be
entitled to vote in, or to receive notice of, any meeting of the stockholders of
the Company.

     4.  Liquidation, Dissolution or Winding Up.
         -------------------------------------- 

     (a) In the event of the voluntary or involuntary liquidation, dissolution
or winding up of the Company, or in the event of its insolvency, before any
distribution or payment is made to any holders of any shares of the Common Stock
or any other class or series of capital stock of the Company designated to be
junior to the Series A Preferred, the Series B Preferred, the Series C
Preferred, the Series D Preferred, the Series E Preferred and the Series F
Preferred and subject to the liquidation rights and preferences of any class or
series of capital stock of the Company designated to be senior to, or on parity
with, the Series A Preferred, the Series B Preferred, the Series C Preferred,
the Series D Preferred the Series E Preferred and the Series F Preferred, the
holders of outstanding shares of the Series A Preferred, the Series B Preferred,
the Series C Preferred, the Series D Preferred, the Series E Preferred and the
Series F Preferred shall be entitled to have set apart for them, or to be paid
first out of the assets of the Company available for distribution to holders of
the Company's capital stock of all classes, an amount in cash equal to (i) $5.86
per share of Series A Preferred and Series C Preferred, plus all declared but
unpaid dividends, (ii) $10.00 per share of Series B Preferred, plus all accrued
but unpaid dividends, whether or not declared, on the Series B Preferred, (iii)
$7.50 per share of Series D Preferred, plus all declared but unpaid dividends,
(iv) $10.00 per share of the Series E Preferred, plus all accrued but unpaid
dividends, whether or not declared and (v) $100.00 per share of the Series F
Preferred, plus all accrued but unpaid dividends, whether or not declared (and
in all instances specified in (i), (ii), (iii), (iv) and (v) subject to
equitable adjustment in the event of any stock dividend, stock split,

                                       2
<PAGE>
 
combination reorganization, recapitalization or other similar event affecting
such shares). If, upon any voluntary or involuntary liquidation, dissolution or
winding up of the Company, the assets of the Company available for distribution
to stockholders shall be insufficient to set aside for or to pay such amounts to
the holders of shares of Series A Preferred, Series B Preferred, Series C
Preferred, Series D Preferred, the Series E Preferred and Series F Preferred the
total amount of the Company's assets which is available to be paid to
stockholders of the Company shall be distributed ratably among the holders of
the Series A Preferred, the Series B Preferred, the Series C Preferred, the
Series D Preferred, the Series E Preferred and the Series F Preferred in
proportion to their preferential liquidation amounts as specified above, subject
to the liquidation rights and preferences of any other class or series of
capital stock of the Company designated to be senior to, or on a parity with,
the Series A Preferred, the Series B Preferred, the Series C Preferred, the
Series D Preferred, the Series E Preferred and the Series F Preferred, and no
distribution shall be made to or set apart for the holders of Common Stock or
any other class or series of capital stock of the Company which at such time is
junior to the Series A Preferred, the Series B Preferred, the Series C
Preferred, the Series D Preferred, the Series E Preferred and the Series F
Preferred as to liquidation rights and preferences. If the assets of the Company
available for distribution to stockholders exceed such amounts, the balance of
such assets shall be paid to or set aside for payment ratably among the holders
of any class or series of capital stock of the Company designated to be junior
to the Series A Preferred, the Series B Preferred, the Series C Preferred, the
Series D Preferred, the Series E Preferred and the Series F Preferred in
accordance with their relative rights and preferences, and thereafter, to the
holders of Common Stock.

     (b)  The merger or consolidation of the Company into or with another
corporation, or the sale or other conveyance of all or substantially all of the
assets of the Company to another entity, shall be deemed, at the option of any
holder of shares of Series F Preferred, a liquidation, dissolution or winding up
of the Company for purposes of this Section 4 as to such holder.

     5.   Conversion.
          ---------- 

     (a)  Subject to the terms and conditions of this Section 5, at any time
after the issuance of the Series F Preferred, the holder of each share of Series
F Preferred shall have the right, at such holder's option, to convert any such
shares of Series F Preferred into such number of fully paid and non-assessable
shares of Common Stock of the Company as is determined by dividing the Series F
Issue Price (as defined below) by the Conversion Price (as defined below). Such
option to convert shares of Series F Preferred into shares of Common Stock may
be exercised as to all or any portion of such shares of Series F Preferred by,
and only by, giving written notice to the Company at its principal office that
the holder elects to convert a stated number of shares of Series F Preferred
into Common Stock and by surrendering for such purpose to the Company at its
principal office the certificate representing such shares of Series F Preferred,
duly endorsed or accompanied by proper instruments to evidence the conversion
election. At the time of such surrender, the persons exercising such option to
convert shall be deemed to be the holders of the shares of Common Stock issuable
upon such conversion, notwithstanding that the stock transfer books of the
Company may

                                       3
<PAGE>
 
then be closed or that certificates representing such shares of Common Stock
shall not then be actually delivered to such person. All rights with respect to
the Series F Preferred so converted (other than the right to receive declared or
accrued (whether or not declared) but unpaid dividends thereon which may, at the
option of the Company, be paid in additional shares of Common Stock) will then
terminate. As promptly as practicable after the receipt of the written notice
referred to in the preceding paragraph and surrender of the certificate or
certificates for the share or shares of Series F Preferred to be converted, the
Company shall issue and deliver, or cause to be issued and delivered, to the
holder of the shares being converted, a certificate or certificates registered
in the holder's name or designee, for the number of whole shares of Common Stock
issuable upon the conversion of such share or shares of Series F Preferred. In
case the number of shares of Series F Preferred represented by the certificate
or certificates surrendered for conversion pursuant to this Section 5 exceeds
the number of shares converted, the Company shall, upon such conversion, execute
and deliver to the holder at the expense of the Company a new certificate or
certificates for the number of shares of Series F Preferred represented by the
certificate or certificates surrendered which are not to be converted. As used
herein, the "Series F Issue Price" shall mean $100 per share and the term
"Conversion Price" shall mean the fair market value of the shares of Common
Stock of the Company at the time of conversion, determined as follows: if the
shares of Common Stock are traded on the Nasdaq Stock Market the average of the
closing prices as reported by the Nasdaq Stock Market or, if not traded on the
Nasdaq Stock Market, by such other principal securities exchange on which the
shares are traded, as applicable, over the twenty (20) days preceding the date
on which conversion will be made or, if not traded on any other exchange, the
price per share which the Company could obtain from a willing buyer for shares
of Common Stock sold by the Company, as determined in good faith by the Board of
Directors of the Company.


     (b)  Capital Reorganization, Merger or Sale of Assets. If at any time or
          ------------------------------------------------
from time to time there shall be a capital reorganization of the Common Stock or
a consolidation or merger of the Company, or a sale of all or substantially all
of the assets of the Company (a "Reorganization"), then, as a part of and as a
condition to such Reorganization, provision shall be made so that the holders of
shares of the Series F Preferred shall thereafter be entitled to receive upon
conversion of the shares of the Series F Preferred the same kind and amount of
stock or other securities or property (including cash) of the Company, or of the
successor corporation resulting from such Reorganization, to which such holder
would have been entitled if such holder had converted its shares of the Series F
Preferred immediately prior to the effective time of such Reorganization. In any
such case, appropriate adjustment shall be made in the application of the
provisions of this Section 5 to the end that the provisions of this Section 5
(including adjustment of the Conversion Price then in effect and the number of
shares of Common Stock or other securities issuable upon conversion of the
shares of the Series F Preferred) shall be applicable after such Reorganization
in as nearly equivalent manner as may be reasonably practicable. In the case of
a transaction to which both this Subsection 5(b) and Subsection 4(b) hereof
apply, the holders of at least a majority of the outstanding shares of the
Series F Preferred upon the occurrence of a Reorganization shall have the option
to elect treatment either under this Subsection 5(b) or under Subsection 4(b)
hereof, notice of which election shall be given in writing to the Company not
less than fifteen (15) business days

                                       4
<PAGE>
 
prior to the effective date of such Reorganization or not less than fifteen (15)
days after the Company has given notice to the holders of the Series F Preferred
Stock of such Reorganization, whichever is later. If no such election is timely
made, the provisions of Subsection 4(b) and not of this Subsection 5(b) shall
apply.

     (c)    Certain Provisions Regarding Conversion.
            --------------------------------------- 

     (i)    No Fractional Shares. The number of shares of Common Stock issuable
            --------------------
upon conversion of any shares of Series F Preferred shall be rounded to the
nearest whole number, and no fractional shares of Common Stock, and no payment
in lieu thereof, shall be issued upon any such conversion.

     (ii)   Common Stock Reserved. The Company shall at all times reserve and
            ---------------------
keep available out of its authorized but unissued Common Stock the full number
of shares of Common Stock deliverable upon the conversion of all then
outstanding shares of Series F Preferred.

     (iii)  Status of Converted or Unissued Series F Preferred. Shares of Series
            --------------------------------------------------
F Preferred that have been issued and reacquired in any manner, including upon
conversion of such shares, shall (upon compliance with any applicable provisions
of the laws of the State of Delaware) have the status of authorized and unissued
shares of the Company's Preferred Stock, par value $.01 per share, undesignated
as to series and may be redesignated and reissued as part of any series of the
Preferred Stock.

     (iv)   Certificate as to Adjustments. Upon the occurrence of each
            -----------------------------
adjustment or readjustment of the number of shares receivable pursuant to this
Section 5, the Company at its expense shall promptly compute such adjustment or
readjustment in accordance with the terms hereof and furnish to each holder of
Series F Preferred a certificate setting forth such adjustment or readjustment
and showing in detail the facts upon which such adjustment or readjustment is
based. The Company shall, upon the written request at any time of any holder of
Series F Preferred, furnish or cause to be furnished to such holder a like
certificate setting forth (i) such adjustments and readjustments, and (ii) the
number of shares of Common Stock and the amount, if any, of other property which
at the time would be received upon the conversion of each series of Series F
Preferred.

     6.     (a)  Redemption.  The Company may, at any time after the date of
                 ----------                                                 
its Initial Public Offering (as defined below) redeem from each holder of Series
F Preferred, at a price equal to the Series F Issue Price, plus any accrued but
unpaid dividends thereon, whether or not declared (the "Redemption Price"), one
hundred percent (100%) of the shares of Series F Preferred held by such holder
on such date.  The Company will provide each holder of Series F Preferred with a
written request setting forth its desire to redeem shares of Series F Preferred.
Upon issuance of any such redemption request, the Company will become obligated
to redeem at the time of redemption specified therein (the "Redemption Date")
all shares of Series F Preferred specified therein.  In case 

                                       5
<PAGE>
 
less than all shares of Series F Preferred represented by any certificate are
redeemed in any redemption pursuant to this Section 6, a new certificate will be
issued representing the unredeemed shares of Series F Preferred without cost to
the holder thereof. As used herein, the term "Initial Public Offering" shall
mean a firm commitment underwritten public offering of the Common Stock of the
Company pursuant to a registration statement filed with and declared effective
by the Securities and Exchange Commission under the Securities Act of 1933, as
amended.

          (b)  Status of Redeemed Shares. Unless there shall have been a default
               -------------------------
in payment of the Redemption Price, no shares of redeemed Series F Preferred
shall be entitled to any dividends accrued after the Redemption Date, and on
such Redemption Date all rights of the holder of such redeemed shares as a
stockholder of the Company by reason of the ownership of such shares will cease,
except the right to receive the Redemption Price of such shares, without
interest, plus any declared or accrued (whether or not declared) unpaid
dividends accruing prior to the Redemption Date upon presentation and surrender
of the certificate representing such shares, and such redeemed shares will not
from and after such Redemption Date be deemed to be outstanding.

     7.   No Impairment.  The Company shall not, by amendment of its
          -------------                                             
Certificate of Incorporation or through any reorganization, transfer of assets,
consolidation, merger, dissolution, issue or sale of securities or any other
voluntary action, avoid or seek to avoid the observance or performance of any of
the terms to be observed or performed hereunder by the Company but shall at all
times in good faith assist in the carrying out of all the provisions of this
Certificate of Designation and in the taking of all such action as may be
necessary or appropriate in order to protect the rights and preferences of the
holders of Series F Preferred against impairment in accordance with this
Certificate of Designation and the Delaware General Corporation Law.

     8.   Certain Amendments to the Company's Certificate of Incorporation.
          ----------------------------------------------------------------  
So long as any shares of Series F Preferred Stock shall be outstanding, the
Company shall not, without first obtaining the affirmative vote or written
consent of the holders of a majority of the outstanding shares of Series F
Preferred Stock, voting separately as a class, amend or repeal any provision of,
or add any provision to, the Company's Certificate of Incorporation, including
any amendment, repeal or addition to the Company's Certificate or Incorporation
effected through a merger, if such action would adversely affect or change the
preferences, rights, privileges or powers of the Series F Preferred Stock, or
increase or decrease (other than by conversion) the total number of authorized
shares of Series F Preferred Stock.

                                       6
<PAGE>
 
     IN WITNESS WHEREOF, the Company has caused this Certificate of Designation
to be signed by its President and Chief Executive Officer this ____day of ____,
____.


                                        CURAGEN CORPORATION



                                        By:________________________________
                                         Jonathan M. Rothberg, Ph.D.
                                         President and Chief
                                         Executive Officer

                                       7
<PAGE>
 
                                  APPENDIX C
                                  ----------
                                        
                           FORM OF LICENSE AGREEMENT
<PAGE>
 
                               LICENSE AGREEMENT

     This License Agreement ("Agreement") is made effective as of
_______________ ("Effective Date") by and between GENENTECH, INC., a Delaware
corporation having its principal business office at 1 DNA Way, South San
Francisco, CA 94080 ("GENENTECH"), and CURAGEN CORPORATION, a Delaware
corporation with its principal place of business at 555 Long Wharf Drive, 11th
Floor, New Haven, Connecticut 06511 ("CURAGEN").  GENENTECH and CURAGEN are each
hereafter referred to individually as a "Party" and together as the "Parties".

     WHEREAS, GENENTECH wishes to obtain a license to certain inventions made or
owned by CURAGEN as provided in that certain Research and Option Agreement
between the Parties hereto dated as of November 20, 1997 which is attached
hereto (the "Research Agreement");

     WHEREAS, CURAGEN has agreed to provide such license under the terms and
conditions set forth herein.

     NOW, THEREFORE, in consideration of the mutual covenants contained herein,
and for other good and valuable consideration, the receipt and adequacy of which
is hereby acknowledged, the Parties hereby agrees as follows:

                                1.  DEFINITIONS

     Whenever used in the Agreement with an initial capital letter, the terms
defined in this Section 1 shall have the meanings specified.

     1.1  "AFFILIATE" shall mean any corporation, firm, limited liability
company, partnership or other entity which directly or indirectly controls or is
controlled by or is under common control with a Party to this Agreement.
"Control" means ownership, directly or through one or more Affiliates, of fifty
percent (50%) or more of the shares of stock entitled to vote for 
<PAGE>
 
the election of directors, in the case of a corporation, or fifty percent (50%)
or more of the equity interests in the case of any other type of legal entity,
status as a general partner in any partnership, or any other arrangement whereby
a Party controls or has the right to control the Board of Directors or
equivalent governing body of a corporation or other entity.

     1.2  "CLONE" shall mean a segment of DNA representing a whole or partial
gene whose sequence or utility is determined from the analysis of one or more
Data Sets or from the Extended Research during the Term of the Research
Agreement.

     1.3  "CURAGEN BACKGROUND INVENTIONS" shall mean all patent rights and know-
how of CURAGEN, other than those relating primarily to Inventions, which CURAGEN
has the right to license and which would be infringed by, or is reasonably
necessary for, the development, manufacture, use, sale or importation of any
product developed by GENENTECH pursuant to the licenses granted hereunder;
provided, however, that CURAGEN Background Inventions shall expressly exclude:
(i) any patent rights and know-how relating to Clones not licensed by GENENTECH
pursuant to this Agreement and (ii) any patent rights or know-how arising from
any CURAGEN collaboration with a third party, except to the extent permitted
thereby.

     1.4  "CURAGEN DATA" shall mean, with respect to a Licensed Clone, all
information pertaining to such Licensed Clone obtained from the processing of
specified CURAGEN samples, including QC data.  QEA/GeneCalling data,
MIM/PathCalling data, sequence data and any other information obtained or
generated by CURAGEN in the performance of the CURAGEN Project relating to such
Licensed Clone.

     1.5  "CURAGEN DATA SET" shall mean all CURAGEN Data resulting from a
discrete CURAGEN Project that CURAGEN can make exclusively available to
GENENTECH.

     1.6  "CURAGEN PROJECT" shall mean a particular project undertaken by
CURAGEN on its own outside the Research Program to process and analyze a
specified set of samples which do not contain GENENTECH Proprietary Material,
and as to which CURAGEN is free to grant rights to GENENTECH hereunder.

                                       2
<PAGE>
 
     1.7  "CURAGEN PROJECT INVENTION" shall mean any discovery, invention, know-
how or trade secret conceived or made by employees of CURAGEN (i) in the
performance of a CURAGEN Project that results in CURAGEN Data that becomes part
of an Exclusive Data Set, that is based on, incorporates or makes material use
of the corresponding CURAGEN Data or (ii) relating to a Lead generated outside
of the Extended Research.

     1.8  "CURAGEN PROJECT PATENT RIGHTS" shall mean Patent Rights containing a
claim or claims covering CURAGEN Project Inventions.  CURAGEN Project Patent
Rights shall also include Patent Rights containing a claim or claims covering
CURAGEN Project Inventions exclusively licensed in by CURAGEN, with the right to
sublicense, now or in the future.

     1.9  "CURAGEN PROJECT PROPRIETARY MATERIAL" shall mean, with respect to a
Licensed Clone, all substances made by CURAGEN in the performance of the CURAGEN
Project relating to such Licensed Clone, including mRNA pools.  CURAGEN Project
Proprietary Material shall include, without limitation, QEA fragments, MIM
constructs and materials derived or constructed from QEA fragments and MIM
constructs, including, without limitation, fragment and full length cDNA clones
made by CURAGEN.

     1.10 "DATA SET," which may be either a Project Data Set or a CURAGEN Data
Set, with respect to a Licensed Clone, shall mean all Project Data resulting
from the discrete Research Project relating to the Licensed Clone or all CURAGEN
Data resulting from the discrete CURAGEN Project relating to the Licensed Clone,
respectively.

     1.11 "EXCLUSIVE DATA SET" shall mean any Project Data Set during the
corresponding Exclusive Evaluation Period as provided in Section 2.4 of the
Research Agreement or any CURAGEN Data Set during the corresponding Exclusive
Evaluation Period as provided in Section 2.5.2 of the Research Agreement.

     1.12 "EXCLUSIVE EVALUATION PERIOD" shall have the meaning set forth in
Section 2.4 or 2.5.2 of the Research Agreement.

     1.13 "EXTENDED LICENSE PATENT RIGHTS" shall have the meaning set forth in
Section 2.3.

                                       3
<PAGE>
 
     1.14 "EXTENDED RESEARCH" shall mean, as to each Licensed Clone, the
research undertaken by CURAGEN before or after the Effective Date hereof
pursuant to Sections 2.4.1, 2.5.2 and/or  7.1.3 of the Research Agreement
relating to or using such Licensed Clone.

     1.15 "EXTENDED RESEARCH DATA" shall mean all information and results
obtained by CURAGEN from its performance of Extended Research.

     1.16 "EXTENDED RESEARCH INVENTIONS" shall mean any discovery, invention,
know-how or trade secret conceived or made by employees of CURAGEN  in the
performance of Extended Research, other than such discoveries, inventions,
know-how or trade secrets that are deemed to be defined as Research Project
Inventions pursuant to the terms of the Research Agreement or this Agreement.

     1.17 "EXTENDED RESEARCH PATENT RIGHTS" shall mean all rights and interests
in and to issued patents and pending patent applications in any country,
including, but not limited to, all provisional applications, substitutions,
continuations, continuations-in-part (solely to the extent that the claims of
such continuations-in-part cover Extended Research Inventions), divisions, and
renewals thereof, all letters patent granted thereon, and all reissues,
reexaminations and extensions thereof, whether owned now or hereafter solely or
jointly by CURAGEN, and wherein at least one claim of such patent right covers
an Extended Research Invention, and including, without limitation, those
Extended Research Patent Rights listed on Schedule I attached hereto.

     1.18 "GENESCAPE"(R) shall mean the web-based software and database product
for accessing and storing Data Sets generated through the application of
CURAGEN's QEA/GeneCalling and MIM/PathCalling.

     1.19 "INVENTION," as to each Licensed Clone, shall mean  CURAGEN Project
Inventions and Research Project Inventions relating to the Licensed Clone.

     1.20 "KNOW- HOW" shall mean: (a) as to each Licensed Clone, all unpatented
Project Data, Research Project Inventions, CURAGEN Data and CURAGEN Project
Inventions relating to such Licensed Clone; (b) as to each Lead, all unpatented
information, inventions, discoveries 

                                       4
<PAGE>
 
and trade secrets relating to the Lead; and (c) as to Extended Research using a
Licensed Clone, all unpatented Extended Research Data and all Extended Research
Inventions relating thereto.

     1.21 "LEAD" shall mean, as to each Licensed Clone,  a small molecule which
was discovered or developed to bind to a protein or inhibit protein function,
and which was developed directly and materially from the use of a Licensed Clone
or the protein encoded thereby by CURAGEN outside of the Research Program prior
to the point in time at which the Clone became a Licensed Clone, including,
without limitation, in the course of the Extended Research.

     1.22 "LICENSED CLONE" shall have the meaning set forth in Section 2.1.

     1.23 "LICENSED PRODUCT," as to each Licensed Clone, shall mean:

     [XXXXX]

     [XXXXX]

     [XXXXX]

     [XXXXX]

     [XXXXX]

                                       5

                       Confidential Treatment Requested
<PAGE>
 
     [XXXXX]

     [XXXXX]

     [XXXXX]

     [XXXXX]

     [XXXXX]

     1.24 "MIM/PATHCALLING" shall mean the technology employed by CURAGEN for
identifying protein-protein interactions from libraries of cDNAs.

     1.25 "NET SALES" shall mean [XXXXX]

     [XXXXX]

                                       6

                       Confidential Treatment Requested
<PAGE>
 
[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]

[XXXXX]
[XXXXX]
[XXXXX]
[XXXXX]

                                       7

                       Confidential Treatment Requested
<PAGE>
 
[XXXXX]

     1.26 "OPTIONED CLONE" shall have the meaning set forth in Section 7.1 of
the Research Agreement.

     1.27 "PATENT COORDINATORS" shall mean a patent attorney or patent agent
representing CURAGEN and a patent attorney or patent agent representing
GENENTECH, as further described in Section 5.1.

     1.28 "PATENT RIGHTS" shall mean, as to each Licensed Clone, all rights and
interests in and to issued patents and pending patent applications in any
country, including, but not limited to, all provisional applications,
substitutions, continuations, continuations-in-part (solely to the extent that
the claims of such continuations-in-part cover Research Project Inventions or
CURAGEN Project Inventions), divisions, and renewals thereof, all letters patent
granted thereon, and all reissues, reexaminations and extensions thereof,
whether owned now or hereafter, solely or jointly by a Party, and wherein at
least one claim of such patent right covers an Invention, and including, without
limitation, those Patent Rights listed on Schedule I attached hereto.

     1.29 "PRIME RATE" shall mean the prime rate of interest as reported by
Citibank, N.A.  In the event that Citibank, N.A. ceases to report such a rate,
the term "Prime Rate" shall mean the generally prevailing base corporate lending
rate of Fleet National Bank.

     1.30 "PROJECT DATA" shall mean all information obtained from the processing
of GENENTECH Proprietary Material in a particular Research Project, including QC
data, expression data, sequence data and any other information obtained or
generated by CURAGEN in the performance of the Research Project relating to such
Licensed Clone.

     1.31 "PROJECT DATA SET" shall mean all Project Data resulting from a
discrete Research Project.

                                       8

                       Confidential Treatment Requested
<PAGE>
 
     1.32 "QEA/GENECALLING" shall mean the technology employed by CURAGEN for
tagging and identifying the expression level of specific gene fragments within a
cDNA pool.

     1.33 "RESEARCH PROGRAM" shall mean the Research Projects to be performed by
CURAGEN and GENENTECH under the Research Agreement.

     1.34 "RESEARCH PROJECT" shall mean a particular project to process and
analyze a specified set of samples under the Research Agreement.

     1.35 "RESEARCH PROJECT INVENTION" shall mean any discovery, invention,
know-how or trade secret conceived or made:  (a) by employees of CURAGEN or
GENENTECH or jointly by employees of both in the performance of the Research
Program, (b) by GENENTECH employees in performing the following specific
activities utilizing any Data Set:  (i) QEA or MIM data analysis, confirmation
of QEA or MIM data, fragment cloning and sequencing of a Clone, and (ii) full-
length cloning of a Clone, or (c) any discovery, invention, know-how or trade
secret deemed to be a Research Project Invention pursuant to the terms of the
Research Agreement or this Agreement.  Research Project Inventions shall not
include inventions conceived or made solely by GENENTECH outside of the Research
Program, except as specifically set forth in (b) above.

     1.36 "RESEARCH PROJECT PATENT RIGHTS" shall mean Patent Rights containing a
claim or claims covering Research Project Inventions.

     1.37 "RESEARCH PROJECT PROPRIETARY MATERIAL" shall mean, with respect to a
Licensed Clone, all substances made by CURAGEN in the performance of the
Research Project relating to such Licensed Clone other than mRNA pools extracted
from GENENTECH Proprietary Material.  Research Project Proprietary Material
shall include, without limitation, QEA fragments, MIM constructs and materials
derived or constructed from QEA fragments and MIM constructs, including, without
limitation, fragment and full length cDNA clones made by CURAGEN.

                                       9
<PAGE>
 
     1.38 "SUBLICENSEE" shall mean any non-Affiliate third party sublicensed by
GENENTECH under the license granted to GENENTECH hereunder, to make, have made,
use, have used, offer to sell, sell, have sold, import or have imported any
Licensed Product.

     1.39 "TERM" shall have the meaning set forth in Section 3.10.

     1.40 "TERRITORY" shall mean the world.

     1.41 "VALID CLAIM(S)" shall mean an unexpired claim of any issued patent
within Patent Rights or Extended License Patent Rights which has not been
finally declared invalid or unenforceable by a patent office or by a court or
other body of competent jurisdiction in any unappealed or unappealable decision
and which has not been lost through an interference or opposition proceeding.


                               2.  LICENSE GRANT

     2.1  LICENSE GRANT.  Upon exercise of an Option pursuant to Section 7.4 of
          -------------                                                        
the Research Agreement for any Optioned Clone, GENENTECH shall elect one of the
types of licenses set forth below.  The Parties shall indicate such election and
complete the information for such Optioned Clone on Schedule I attached hereto
and incorporated herein, and sign such Schedule I.  Such Optioned Clone shall
thereafter be deemed a Licensed Clone.  With respect to the license types set
forth in (a) and (b) below, GENENTECH shall also indicate on Schedule I its
election , if any, to obtain an exclusive license hereunder to CURAGEN's rights
and interests in any Lead relating to such Licensed Clone.

     (a)  For each Licensed Clone and corresponding Lead(s) listed on Schedule I
          for which this Section 2.1(a) exclusive license is elected, subject to
          the rights reserved to CURAGEN in Section 2.5 below, CURAGEN hereby
          grants to GENENTECH an exclusive license (even as to CURAGEN) in the
          Territory, to develop, make, have made, use, have used, sell, have
          sold, offer for sale, import and have imported any and all products
          for any and all human uses, under:  (x) all Patent 

                                      10
<PAGE>
 
          Rights, Inventions, Know-How, CURAGEN Project Proprietary Material and
          Research Project Proprietary Material that pertain to such Licensed
          Clone, related Licensed Products and the uses thereof, including but
          not limited to Patent Rights claiming whole or partial sequences or
          utility; and (y) all Patent Rights and Know-How of CURAGEN which
          CURAGEN has the right to license to GENENTECH relating to Leads
          discovered or developed using such Licensed Clone or the protein
          encoded thereby as a target, and which GENENTECH has elected to
          license. Such license shall be for the Term specified in Section 3.10,
          unless terminated as set forth in this Agreement.

     (b)  For each Licensed Clone and corresponding Lead(s) listed on Schedule I
          for which this Section 2.1(b) exclusive license is elected and which
          were "known" by third parties prior to the exercise of the
          corresponding Option as determined pursuant to subsection (d) below,
          subject to the rights reserved to CURAGEN in Section 2.5 below,
          CURAGEN hereby grants to GENENTECH an exclusive license (even as to
          CURAGEN) in the Territory, to develop, make, have made, use, have
          used, sell, have sold, offer for sale, import and have imported any
          and all products for any and all human uses, under: (x) all Patent
          Rights, Inventions, Know-How, CURAGEN Project Proprietary Material and
          Research Project Proprietary Material that pertain to such Licensed
          Clone, related Licensed Products and the uses thereof, including but
          not limited to Patent Rights claiming whole or partial sequences or
          utility; and (y) all Patent Rights and Know-How of CURAGEN which
          CURAGEN has the right to license to GENENTECH relating to Leads
          discovered or developed using the Licensed Clone or the protein
          encoded thereby as a target, and which GENENTECH has elected to
          license.  Such license shall be for the Term specified in Section
          3.10, unless terminated as set forth in this Agreement.

     (c)  For each Licensed Clone listed on Schedule I for which this Section
          2.1(c) non-exclusive license is elected and for Licensed Products
          related to such Licensed Clone that are discovered or developed by
          GENENTECH, CURAGEN hereby

                                      11
<PAGE>
 
          grants to GENENTECH a non-exclusive license in the Territory to use
          such Licensed Clone or the protein encoded thereby as a reagent for
          discovering or developing Licensed Products and to develop, make, have
          made, use, have used, sell, have sold, offer for sale, import and have
          imported Licensed Products for any and all human uses, under all
          Patent Rights, Inventions, Know-How, Research Project Proprietary
          Materials and CURAGEN Project Proprietary Materials pertaining to such
          Licensed Clone, related Licensed Products and the uses thereof,
          including but not limited to Patent Rights claiming whole or partial
          sequences or utility. Such license shall be for the Term specified in
          Section 3.10, unless terminated as set forth in this Agreement.

     (d)  The Parties shall mutually agree in good faith on whether any Licensed
          Clone is "known" by third parties prior to the exercise of an Option,
          based primarily on the availability of whole or substantially whole
          coding domains substantially the same as such Licensed Clone in
          publicly available literature, patent applications or databases or on
          knowledge of such information by GENENTECH as evidenced by written or
          computer records.  Licensed Clones which are "known" only as a result
          of either a previous Research Project or a CURAGEN Project from which
          GENENTECH received access to an Exclusive Data Set from which the
          Licensed Clone was optioned, and are not "known" to third parties or
          to GENENTECH other than through any public disclosure of research
          results related to such Research Project or CURAGEN Project, shall not
          be deemed "known" for the purposes hereof.

     2.2  NON-EXCLUSIVE LICENSE.  CURAGEN hereby grants to GENENTECH a non-
          ---------------------                                           
exclusive license, coterminous with each license grant in Section 2.1, under
CURAGEN Background Inventions solely to the extent necessary to allow GENENTECH
to practice the license granted in Section 2.1 and for no other purpose.

     2.3  EXTENDED LICENSE.  Any license granted to GENENTECH under Section
          ----------------                                                 
2.1(a) or (b) shall also include, with respect to each Licensed Clone and
corresponding Lead(s) listed on

                                      12
<PAGE>
 
Schedule I, an exclusive license under the know-how, patents and patent
applications set forth below to the extent CURAGEN has the right to grant such
license (an "Extended License"); provided, however, that GENENTECH may elect, at
its sole discretion, not to accept a license under any Extended License Patent
Rights (as defined below), such election to be made within sixty (60) days of
the license grant to the corresponding Licensed Clone, or within sixty (60) days
of CURAGEN's notice to GENENTECH of the filing of any patent application within
Extended License Patent Rights for patent applications filed after execution of
this Agreement with respect to the relevant Licensed Clone:

     (a)  Any patents or patent applications (including all provisional
applications, substitutions, continuations, continuations-in-part, divisions and
renewals thereof, all letters patent granted thereon, and all reissues,
reexaminations and extensions thereof) owned by CURAGEN that result from any
activities other than the Research Program (x) that are not Extended Research
Patent Rights and do not arise from CURAGEN's exercise of its rights under
Section 2.5 hereof but claim any Licensed Product relating to such Licensed
Clone, provided that CURAGEN is not utilizing the invention or inventions
claimed in such patent or application in a preclinical or clinical development
project being actively planned or conducted by CURAGEN (alone or in
collaboration with any third party) on the date such Licensed Clone was optioned
by GENENTECH pursuant to the Research Agreement as evidenced by written or
computer records; or (y) that are Extended Research Patent Rights arising from
the use of such Licensed Clone ((x) and (y) collectively, the "Extended License
Patent Rights"); and

     (b)  Know-How as described in Section 1.20(c).

     2.4  DUE DILIGENCE.  GENENTECH agrees to use commercially reasonable
          -------------                                                  
efforts in pursuing research and development of at least one Licensed Product
based upon each Licensed Clone in a manner similar to other products in research
and development at GENENTECH at a similar development stage and of similar
commercial value.  If GENENTECH ceases to use such commercially reasonable
efforts for a commercially unreasonable period of time with respect to at least
one Licensed Product for any Licensed Clone, CURAGEN shall have the right to
terminate the license granted to GENENTECH hereunder with respect to such
Licensed Clone

                                      13
<PAGE>
 
only, provided that: (a) CURAGEN refunds to GENENTECH on the effective date of
such termination all licensing and milestone payments which have previously been
paid to CURAGEN hereunder for such Licensed Clone and (b) that CURAGEN pays to
GENENTECH royalties on Net Sales of Licensed Products based upon such Licensed
Clone that are sold by CURAGEN, its Affiliates and its sublicensees under the
same royalty rates and terms as are set forth in Section 7.7 of the Research
Agreement. Such termination by CURAGEN shall be effective sixty (60) days after
giving GENENTECH written notice of such termination, describing the lack of
diligence and shall have the consequences set forth in Section 6.2. The
foregoing notwithstanding, if such breach of diligence is shown to be non-
existent within the aforesaid sixty (60) day period, CURAGEN'S notice shall be
deemed automatically withdrawn and of no effect.

     2.5  RESERVATION OF RIGHTS.  Notwithstanding anything in this Agreement to
          ---------------------                                                
the contrary, CURAGEN hereby retains for itself the right to use each Licensed
Clone and the protein encoded thereby for CURAGEN's internal, general, non-
directed, research purposes (including, without limitation, full-length cloning,
expression analysis, protein-protein interactions and drug screening).  For
example, but without limitation, inclusion of the Licensed Clone together with
other clones in research to determine multiple protein-protein interactions, or
inclusion of the Licensed Clone together with other clones in a screen against
one or more molecules to determine inhibition would be "non-directed" research,
whereas activities associated with choosing a specific Licensed Clone and
working to elucidate the biological activity of such Licensed Clone (e.g.,
generating antibodies to the Licensed Clone, testing the Licensed Clone or
protein encoded thereby in preclinical models, enriching libraries with such
Licensed Clone to purposefully look for proteins which bind to such Licensed
Clone) would be considered "directed" research and CURAGEN would not be
permitted to perform such activities under this Section 2.5.  CURAGEN shall
promptly report to GENENTECH a summary of all such research results.  Any
inventions conceived or made during such research which relate to the sequence
or utility of the Licensed Clone, the proteins derived therefrom (including
antibodies), homologs and mutants with substantially the same biological
activity as such Licensed Clone or protein, or antibodies or small molecules
which interact with such Licensed

                                      14
<PAGE>
 
Clone or protein or homolog or mutant thereof, shall be deemed Research Project
Inventions and shall be subject to the licenses granted pursuant to Section
2.1(a) or (b) hereof, without payment of any additional license or option fee by
GENENTECH. With respect to all other inventions resulting from such research, in
the event that such Licensed Clone is subject to an exclusive license hereunder,
CURAGEN shall, prior to disclosure to any other party, offer all such inventions
and related research results to GENENTECH as a CURAGEN Project pursuant to the
provisions of Section 2.5 of the Research Agreement for an initial Exclusive
Evaluation Period of ninety (90) days, which shall be granted to GENENTECH upon
its request at no additional fee. Extensions of such Exclusive Evaluation
Period, Options, extensions of Options and the exercise of Options shall be
governed by Section 2.5 and Article 7 of the Research Agreement. Notwithstanding
any other provisions of this Agreement or the Research Agreement, any such
inventions which are ultimately licensed by GENENTECH after exercise of the
above-granted rights pursuant to Section 2.5 and Article 7 of the Research
Agreement relating to research performed under Section 2.5 of this Agreement
shall be deemed Research Project Inventions for all purposes under this License
Agreement, including, without limitation, the determination of royalties.

     2.6  SUBLICENSES.  GENENTECH shall have the right to grant sublicenses to
          -----------                                                         
all or any portion of its rights under any license granted herein to any
Affiliate or Sublicensee, provided, however, that GENENTECH shall remain
obligated to ensure payment of royalty and milestone obligations as set forth in
Article 3.

                               3.  CONSIDERATION

     3.1  LICENSE FEES.  Upon exercise of an Option pursuant to Section 7.1.2 of
          ------------                                                          
the Research Agreement for any Optioned Clone and execution of Schedule I by the
Parties with respect to such Optioned Clone and corresponding Lead(s), GENENTECH
shall pay to CURAGEN a license fee as set forth below:

          LICENSE TYPE                                 $ (THOUSANDS)  
          ------------                                 -------------  
                                               
          [XXXXX]

                                      15

                       Confidential Treatment Requested
<PAGE>
 
                                    [XXXXX]
                                    [XXXXX]


     3.2  MILESTONE PAYMENTS FOR THERAPEUTIC OR PROPHYLACTIC PRODUCTS.
          -----------------------------------------------------------

          3.2.1  Milestone Payments under Exclusive License. GENENTECH shall
                 ------------------------------------------
make the following milestone payments to CURAGEN for each therapeutic or
prophylactic Licensed Product covered by an exclusive license under Section
2.1(a):

     (a)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee files the first Investigational New Drug
          application (or foreign equivalent) with the FDA (or equivalent
          foreign regulatory agency) for the Licensed Product ("IND");

     (b)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee commences the first Phase III or Phase II/III
          clinical trial in any country for the Licensed Product;

     (c)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee submits the first Biologics License
          Application, Product License Application, New Drug Application or
          other application for approval to sell the Licensed Product to the FDA
          (or equivalent foreign regulatory agency) for the Licensed Product;

     (d)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee receives FDA approval of the Licensed Product
          for commercial sale in the United States;

     (e)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee first receives all required regulatory
          approval to commence sales of the Licensed Product in Germany, France,
          Italy, Spain, the United Kingdom or Japan; and

                                      16

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     (f)  [XXXXX] within forty-five (45) days following the end of the first
          calendar year in which Net Sales of such Licensed Product exceed
          [XXXXX].

          3.2.2  Milestone Payments under Exclusive License.  GENENTECH shall
                 ------------------------------------------                  
make the following milestone payments to CURAGEN for each therapeutic or
prophylactic Licensed Product covered by an exclusive license under Section
2.1(b) but only in the event that a therapeutic or prophylactic use for such
Licensed Product is a Research Project Invention, a Curagen Research Project
Invention or an Extended Research Invention licensed hereunder:

     (a)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee files the first Investigational New Drug
          application (or foreign equivalent) with the FDA (or equivalent
          foreign regulatory agency) for the Licensed Product for a use covered
          by the exclusive licenses granted herein ("IND");

     (b)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee commences the first Phase III or Phase II/III
          clinical trial in any country for the Licensed Product for a use
          covered by the exclusive licenses granted herein;

     (c)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee submits the first Biologics License
          Application, Product License Application, New Drug Application or
          other application for approval to sell the Licensed Product to the FDA
          (or equivalent foreign regulatory agency) for the Licensed Product for
          a use covered by the exclusive licenses granted herein;

     (d)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee receives FDA approval of the Licensed Product
          for commercial sale for a use covered by the exclusive licenses
          granted herein;

                                      17

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     (e)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee first receives approval to commence sales of
          the Licensed Product for a use covered by the exclusive licenses
          granted herein in Germany, France, Italy, Spain, the United Kingdom or
          Japan; and

     (f)  [XXXXX] within forty-five (45) days following the end of the first
          calendar year in which Net Sales of such Licensed Product for a use
          covered by the exclusive licenses granted herein exceed [XXXXX].

          3.2.3  Milestone Payments under Non-exclusive License.  GENENTECH
                 ----------------------------------------------            
shall make the following milestone payments to CURAGEN for each therapeutic or
prophylactic Licensed Product covered by a non-exclusive license under Section
2.1(c):

     (a)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee files the first Investigational New Drug
          application (or foreign equivalent) with the FDA (or equivalent
          foreign regulatory agency) for the Licensed Product ("IND");

     (b)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee commences the first Phase III or Phase II/III
          clinical trial in any country for the Licensed Product;

     (c)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee submits the first Biologics License
          Application, Product License Application, NDA or other application for
          approval to sell the Licensed Product to the FDA (or equivalent
          foreign regulatory agency) for the Licensed Product;

     (d)  [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee receives FDA (or equivalent foreign
          regulatory agency) approval of the Licensed Product for commercial
          sale; and

                                      18

                       Confidential Treatment Requested
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     (e)  [XXXXX] within thirty (30) days following the end of the first
          calendar year in which Net Sales of such Licensed Product exceed
          [XXXXX].

     3.3  MILESTONE PAYMENTS FOR DIAGNOSTIC PRODUCTS.  GENENTECH shall make the
          ------------------------------------------                           
following milestone payment to CURAGEN for each Licensed Product described in
Subsection (h) of the definition of Licensed Products covered by an exclusive
license under Section 2.1(a) or 2.1(b):

          [XXXXX] within thirty (30) days following the date GENENTECH or an
          Affiliate or Sublicensee receives FDA (or equivalent foreign
          regulatory agency) approval of the Licensed Product for commercial
          sale.

     3.4  ROYALTIES ON LICENSED PRODUCTS LICENSED EXCLUSIVELY TO GENENTECH AND
          --------------------------------------------------------------------
COVERED SOLELY BY RESEARCH PROJECT PATENT RIGHTS.  GENENTECH shall pay to
- ------------------------------------------------                         
CURAGEN a royalty on Net Sales of Licensed Products in those countries where the
manufacture, use, importation or sale of such Licensed Product by a third party
(i) would infringe a Valid Claim of a Research Project Patent Right and (ii)
would not infringe a Valid Claim of an Extended License Patent Right or a
CURAGEN Project Patent Right, as follows:

     [XXXXX]

     [XXXXX]

     [XXXXX]

                                      19

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     (d)  Royalties due to CURAGEN pursuant to subsections (a), (b) and (c)
          above for a given Licensed Product may be reduced by [XXXXX] of any
          royalties paid to third parties by GENENTECH, its Affiliates or
          Sublicensees on net sales of such Licensed Product that are required
          in order to allow GENENTECH, its Affiliates or Sublicensees to
          manufacture, use or sell such Licensed Product; provided, however,
          that such reductions shall in no event reduce the royalty for such
          Licensed Product payable pursuant to such subsection by more than
          [XXXXX].

     3.5  ROYALTIES ON LICENSED PRODUCTS LICENSED EXCLUSIVELY TO GENENTECH AND
          --------------------------------------------------------------------
COVERED BY RESEARCH PROJECT PATENT RIGHTS AND CURAGEN PROJECT PATENT RIGHTS OR
- ------------------------------------------------------------------------------
EXTENDED LICENSE PATENT RIGHTS.  GENENTECH shall pay to CURAGEN a royalty on Net
- ------------------------------                                                  
Sales of Licensed Products in those countries where the manufacture, use,
importation or sale of such Licensed Product by a third party (i) would infringe
a Valid Claim of a Research Project Patent Right and (ii) would infringe a Valid
Claim of an Extended License Patent Right or a CURAGEN Project Patent Right, as
follows:

     (a)  If the Licensed Product is as described in subsections (a)-(c) or (e)
          of the definition of Licensed Product, the royalty rate on Net Sales
          of such Licensed Product shall be as follows:

               [XXXXX]

               [XXXXX]

               [XXXXX]

     (b)  If the Licensed Product is as described in subsections (d) or (f) of
          the definition of Licensed Product, or is a product as described in
          subsection (g) of the definition of Licensed Product and is not
          discovered from material use of a Lead by GENENTECH, its Affiliates or
          Sublicensees, the royalty rate on Net Sales of such Licensed Product
          shall be:

                                      20

                       Confidential Treatment Requested
<PAGE>
 
               [XXXXX]

               [XXXXX]

               [XXXXX]

     (c)  If the Licensed Product is as described in subsection (g) of the
          definition of Licensed Product and is discovered from the material use
          by GENENTECH, its Affiliates or Sublicensees of a Lead identified by
          CURAGEN and provided to GENENTECH pursuant to an exclusive license
          granted pursuant to the provisions of Section 2.1(a) or (b), the
          royalty rate on Net Sales of such Licensed Product shall be:

               [XXXXX]

               [XXXXX]

               [XXXXX]

     (d)  If the Licensed Product is as described in subsections (h) or (i) of
          the definition of Licensed Product, the royalty rate on Net Sales of
          such Licensed Product shall be [XXXXX].

     (e)  Royalties due to CURAGEN pursuant to subsections (a), (b) , (c) and
          (d) above for a given Licensed Product may be reduced by [XXXXX] of
          any royalties paid to third parties by GENENTECH, its Affiliates or
          Sublicensees on net sales of such Licensed Product that are required
          in order to allow GENENTECH, its Affiliates or Sublicensees to
          manufacture, use or sell such Licensed Product; provided, however,
          that such reductions shall in no event reduce the royalty for such
          Licensed Product payable pursuant to such subsection by more than
          [XXXXX].

     3.6  ROYALTIES ON LICENSED PRODUCTS LICENSED EXCLUSIVELY TO GENENTECH AND
          --------------------------------------------------------------------
COVERED SOLELY BY CURAGEN PROJECT  PATENT RIGHTS OR EXTENDED LICENSE PATENT
- ---------------------------------------------------------------------------
RIGHTS.  GENENTECH shall pay to CURAGEN a royalty on Net Sales of Licensed
- ------                                                                    
Products in those 

                                      21

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countries where the manufacture, use, importation or sale of such Licensed
Product by a third party (i) would not infringe a Valid Claim of a Research
Project Patent Right and (ii) would infringe a Valid Claim of an Extended
License Patent Right or a CURAGEN Project Patent Right, as follows:

     (a)  If the Licensed Product is as described in subsections (a)-(c) or (e)
          of the definition of Licensed Product, the royalty rate on Net Sales
          of such Licensed Product shall be as follows:

               [XXXXX]

               [XXXXX]

               [XXXXX]

     (b)  If the Licensed Product is as described in subsections (d) or (f) of
          the definition of Licensed Product, or is a product as described in
          subsection (g) of the definition of Licensed Product and is not
          discovered from material use of a Lead by GENENTECH, its Affiliates or
          Sublicensees, the royalty rate on Net Sales of such Licensed Product
          shall be:

               [XXXXX]

               [XXXXX]

               [XXXXX]

     (c)  If the Licensed Product is as described in subsection (g) of the
          definition of Licensed Product and is discovered from material use by
          GENENTECH, its Affiliates or Sublicensees of a Lead identified by
          CURAGEN and provided to GENENTECH pursuant to an exclusive license
          granted pursuant to the provisions of Section 2.1(a) or (b), the
          royalty rate on Net Sales of such Licensed Product shall be:

                                      22

                       Confidential Treatment Requested
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                                    [XXXXX]

                                    [XXXXX]

                                    [XXXXX]

     (d)  If the Licensed Product is as described in subsections (h) or (i) of
          the definition of Licensed Product, the royalty rate on Net Sales of
          such Licensed Product shall be [XXXXX].

     (e)  Royalties due to CURAGEN pursuant to subsections (a), (b), (c) and (d)
          above for a given Licensed Product may be reduced by [XXXXX] of any
          royalties paid to third parties by GENENTECH, its Affiliates or
          Sublicensees on net sales of such Licensed Product that are required
          in order to allow GENENTECH, its Affiliates or Sublicensees to
          manufacture, use or sell such Licensed Product; provided, however,
          that such reductions shall in no event reduce the royalty for such
          Licensed Product payable pursuant to such subsection by more than
          [XXXXX].

     3.7  LICENSED PRODUCTS NON EXCLUSIVELY LICENSED TO GENENTECH OR EXCLUSIVELY
          ----------------------------------------------------------------------
LICENSED BUT NOT COVERED BY PATENT RIGHTS OR EXTENDED LICENSE PATENT RIGHTS.
- ---------------------------------------------------------------------------- 
For Licensed Products that are discovered under a license to GENENTECH pursuant
to Section 2.1(c) above, or that are licensed exclusively to GENENTECH hereunder
and are made, used or sold by GENENTECH, its Affiliates or Sublicensees, where
the manufacture, use, importation or sale of such Licensed Product by a third
party would not infringe a Valid Claim of any Patent Right or Extended License
Patent Right, GENENTECH shall pay to CURAGEN a royalty on Net Sales as follows:

     (a)  For Licensed Products as described in subsections (a)-(c) or (e) of
          the definition of Licensed Product, the royalty rate on Net Sales of
          such Licensed Product shall be [XXXXX].

                                      23

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     (b)  For Licensed Products as described in subsections (d) or (f) of the
          definition of Licensed Product or as described in subsection (g) of
          the definition of Licensed Product which are not discovered from
          material use of a Lead by GENENTECH, its Affiliates or Sublicensees,
          the royalty rate on Net Sales of such Licensed Product shall be 
          [XXXXX].

     (c)  For Licensed Products as described in subsection (g) of the definition
          of Licensed Product which are discovered from material use by
          GENENTECH, its Affiliates or Sublicensees of a Lead, the royalty rate
          on Net Sales of such Licensed Products shall be [XXXXX].

     (d)  For Licensed Products as described in subsections (h) or (i) of the
          definition of Licensed Product, the royalty rate on Net Sales of such
          Licensed Products shall be [XXXXX].

     (e)  Royalties due to CURAGEN pursuant to subsections (a), (b) , (c), 
          and (d) above for a given Licensed Product may be reduced by [XXXXX]
          of any royalties paid to third parties by GENENTECH, its Affiliates or
          Sublicensees on net sales of such Licensed Product that are required
          in order to allow GENENTECH, its Affiliates or Sublicensees to
          manufacture, use or sell such Licensed Product; provided, however,
          that such reductions shall in no event reduce the royalty for such
          Licensed Product payable pursuant to such subsection by more than
          [XXXXX].

     3.8  ONE ROYALTY.  Only one royalty, calculated at the highest applicable
          -----------                                                         
royalty rate hereunder, shall be payable to CURAGEN hereunder for each sale of a
Licensed Product, regardless of the number of patents, patent applications or
Valid Claims directed to or covering such Licensed Product.

     3.9  PAYMENT TERMS.
          ------------- 

     (a)  Royalty payments shall be made to CURAGEN in United States Dollars
          quarterly within sixty (60) days following the end of each calendar
          quarter for which 

                                      24

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<PAGE>
 
          royalties are due. Each royalty payment shall be accompanied by a
          report summarizing the total Net Sales for each Licensed Product
          during the relevant three-month period and the calculation of
          royalties, if any, due thereon pursuant to this Article 3.

     (b)  All royalties shall be payable in full in the United States in United
          States Dollars, regardless of the countries in which sales are made.
          For the purpose of computing Net Sales for Licensed Products sold in a
          currency other than United States dollars, such currency shall be
          converted into United States dollars at the exchange rate for buying
          U.S. dollars set forth in The Wall Street Journal for the last
                                    -----------------------             
          business day of the calendar quarter.

     3.10 ROYALTY TERM.  GENENTECH shall pay royalties with respect to each
          ------------                                                     
Licensed Product on a country-by-country basis until (i) the expiration or 
revocation or complete rejection of the last to expire or to be revoked or to be
completely rejected of any Valid Claim of a Patent Right or Extended License
Patent Right covering such Licensed Product in such country, or (ii) ten (10)
years from the first commercial sale of such Licensed Product in such country,
whichever is later. The term of each license under this Agreement (the "Term")
shall commence upon execution of Schedule I with respect thereto, and shall
continue as long as any royalties are due hereunder for Licensed Products under
such license. Following such period, unless the license pertaining to such
Licensed Product has previously been terminated, GENENTECH shall have a fully
paid-up, irrevocable license in such country under the Patent Rights, Extended
License Patent Rights, Inventions, Know-How and CURAGEN Background Inventions
relating to the relevant Licensed Clone, to make, have made, use, have used,
sell, have sold, offer for sale, import and have imported such Licensed Product
in such country.

     3.11 OVERDUE ROYALTIES.  Royalties not paid within the time period set
          -----------------                                                
forth in this Article 3 shall bear interest at [XXXXX], accruing monthly, from
the due date until paid in full.

     3.12 RECORDS RETENTION.  AUDITS.  GENENTECH, its Affiliates and
          --------------------------                                
Sublicensees shall keep for [XXXXX] from the date of each payment of royalties
complete and accurate records

                                      25

                       Confidential Treatment Requested
<PAGE>
 
of sales by GENENTECH and its Affiliates and Sublicensees of each Licensed
Product in sufficient detail to allow the accruing royalties to be determined
accurately. CURAGEN shall have the right for a period of [XXXXX] after receiving
any report or statement with respect to royalties due and payable to appoint an
independent certified public accountant reasonably acceptable to GENENTECH to
inspect the relevant records of GENENTECH and its Affiliates and Sublicensees to
verify such report or statement. GENENTECH and its Affiliates and Sublicensees
shall each make its records available for inspection by such independent
certified public accountant during regular business hours at such place or
places where such records are customarily kept, upon reasonable notice from
CURAGEN, solely to verify the accuracy of the reports and payments. Such
inspection right shall not be exercised more than once in any calendar year nor
more than once with respect to sales of any Licensed Product in any given
payment period. CURAGEN agrees to hold in strict confidence all information
concerning royalty payments and reports, and all information learned in the
course of any audit or inspection, except to the extent necessary for CURAGEN to
reveal such information in order to enforce its rights under this Agreement or
if disclosure is required by law, regulation or judicial order. The results of
each inspection, if any, shall be binding on both Parties. CURAGEN shall pay for
such inspections, except that in the event there is any upward adjustment in
aggregate royalties payable for any year shown by such inspection of more than
[XXXXX] of the amount paid, GENENTECH shall pay for such inspection.

                   4.  TREATMENT OF CONFIDENTIAL INFORMATION

     4.1  CONFIDENTIAL INFORMATION.  During the Term of this Agreement, each
          ------------------------                                          
Party may disclose to the other proprietary technical, research and business
information (collectively, "Confidential Information").  For a period of [XXXXX]
after the receipt of any such Confidential Information, the receiving Party
shall keep confidential all such Confidential Information of the other Party and
will not disclose such Confidential Information of the other Party to third
parties by publication or otherwise. Each Party further agrees not to use
Confidential Information of the other Party for any purpose other than
exercising any rights granted to it or reserved by it under this Agreement.
Notwithstanding the foregoing, it is

                                      26

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<PAGE>
 
understood and agreed that the receiving Party's obligations of confidentiality
and nonuse herein shall not apply to any information which:

     (a)  is, at the time of disclosure by the disclosing Party hereunder, or
          thereafter becomes, a part of the public domain or publicly known or
          available through no fault or negligence of the receiving Party or any
          of its Affiliates; or

     (b)  was otherwise in the receiving Party's lawful possession prior to
          disclosure by the disclosing Party, as demonstrated by the receiving
          Party's written records; or

     (c)  is lawfully disclosed to the receiving Party on a non-confidential
          basis by a third party who is not in violation of an obligation of
          confidentiality to the disclosing Party relative to such information.

Each Party may disclose the other Party's Confidential Information to the extent
reasonably necessary to comply with applicable government laws or regulations,
provided that prompt notice of any such disclosure shall be given to the other
Party.

     Information disclosed other than in written or electronic form shall be
subject to the terms of this Section 4.1 only if confirmed in writing to other
Party within thirty (30) days of initial disclosure and specifying with
particularity that Confidential Information disclosed other than in written form
which is subject to the provisions of this Section 4.1.

     4.2  PRESS RELEASE AND REGULATORY FILINGS.  The Parties shall mutually
          -------------------------------------                            
agree on a press release announcing the execution of this Agreement and on any
confidential treatment request to be filed with the Securities and Exchange
Commission with respect to this Agreement.  Neither Party shall make any
disclosure of the terms of this Agreement except as required by applicable law
or as set forth above without the prior written consent of the other Party.
Once any written statement is approved for disclosure by both Parties, either
Party may make subsequent public disclosures of the contents of such statement
without the further approval of the other Party.

                                      27
<PAGE>
 
             5.  PROVISIONS CONCERNING THE FILING, PROSECUTION AND

                         MAINTENANCE OF PATENT RIGHTS

     5.1  PATENT FILING.  During the Term of this Agreement, with respect to any
          -------------                                                         
Patent Rights, Extended Patent Rights, Inventions or Extended Research
Inventions licensed hereunder:

     (a)  Upon granting an exclusive license to GENENTECH hereunder for a
          Licensed Clone, Lead(s), Extended Research Invention or Extended
          License Patent Right, CURAGEN and GENENTECH shall file requests for
          CFR Rule 1.60 continuation patent applications in order to create
          patent rights relating solely to Licensed Clones, Leads, Extended
          Research Inventions and Extended License Patent Rights which are
          exclusively licensed hereunder and not to other Clones or inventions.
          CURAGEN shall cause such actions to be taken unless the Parties
          reasonably agree that such actions are not feasible or desirable.

     (b)  GENENTECH shall have the right to prepare, file, prosecute, obtain and
          maintain, at its expense, all Patent Rights and Extended License
          Patent Rights relating solely to Licensed Clones or Licensed Products
          relating to Licensed Clones or Leads which are exclusively licensed
          hereunder. Initial patent filings shall be made in the form of a
          regular CFR Rule 1.51 U.S. Priority patent application or a
          provisional application, as determined by the Patent Coordinators. The
          Patent Coordinators for each Party will be designated by such Party
          from time to time. Patent applications will be perfected by making, as
          soon as available, an ATCC deposit of Licensed Clone(s) and making any
          subsequent application filings necessary to perfect U.S. or foreign
          priority patent rights in the countries of Europe that are members of
          the European Patent Organization, Japan, Canada, Mexico and at least
          such other countries as mutually agreed by the Parties. CURAGEN agrees
          to provide reasonable assistance and cooperation to GENENTECH to
          facilitate such filing, prosecution and maintenance including, without
          limitation, the execution of appropriate powers of attorney. GENENTECH
          agrees that any such preparation, filing, prosecution and 

                                      28
<PAGE>
 
          maintenance shall be conducted diligently and in a timely fashion and
          that CURAGEN shall be kept reasonably informed of the progress
          thereof. Upon request GENENTECH will provide copies of the following
          documents to CURAGEN: information regarding inventorship, sequences
          and sequence listings, serial numbers, filing dates, foreign filing
          licenses, copies of patent applications and official correspondence
          with the patent office. CURAGEN shall, whenever practical, be given
          the opportunity to review and comment in advance on any patent filings
          or other correspondence with the patent office during such periods and
          GENENTECH shall use reasonable efforts to incorporate any comments
          provided by CURAGEN. GENENTECH shall, if warranted in its commercially
          reasonable judgment, pursue its priority to claims on Inventions by
          filing all necessary interferences and opposition papers, motions and
          the like. GENENTECH shall conduct any interference proceeding in good
          faith, applying its commercially reasonable efforts to prevail
          therein. CURAGEN shall be given the opportunity to review and comment
          upon any proposed settlement of an interference relating to Patent
          Rights or Extended Patent Rights subject to license hereunder.
          GENENTECH will consider CURAGEN's comments in good faith, but shall
          have the right to enter into a good faith settlement of the
          interference.

     (c)  Except as provided in (b) above, CURAGEN shall have the responsibility
          to prepare, file, prosecute, obtain and maintain patent applications
          and patents on Inventions and Extended Research Inventions licensed
          hereunder, relating to the Licensed Clones and Leads which are
          licensed hereunder at its sole expense.  GENENTECH agrees to provide
          reasonable assistance and cooperation to CURAGEN to facilitate such
          filing, prosecution and maintenance.  CURAGEN agrees that any such
          preparation, filing, prosecution and maintenance shall be conducted as
          outlined in subsection (b) above and shall be conducted with
          reasonable diligence and that GENENTECH shall be kept fully informed
          of the progress thereof and provided with copies of all material
          documents pertaining thereto during the term of this Agreement.
          GENENTECH shall, whenever 

                                      29
<PAGE>
 
          possible, be given the opportunity to review and comment in advance on
          any patent filings or other correspondence with the patent office
          during such periods and CURAGEN shall consider incorporating any
          comments provided by GENENTECH in good faith.

     (d)  The Parties shall mutually agree before permitting any patent
          application or patent within Patent Rights or Extended License Patent
          Rights exclusively licensed hereunder to lapse as well as before
          authorizing any amendment to any patent application or patent within
          such Patent Rights or Extended License Patent Rights that would
          irrevocably limit the lawful scope of the Patent Rights or Extended
          License Patent Rights.

     (e)  Before GENENTECH elects to abandon its right to prepare, file,
          prosecute, obtain and maintain patent applications and patents as
          described in Section 5.1(b), it shall give at least thirty (30) days
          prior written notice thereof to CURAGEN. Such notice shall
          specifically identify the patent application(s) and/or patent(s) for
          which GENENTECH wishes to relinquish such right. Following the receipt
          of such notice, CURAGEN shall have the right to prepare, file,
          prosecute, obtain and maintain the patent application(s) and patent(s)
          identified in the notice, at its sole expense, and any such patents
          and patent applications shall be removed from operation of this
          Agreement. In addition, GENENTECH shall be deemed without any further
          action to have granted to CURAGEN an exclusive, worldwide license
          (including the right to grant sublicenses), under GENENTECH's
          ownership interest in any such patents and applications to develop,
          have developed, make, have made, use, have used, offer for sale, sell,
          have sold, import and have imported any and all products in all fields
          XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
          XXXXXXXXXXXXXXXXX.
 
     (f)  No Party shall have any obligation under this Agreement to pay any
          fees or costs: (i) for bringing a lawsuit or other action to enforce
          any of the Patent Rights or Extended License Patent Rights against an
          actual or suspected infringement or (ii) 


                       Confidential Treatment Requested
                                      30
<PAGE>
 
          for any other Party to obtain for its own benefit independent business
          or legal advice concerning any of the Patent Rights or Extended
          License Patent Rights.

     5.2  NOTICE OF INFRINGEMENT.  If, during the Term of this Agreement or the
          ----------------------                                               
term of any license hereunder, either Party learns of any infringement by a
third party of the patents within Patent Rights or Extended License Patent
Rights exclusively licensed hereunder, such Party shall promptly notify the
other Party and shall provide such other Party with available evidence of such
infringement.

     5.3  INFRINGEMENT.
          ------------ 

     (a)  GENENTECH shall have the first right (but not the obligation), at its
          own expense, to take appropriate action to enforce Patent Rights or
          Extended License Patent Rights licensed exclusively to GENENTECH
          hereunder in the event of any actual or suspected infringement of such
          rights.  GENENTECH may, in its sole judgment, institute suit against
          any such infringer or alleged infringer and control and defend and
          settle such suit in a manner consistent with the terms and provisions
          hereof.  If GENENTECH has not commenced reasonable action to enforce
          such Patent Rights and Extended License Patent Rights, in the case of
          significant infringement, or has ceased to pursue such action within
          one hundred twenty (120) days after written notice from CURAGEN of the
          infringement, which notice includes all of CURAGEN's then available
          supporting evidence and a request by CURAGEN that action should be
          taken against such alleged infringer, CURAGEN shall have the right
          (but not the obligation), at its own expense, to bring suit against
          such infringement.  Any amount recovered, whether by judgment or
          settlement, shall first be applied to reimburse the costs and expenses
          (including attorneys' fees) of the Party bringing suit, and then to
          reimburse the costs and expenses (including attorneys' fees), if any,
          of the other Party and then to reimburse CURAGEN for any royalties
          withheld by GENENTECH as provided in Section 5.3(b) below, which shall
          be paid with interest as specified in Section 3.11.  [XXXXX]

                                      31

                       Confidential Treatment Requested
<PAGE>
 
          [XXXXX]

     (b)  In the event that GENENTECH brings any suit in any country as
          permitted in Section 5.3(a) above with respect to a Material
          Infringement as defined in (c) below, GENENTECH shall be entitled to
          reduce royalties payable to CURAGEN hereunder with respect to Licensed
          Products substantially similar to the product alleged to be infringing
          the Patent Right(s) or Extended License Patent Right(s) which are the
          subject of the suit in such country and for so long as a Material
          Infringement exists, by [XXXXX] of the amounts otherwise due hereunder
          with respect to such Licensed Products in such country.

     (c)  For purposes of this Section 5.3, a Material Infringement shall be
          deemed to exist with respect to a Licensed Product on a country-by-
          country basis when sales by a third party of allegedly infringing
          products in such country reach a level of [XXXXX] or more of the
          combined sales of such allegedly infringing product(s) and sales of
          the Licensed Product in such country.

     5.4  COOPERATION.  Each Party shall execute all papers and perform such
          -----------                                                       
other acts as may be reasonably required to cooperate with the Party bringing
any infringement suit brought in accordance with Section 5.3 above (including
giving legal consent for bringing such suit, and agreeing to be named as a
plaintiff or otherwise joined in such suit), and at its option and expense, may
be represented in such suit by counsel of its choice.

                           6.  TERM AND TERMINATION

     6.1. TERMINATION PROVISIONS.
          ---------------------- 

     The Term of any license hereunder shall be as specified in Section 3.10,
unless terminated as set forth below:

     (a)  Any license hereunder with respect to any Licensed Clone and the
          related Leads, Extended Research Inventions or Extended License Patent
          Rights, may be 

                                      32

                       Confidential Treatment Requested
<PAGE>
 
          terminated by either Party upon any material breach by the other Party
          of any material obligation or condition of such license, effective
          thirty (30) days after giving written notice to the breaching Party of
          such termination in the case of a payment breach and sixty (60) days
          after giving written notice to the breaching Party of such termination
          in the case of any other breach, which notice shall describe such
          breach in reasonable detail; provided, however, that a breach of
          Section 2.4 shall only give rise to the termination rights specified
          therein. The foregoing notwithstanding, if the default or breach is
          cured or shown to be non-existent within the aforesaid thirty (30) or
          sixty (60) day period, the notice shall be deemed automatically
          withdrawn and of no effect.

     (b)  If either Party files for protection under bankruptcy laws, makes an
          assignment for the benefit of creditors, appoints or suffers
          appointment of a receiver or trustee over its property, files a
          petition under any bankruptcy or insolvency act or has any such
          petition filed against it which is not discharged within sixty (60)
          days of the filing thereof, then the other Party may terminate this
          Agreement by notice to such Party.

     (c)  The licenses granted hereunder with respect to certain Licensed Clones
          shall terminate as specified in Section 2.3.4 of the Research
          Agreement without any requirement of further action by CURAGEN
          hereunder.

     6.2  EFFECT OF TERMINATION.
          --------------------- 

     (a)  Upon termination of a license or licenses granted hereunder by CURAGEN
          pursuant to Section 6.1(a), (b) or (c) or under Section 2.4 with
          respect to any Licensed Clone, all relevant rights to such Licensed
          Clone and the related Leads, Extended Research Inventions and Extended
          License Patent Rights included in any such license(s) granted by
          CURAGEN to GENENTECH hereunder under which GENENTECH is in breach
          shall immediately and automatically revert to CURAGEN, subject to
          GENENTECH's right to sell any remaining quantities of Licensed Product
          remaining in its inventories as of the date of termination.  All
          
                                      33

                       Confidential Treatment Requested
<PAGE>
 
          remaining license rights granted to GENENTECH hereunder shall remain
          in full force and effect.  GENENTECH shall promptly transfer to
          CURAGEN such Licensed Clones, Data Sets and CURAGEN Proprietary
          Material in its possession without retaining any copies thereof, as
          well as any full-length sequence data of such Licensed Clone(s).  In
          addition, upon any termination pursuant to Section 6.1(a) or (c) or
          Section 2.4, GENENTECH shall be deemed without any further action to
          have granted to CURAGEN an exclusive, worldwide, license (including
          the right to grant sublicenses), under GENENTECH's ownership interest
          in any Research Project Inventions and Research Project Patent Rights
          covering or related to the relevant Licensed Clone(s) for which
          GENENTECH's license rights have been terminated to develop, have
          developed, make, have made, use, have used, offer for sale, sell, have
          sold, import and have imported any and all products in all fields with
          royalties payable only as set forth in Section 7.7 of the Research
          Agreement.

     (b)  Documentation.  At the request of CURAGEN, GENENTECH shall execute and
          -------------                                                         
          deliver such bills of sale, assignments and licenses and other
          documents as may be necessary to fully vest in CURAGEN all right,
          title and interest to which it is entitled as aforesaid pursuant to
          this Section 6.2.

     (c)  Payment Obligations.  GENENTECH shall have no obligation to make any
          -------------------                                                 
          milestone or royalty payment to CURAGEN that has not accrued prior to
          the effective date of any termination, except for royalties due on
          sales of remaining inventory, but shall remain liable for all
          obligations accruing prior to termination.

     (d)  In the event of a material breach by CURAGEN of any material
          obligation or condition under this Agreement relating to any license
          hereunder with respect to any Licensed Clone, in lieu of terminating
          this Agreement as provided in Section 6.1(a), GENENTECH may, effective
          sixty (60) days after giving written notice to CURAGEN, which notice
          shall describe such breach in reasonable detail, elect to maintain the
          license to the Licensed Clone to which the breach relates with a 
          [XXXXX]

                                      34

                       Confidential Treatment Requested
<PAGE>
 
          [XXXXX] reduction in the royalties otherwise due hereunder with
          respect to Licensed Products relating to such Licensed Clone. The
          foregoing notwithstanding, if the material breach is cured or shown to
          be non-existent within the aforesaid sixty (60) day period, such
          notice and election shall be deemed automatically withdrawn and of no
          effect.

     6.3  OTHER TERMINATION BY GENENTECH.  GENENTECH may terminate this
          -------------------------------                              
Agreement, or any license or licenses granted hereunder with respect to any
Licensed Clone(s), Lead(s) or Extended Research Inventions or Extended License
Patent Rights, and the related rights and obligations hereunder, in its sole
discretion at any time by giving written notice thereof to CURAGEN.  Such
termination shall be effective fifteen (15) days following the date such notice
is received by CURAGEN and shall have all consequences as set forth in Section
6.2 above, but only with respect to such Licensed Clone or Lead, as if this
Agreement had been terminated pursuant to Section 6.1(a).

     6.4  REMEDIES.  If either Party shall fail to perform or observe or
          ---------                                                     
otherwise breaches any of its material obligations under this Agreement, in
addition to any right to terminate this Agreement, the non-defaulting Party may
elect to obtain other relief and remedies available under law.

     6.5  SURVIVING PROVISIONS.  Notwithstanding any provision herein to the
          ---------------------                                             
contrary, the rights and obligations set forth in Sections 3.9, 3.11 and 3.12,
Article 4, Sections 6.2 and 6.4, and Article 7 hereof, as well as any rights and
obligations otherwise accrued, shall survive the expiration or termination of
this Agreement.

                               7.  MISCELLANEOUS

     7.1  CURAGEN REPRESENTATIONS.  CURAGEN represents and warrants that:  (a)
          -----------------------                                             
the execution and delivery of this Agreement and the performance of the
transactions contemplated hereby have been duly authorized by all appropriate
CURAGEN corporate action; (b) CURAGEN is under no obligation which is
inconsistent with this Agreement; and (c) 

                                      35

                       Confidential Treatment Requested
<PAGE>
 
CURAGEN has the full right and legal capacity to grant the rights to GENENTECH
pursuant to Article 2 above without violating the rights of any third party.

     7.2  GENENTECH REPRESENTATIONS.  GENENTECH represents and warrants that:
          -------------------------                                           
(a) the execution and delivery of this Agreement and the performance of the
transactions contemplated hereby have been duly authorized by all appropriate
GENENTECH corporate action; and (b) GENENTECH is under no obligation which is
inconsistent with this Agreement.

     7.3  NO WARRANTIES.
          ------------- 

     (a)  Nothing in this Agreement is or shall be construed as:

          (i)  a warranty or representation by CURAGEN or GENENTECH as to the
               validity or scope of any application or patent within the Patent
               Rights;

          (ii) a warranty or representation that anything made, used, sold or
               otherwise disposed of under any license granted in this Agreement
               is or will be free from infringement of patents, copyrights, and
               other rights of third parties.

     (b)  Except as expressly set forth in this Agreement, NEITHER PARTY MAKES
          ANY REPRESENTATIONS OR EXTENDS ANY WARRANTIES OF ANY KIND, EITHER
          EXPRESS OR IMPLIED.  THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF
          MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE
          DEVELOPMENT, MANUFACTURE, SALE, IMPORTATION OR USE OF THE LICENSED
          PRODUCT(S) WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK, OR
          OTHER RIGHTS, OR ANY OTHER EXPRESS OR IMPLIED WARRANTIES.

     7.4  LIABILITY.  NOTWITHSTANDING ANYTHING ELSE IN THIS AGREEMENT OR
          ---------                                                     
OTHERWISE, NEITHER PARTY WILL BE LIABLE WITH RESPECT TO ANY SUBJECT MATTER OF
THIS AGREEMENT UNDER ANY CONTRACT, NEGLIGENCE, STRICT LIABILITY OR OTHER LEGAL
OR EQUITABLE THEORY FOR (I) ANY 

                                      36
<PAGE>
 
INDIRECT, INCIDENTAL, CONSEQUENTIAL OR PUNITIVE DAMAGES OR LOST PROFITS OR (II)
COST OF PROCUREMENT OF SUBSTITUTE GOODS, TECHNOLOGY OR SERVICES

     7.5  NOTICES.  Any notices, requests, deliveries, approvals or consents
          -------                                                           
required or permitted to be given under this Agreement to GENENTECH or CURAGEN
shall be in writing and shall be personally delivered or sent by telecopy (with
written confirmation to follow via United States first class mail), overnight
courier providing evidence of receipt or certified mail, return receipt
requested, postage prepaid, in each case to the respective address specified
below (or to such address as may be specified in writing to the other Party
hereto):

          CURAGEN:       555 Long Wharf, 11th Floor
                         New Haven, CT 06511
                         Attn: Vice President, Business Development
                         Telecopy: (203) 401-3333

          GENENTECH:     1 DNA Way
                         South San Francisco, CA  94080
                         Attn: Corporate Secretary
                         Telecopy: (650) 952-9881

     Such notices shall be deemed to have been sufficiently given on:  (a) the
date sent if delivered in person or transmitted by telecopy, (b) the next
business day after dispatch in the case of overnight courier or (c) five (5)
business days after deposit in the U.S. mail in the case of certified mail.

     7.6  GOVERNING LAW.  This Agreement will be construed, interpreted and
          -------------                                                    
applied in accordance with the laws of the State of New York (excluding its body
of law controlling conflicts of law).

     7.7  LIMITATIONS.  Except as set forth elsewhere in this Agreement, neither
          -----------                                                           
Party grants to the other Party any right or license to any of its intellectual
property.

     7.8  ENTIRE AGREEMENT.  This is the entire Agreement between the Parties
          ----------------                                                   
with respect to the subject matter herein.  No modification shall be effective
unless in writing and signed by the Parties.

                                      37
<PAGE>
 
     7.9  WAIVER.  The terms or conditions of this Agreement may be waived only
          ------                                                               
by a written instrument executed by the Party waiving compliance.  The failure
of either Party at any time or times to require performance of any provision
hereof shall in no manner affect its rights at a later time to enforce the same.
No waiver by either Party of any condition or term shall be deemed as a
continuing waiver of such condition or term or of another condition or term.

     7.10 HEADINGS.  Section and subsection headings are inserted for
          --------                                                   
convenience of reference only and do not form part of this Agreement.

     7.11 ASSIGNMENT.  This Agreement may not be assigned by either Party
          ----------                                                     
without the consent of the other, except that each Party may, without such
consent, assign this Agreement and the rights, obligations and interests of such
Party, in whole or in part, to any of its wholly-owned subsidiaries, to any
purchaser of all or substantially all of its assets in the line of business to
which this Agreement pertains, or of all of its capital stock, or to any
successor corporation resulting from any merger or consolidation of such Party
with or into such corporation.

     7.12 FORCE MAJEURE.  Neither Party shall be liable for failure of or delay
          -------------                                                        
in performing obligations set forth in this Agreement, and neither shall be
deemed in breach of its obligations, if such failure or delay is due to natural
disasters or any causes beyond the reasonable control of such Party.  In event
of such force majeure, the Party affected thereby shall use reasonable efforts
to cure or overcome the same and resume performance of its obligations
hereunder.

     7.13 CONSTRUCTION.  The Parties hereto acknowledge and agree that:  (i)
          ------------                                                      
each  Party and its counsel reviewed and negotiated the terms and provisions of
this Agreement and have contributed to its revision; (ii) the rule of
construction to the effect that any ambiguities are resolved against the
drafting Party shall not be employed in the interpretation of this Agreement;
and (iii) the terms and provisions of this Agreement shall be construed fairly
as to all Parties hereto and not in a favor of or against any Party, regardless
of which Party was generally responsible for the preparation of this Agreement.

     7.14 SEVERABILITY.  If any provision(s) of this Agreement are or become
          ------------                                                      
invalid, are ruled illegal by any court of competent jurisdiction or are deemed
unenforceable under then 

                                      38
<PAGE>
 
current applicable law from time to time in effect during the Term hereof, it is
the intention of the Parties that the remainder of this Agreement shall not be
affected thereby provided that a Party's rights under this Agreement are not
materially affected. The Parties hereto covenant and agree to renegotiate any
such term, covenant or application thereof in good faith in order to provide a
reasonably acceptable alternative to the term, covenant or condition of this
Agreement or the application thereof that is invalid, illegal or unenforceable,
it being the intent of the Parties that the basic purposes of this Agreement are
to be effectuated.

     7.15 STATUS.  Nothing in this Agreement is intended or shall be deemed to
          ------                                                              
constitute a partner, agency, employer-employee, or joint venture relationship
between the Parties.

     7.16 INDEMNIFICATION.
          ---------------   

     (a)  GENENTECH shall indemnify, defend and hold harmless CURAGEN, its
Affiliates and their respective directors, officers, employees, and agents and
their respective successors, heirs and assigns (the "CURAGEN Indemnitees"),
against any liability, damage, loss or expense (including reasonable attorneys'
fees and expenses of litigation) incurred by or imposed upon the CURAGEN
Indemnitees, or any of them, in connection with any claims, suits, actions,
demands or judgments ("Claims") of third parties for personal injury and product
liability matters (except in cases where such Claims result from a willful
material breach of this Agreement or the gross negligence or willful misconduct
on the part of a CURAGEN Indemnitee) arising out of or relating to any actions
of GENENTECH or any Affiliate, licensee, sublicensee, distributor or agent of
GENENTECH in the development, testing, production, manufacture, promotion,
import, sale or use by any person of any Licensed Product manufactured or sold
by GENENTECH or by an Affiliate, licensee, sublicensee, distributor or agent of
GENENTECH.

     (b)  GENENTECH's obligation to indemnify, defend and hold the CURAGEN
Indemnitees harmless pursuant to Section 9.16(a) are conditioned on the
indemnified Party:  (i) providing written notice to the indemnifying Party of
any Claim arising out of the indemnified activities promptly after the
indemnified Party has knowledge of such Claim, (ii) permitting the indemnifying
Party to assume, at its discretion, sole and full control of the investigation,

                                      39
<PAGE>
 
preparation, defense, trial and settlement in connection with such Claim, (iii)
assisting and cooperating with the indemnifying Party, at the indemnifying
Party's reasonable expense, in the investigation of, preparation for and defense
of any such Claim, and (iv) not compromising, negotiating or settling such Claim
without the indemnifying Party's prior written consent.

     7.17 COUNTERPARTS.
          ------------   

     This Agreement may be executed in any number of counterparts, each of which
counterparts, when so executed and delivered, shall be deemed to be an original,
and all of which counterparts, taken together, shall constitute one and the same
instrument.


     IN WITNESS WHEREOF, the Parties have caused this Agreement to be executed
by their duly authorized representative in two (2) originals.


GENENTECH, INC.                     CURAGEN CORPORATION



By: ______________________________  By: ______________________________

Title: ___________________________  Title: ___________________________

                                      40
<PAGE>
 
                                  SCHEDULE I

                   (To be completed for each Licensed Clone)

LICENSED CLONE:
- ---------------


TYPE OF LICENSE:
- ----------------


PROJECT DATA SET
- ----------------
OR
- --
CURAGEN DATA SET
- ----------------
PERTAINING TO LICENSED CLONE:
- -----------------------------


CURAGEN PROPRIETARY
- -------------------
MATERIAL PERTAINING TO
- ----------------------
LICENSED CLONE:
- ---------------


CURAGEN PATENT RIGHTS
- ---------------------
PERTAINING TO LICENSED CLONE:
- -----------------------------


RIGHTS UNDER
- ------------
EXTENDED LICENSE:
- -----------------


                         Signed this ______ day of __________________, _____

                         CURAGEN CORPORATION

                         By: ______________________________________

                              Name:
                              Title:


                         GENENTECH, INC.

                         By: ______________________________________

                              Name:
                              Title:

                                      41
<PAGE>
 
                                  APPENDIX D
                                  ----------

                              EXISTING DATA SETS


                                   [XXXXX]


                                   [XXXXX]


                                   [XXXXX]


                                   [XXXXX]


                       Confidential Treatment Requested
<PAGE>
 
                                  APPENDIX E
                                  ----------
                                        
                       TERMS OF SUBSCRIPTION AGREEMENTS
                                        

QEA/Gene Calling
- ----------------

Subscriber will receive secure access to CURAGEN's QEA/GeneCalling subscription
database through the GeneScape( data base and software.  Access will be provided
for up to [XXXXX] users on equipment to be provided by Subscriber.

CURAGEN will support and maintain the software provided for such access and will
use commercially reasonable efforts to update and maintain the database and to
keep it reasonably available for use.

Options and Licenses to clones identified using the database shall be provided
on terms substantially similar to those contained in this Agreement and the
License Agreement.

MIM/Path Calling
- ----------------

Subscriber will receive access to the MIM/PathCalling database through the
GeneScape(R) data base and software.  Access will be provided for up to [XXXXX]
users on equipment to be provided by Subscriber.

CURAGEN will support and maintain the software provided for such access and will
use commercially reasonable efforts to update and maintain the database and to
keep it reasonably available for use.

Options and Licenses to clones identified using the database shall be provided
on terms substantially similar to those contained in this Agreement and the
License Agreement.

GeneTools
- ---------

Pursuant to any subscription agreement as described above Subscriber will also
receive secure access to the GeneTools database through the GeneScape(R)
software.  Access will be provided for up to [XXXXX] users on equipment to be
provided by Subscriber.

                       Confidential Treatment Requested
<PAGE>
 
                                  APPENDIX F
                                  ----------
                                        
                           STOCK PURCHASE AGREEMENT
                                        
<PAGE>
 
                              CURAGEN CORPORATION

                                        

                           STOCK PURCHASE AGREEMENT

                        DATED AS OF ____________, 1997

<PAGE>
 
                              CURAGEN CORPORATION

                           STOCK PURCHASE AGREEMENT

     THIS AGREEMENT is dated as of ___________, 1997 by and between CURAGEN
CORPORATION (the "Company"), a Delaware corporation with principal offices at
555 Long Wharf Drive, 11/th/ Floor, New Haven, CT, 06511 and Genentech, Inc.
(the "Purchaser"), a Delaware corporation with principal offices at 1 DNA Way,
South San Francisco, CA 94080.

     WHEREAS the Company wishes to obtain equity financing and the Purchaser is
willing, on the terms and conditions contained in this Agreement,  to purchase
Shares of the Company.

     IN CONSIDERATION of the mutual covenants contained in this Agreement, the
parties agree as follows:

     SECTION 1. Authorization of Sale of the Shares. The Company has authorized
                ------------------------------------
the sale to the Purchaser of that number of shares (the "Shares") of the Common
Stock, $.01 par value per share (the "Common Stock"), of the Company, as is
equal to the quotient obtained by dividing $5,000,000 by the Offering Price (as
defined below).

     SECTION 2. Agreement to Sell and Purchase Shares. At the Closing (as
                --------------------------------------
defined in Section 3), the Company will sell to the Purchaser, and the Purchaser
will buy from the Company, upon the terms and conditions hereinafter set forth,
the Shares, at a purchase price per Share equal to the Offering Price for an
aggregate purchase price of $5,000,000 (the "Purchase Price"). As used herein,
the term "Offering Price" shall mean the price per share of the shares of Common
Stock sold to the public in connection with the closing by the Company of its
initial public offering (the "Public Offering Closing") pursuant to an effective
registration statement under the Securities Act of 1933, as amended (the
"Securities Act").

     SECTION 3. Closings.
                -------- 

          3.1  Delivery of the Shares at the Closing. The completion of the
               --------------------------------------
purchase and sale of the Shares being purchased and sold pursuant to this
Agreement (the "Closing") shall occur at the offices of Mintz, Levin, Cohn,
Ferris, Glovsky and Popeo, P.C., One Financial Center, Boston, Massachusetts
02111 contemporaneously with the Public Offering Closing (the "Closing
<PAGE>
 
Date"), or such other time and place as shall be agreed to by the Company and
the Purchaser. At the Closing, the Purchaser shall pay to the Company an amount
in cash or by wire transfer equal to the Purchase Price and the Company shall
deliver to the Purchaser one or more stock certificates representing the Shares
purchased by the Purchaser, each such certificate to be registered in the name
of the Purchaser. The Company's obligation to close the transaction shall be
subject to the following conditions, any of which may be waived by the Company:
(a) receipt by the Company of a certified or official bank check or checks or
wire transfer of funds in the full amount of the Purchase Price for the Shares
being purchased hereunder; (b) execution and delivery by the Purchaser of the
Registration Rights Agreement substantially in the form attached as Exhibit 1
                                                                    ---------
(the "Registration Rights Agreement"); and (c) the accuracy of the
representations and warranties made by the Purchaser and the fulfillment of
those undertakings of the Purchaser to be fulfilled prior to the Closing. The
Purchaser's obligation to close the transaction shall be subject to the
fulfillment of the following conditions: (a) the occurrence of the Public
Offering Closing, (b) the execution and delivery by the Company of the
Registration Rights Agreement; (c) the receipt by the Purchaser of an opinion of
Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C., counsel to the Company, in
form and substance reasonably satisfactory to the Purchaser; (d) the receipt by
the Purchaser of a certificate, signed by the Secretary of the Company, in the
form attached hereto as Exhibit 2, (e) the receipt by the Purchaser, of a
                        ---------
certificate, dated as of the Closing Date, as to the good standing of the
Company in the state of Delaware, (f) the receipt by the Purchaser of a stock
certificate, representing the Shares, and (g) the accuracy of the
representations and warranties made by the Company herein as of the Closing as
though such representations and warranties had been made on and as of Closing
and the fulfillment of those undertakings of the Company to be fulfilled prior
to Closing, and Purchaser's receipt of a certificate executed by the Senior Vice
President of the Company in the form attached hereto as Exhibit 3 certifying as
                                                        ---------
to the same. This Agreement and the Registration Rights Agreement are
collectively referred to herein as the "Transaction Documents".

          3.2.  Delivery of Preferred Shares at Subsequent Closing. In the event
                ---------------------------------------------------   
that the Public Offering Closing does not occur on or before May 30, 1999, then
the Company may, at its option, sell to the Purchaser, and the Purchaser will
buy from the Company, on or before June 30, 1999 (the "Subsequent Closing
Date"), upon the terms and conditions hereinafter set forth, that number of
Preferred Shares (as defined below) of the Company as is equal to the quotient
obtained

                                       2
<PAGE>
 
by dividing $5,000,000 by the Private Placement Price (as defined below). As
used herein (i) the term "Preferred Shares" shall mean the shares of a new
series of Preferred Stock, $.01 par value per share (the "Preferred Stock"),
having substantially the same rights, preferences and privileges as the
Company's Series A Preferred Stock (other than with respect to (i) the
applicable conversion rate and (ii) those certain adjustments to the applicable
conversion rate set forth in Section 5(c)(ii) of Exhibit A of the Restated
Certificate of Incorporation of the Company dated June 24, 1997) and (ii) the
term "Private Placement Price" shall mean a price per share based upon the price
per share at which the Company sold shares of Preferred Stock in the round of
equity financing immediately preceding the Subsequent Closing Date raising in
excess of $3,000,000 from investors not involved in a collaborative relationship
with the Company. At the Subsequent Closing, the Purchaser shall pay to the
Company an amount in cash or by wire transfer equal to the Private Placement
Price and the Company shall deliver to the Purchaser one or more stock
certificates representing the Preferred Shares purchased by the Purchaser, each
such certificate to be registered in the name of the Purchaser. The Company's
obligation to close the transaction shall be subject to the following
conditions, any of which may be waived by the Company: (a) receipt by the
Company of a certified or official bank check or checks or wire transfer of
funds in the full amount of the Private Placement Price for the Preferred Shares
being purchased hereunder; (b) execution and delivery by the Purchaser of an
amendment to that certain Amended and Restated Registration Rights Agreement
dated as of March 27, 1997, as amended May 16, 1997 (the "Registration Rights
Amendment"); and (c) the accuracy of the representations and warranties made by
the Purchaser as of the Subsequent Closing Date and the fulfillment of those
undertakings of the Purchaser to be fulfilled prior to the Subsequent Closing.
The Purchaser's obligation to close the transaction shall be subject to the
fulfillment of the following conditions: (a) the execution and delivery by the
Company of the Registration Rights Amendment; (b) the receipt by the Purchaser
of an opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C., counsel to
the Company, in form and substance reasonably satisfactory to the Purchaser; (c)
the receipt by the Purchaser of a certificate, signed by the Secretary of the
Company, in the form attached hereto as Exhibit 2; (d) the receipt by the
                                        ---------
Purchaser, of a certificate, dated as of the Subsequent Closing Date, as to the
good standing of the Company in the state of Delaware; (e) the receipt by the
Purchaser of a stock certificate, representing the Preferred Shares; and (f) the
accuracy of the representations and warranties made by the Company herein as of
the Subsequent Closing as though such representations and warranties had been
made on and as of Subsequent Closing and the fulfillment of those undertakings
of the

                                       3
<PAGE>
 
Company to be fulfilled prior to the Subsequent Closing, and Purchaser's receipt
of a certificate executed by the Senior Vice President of the Company in the
form attached hereto as Exhibit 3 certifying as to the same. Except as otherwise
                        ---------
provided herein, any such sale of Preferred Shares shall be upon the same terms
and conditions as those contained herein for the Shares; provided that all
references in this Agreement to the "Closing" and the "Closing Date" shall mean
and refer to the "Subsequent Closing" and the "Subsequent Closing Date"; all
references in this Agreement (other than in Sections 1, 2 and 3) to the "Shares"
shall mean and refer to the "Preferred Shares" and all references to the
"Transaction Documents" in this Agreement shall mean and refer to this Agreement
and the Registration Rights Amendment.

     SECTION 4.  Representations, Warranties and Covenants of the Company. As
                 ---------------------------------------------------------
used herein, "best knowledge" shall mean and include a) actual knowledge of any
officers or directors of the Company and b) that knowledge which a prudent
businessperson would have obtained in the management of his or her business
using due inquiry. The Company hereby represents and warrants to, and covenants
with, the Purchaser as follows:

          4.1.  Organization. The Company is duly organized, validly existing
                -------------
and in good standing under the laws of the State of Delaware. The Company has
full corporate power and authority to own, operate and occupy its properties and
to conduct its business as presently conducted and is registered or qualified to
do business and in good standing in each jurisdiction in which it owns or leases
property or transacts business and where the failure to be so qualified would
have a material adverse effect upon the business, financial condition,
properties or operations of the Company. The Company owns and holds all of the
outstanding capital stock of Genescape, Inc. No other person has any rights to
acquire any interest (equity or otherwise) in Genescape, Inc. As of the date
hereof, Genescape has conducted no business or other activities (other than
activities related to its inception) and holds no assets. Other than Genescape,
Inc., the Company does not own, directly or indirectly, any interest in any
corporation, association, or other entity. The Company is not a participant in
any joint venture, partnership or similar arrangement. The Company has delivered
to the Purchaser an accurate and complete copy of its Certificate of
Incorporation and all Amendments thereto, including without limitation, all
Certificates of Designation filed with the Secretary of State of Delaware.

          4.2.  Due Authorization. The Company has all requisite corporate power
                ------------------
and authority to execute, deliver and perform its obligations under the
Transaction Documents, and the

                                       4
<PAGE>
 
Transaction Documents have been duly authorized and validly executed and
delivered by the Company and constitute legal, valid and binding agreements of
the Company enforceable against the Company in accordance with their terms.

          4.3.  Non-Contravention. The execution and delivery of the Transaction
                ------------------
Documents, the issuance and sale of the Shares to be sold by the Company
hereunder, the fulfillment of the terms of the Transaction Documents and the
consummation of the transactions contemplated by the Transaction Documents will
not conflict with or constitute a violation of, or default or give rise to any
benefits or an acceleration of any rights of any third party (with the passage
of time or otherwise) under, any material agreement or instrument to which the
Company is a party or by which it is bound or the charter, by-laws or other
organizational documents of the Company nor result in the creation or imposition
of any lien, encumbrance, claim, security interest or restriction whatsoever
upon any of the material properties or assets of the Company or an acceleration
of indebtedness pursuant to any obligation, agreement or condition contained in
any material bond, debenture, note or any other evidence of indebtedness or any
material indenture, mortgage, deed of trust or any other agreement or instrument
to which the Company is a party or by which it is bound or to which any of the
property or assets of the Company is subject, nor conflict with, or result in a
violation of, any law, administrative regulation, ordinance or order of any
court or governmental agency, arbitration panel or authority applicable to the
Company. No consent, approval, authorization or other order of, or registration,
qualification or filing with, any regulatory body, administrative agency, or
other governmental body is required for the valid issuance and sale of the
Shares to be sold pursuant to the Agreement, other than such as have been or
will be made or obtained.

          4.4.  Capitalization. As of the date hereof, the Company has the total
                ---------------
authorized capitalization described on Schedule 4.4 attached hereto. The Shares
                                       ------------
to be sold pursuant to this Agreement have been duly authorized, and when issued
and paid for in accordance with the terms of this Agreement will be validly
issued, fully paid and non-assessable and free of restrictions on transfer,
other than restrictions on their transfer under the Transaction Documents and
under applicable state and federal securities laws. The outstanding shares of
capital stock of the Company have been duly and validly issued and are fully
paid and non-assessable. Except as set forth on Schedule 4.4, no options,
                                                ------------
warrants, puts, calls, commitments, convertible exchangeable securities, or
similar rights for issuance of new or additional securities exist with respect
to the Company.

                                       5
<PAGE>
 
Schedule 4.4 contains a true and complete list of each stockholder,
- ------------
warrantholder and optionholder of the Company as of the date hereof.

          4.5  Contracts and Other Commitments. Except as disclosed on Schedule
               --------------------------------                        --------
4.5 the Company does not have any contract, agreement, lease, commitment, or
- ---
proposed transaction, written or oral, absolute or contingent, other than (i)
contracts for the purchase of goods, supplies and services that were entered
into in the ordinary course of business and that do not involve individually
more than $200,000, (ii) sales contracts entered into in the ordinary course of
business, and (iii) contracts terminable at will by the Company on no more than
thirty (30) days' notice without cost or liability to the Company and that do
not involve any employment or consulting arrangement and are not material to the
conduct of the Company's business. For the purpose of this paragraph, employment
and consulting contracts and contracts with labor unions, and license agreements
and any other agreements relating to the acquisition or disposition of the
Company's technology (other than standard end-user license agreements) shall not
be considered to be contracts entered into in the ordinary course of business.

          4.6  Related-Party Transactions. No employee, officer, or director of
               ---------------------------
the Company or member of his or her immediate family is indebted to the Company,
nor is the Company indebted (or committed to make loans or extend or guarantee
credit) to any of them, except that the Company is obligated to pay
approximately $21,000 in interest that accrued on promissory notes issued in
1993 to members of the Rothberg family, which notes were converted into Common
Stock at the end of 1993. To the best of the Company's knowledge, none of such
persons has any direct or indirect ownership interest in any firm or corporation
with which the Company is affiliated or with which the Company has a business
relationship, or any firm or corporation that competes with the Company, except
that employees, officers, or directors of the Company and members of their
immediate families may own stock in publicly traded companies that may compete
with the Company. To the best of the Company's knowledge, no officer or director
or any member of their immediate families is, directly or indirectly, interested
in any material contract with the Company.

          4.7  Registration Rights. Except as provided in the Registration
               --------------------
Rights Agreement dated as of June 25, 1997 by and between the Company and a
certain stockholder, the Amended and Restated Registration Rights Agreement
dated as of March 27, 1997, by and among the Company and certain stockholders of
the Company, as amended, and as provided to Connecticut Innovations,

                                       6
<PAGE>
 
Incorporated and the holders of warrants to purchase 11,111 shares of Common
Stock in separate agreements, the Company is not obligated to register under the
Securities Act any of its presently outstanding securities or any of its
securities that may be subsequently issued.

          4.8  Permits. The Company has all franchises, permits, licenses, and
               --------
any similar authority necessary for the conduct of its business as now being
conducted by it, the lack of which could materially and adversely affect the
business, properties, prospects, or financial condition of the Company and
believes it can obtain, without undue burden or expense, any similar authority
for the conduct of its business as planned to be conducted. The Company is not
in default in any material respect under any of such franchises, permits,
licenses or other similar authority.

          4.9  Compliance With Other Instruments. The Company is not in
               ----------------------------------
violation or default in any material respect of any provision of its Certificate
of Incorporation or Bylaws or in any material respect of any provision of any
mortgage, indenture, agreement, instrument, or contract to which it is a party
or by which it is bound or, to the best of its knowledge, of any federal or
state judgment, order, writ, decree, statute, rule, or regulation applicable to
the Company. The execution, delivery, and performance by the Company of the
Transaction Documents and the consummation of the transactions contemplated
hereby and thereby will not result in any such violation or be in material
conflict with or constitute, with or without the passage of time or giving of
notice, either a material default under any such provision or an event that
results in the creation of any material lien, charge, or encumbrance upon any
assets of the Company or the suspension, revocation, impairment, forfeiture, or
non-renewal of any material permit, license, authorization, or approval
applicable to the Company, its business or operations, or any of its assets or
properties.

          4.10  Litigation. There is no action, suit, proceeding, or
                -----------
investigation, to the best of the Company's knowledge, pending or currently
threatened against the Company that questions the validity of the Transaction
Documents or the right of the Company to enter into such agreements, or to
consummate the transactions contemplated hereby or thereby, or that might
result, either individually or in the aggregate, in any material adverse change
in the assets, business, properties, prospects, or financial condition of the
Company, or in any material change in the current equity ownership of the
Company. The foregoing includes, without limitation, any action, suit,
proceeding, or investigation pending or currently threatened involving the prior
employment of any of the Company's employees, their use in connection with the
Company's business of any information or techniques allegedly proprietary to any
of their former employers, their obligations under any agreements with prior
employers, or negotiations by the Company with potential backers

                                       7
<PAGE>
 
of, or investors in, the Company or its proposed business. The Company is not a
party to, or to the best of its knowledge, named in any order, writ, injunction,
judgment, or decree of any court, government agency, or instrumentality. There
is no action, suit, or proceeding by the Company currently pending or that the
Company currently intends to initiate.

          4.11  Offering. Subject in part to the truth and accuracy of the
                ---------
Purchaser's representations set forth in Section 5.1 of this Agreement, the
offer, sale and issuance of the Shares as contemplated by this Agreement are
exempt from the registration requirements of the Securities Act, and neither the
Company nor any authorized agent acting on its behalf will take any action
hereafter that would cause the loss of such exemption.

          4.12  Title to Property and Assets; Leases. The Company owns no real
                -------------------------------------
estate and leases facilities in Branford, Connecticut, New Haven, Connecticut
and Alachua, Florida. Except (i) as reflected in the Financial Statements (as
defined in paragraph 4.13), (ii) for liens for current taxes not yet delinquent,
(iii) for liens imposed by law and incurred in the ordinary course of business
for obligations not past due to carriers, warehousemen, laborers, materialmen
and the like, (iv) for liens in respect of pledges or deposits under workers'
compensation laws or similar legislation or (v) for minor defects in title, none
of which, individually or in the aggregate, materially interferes with the use
of such property, the Company owns its property and assets free and clear of all
mortgages, liens, claims, and encumbrances. With respect to the property and
assets it leases, the Company is in compliance with such leases and, to the best
of its knowledge, holds a valid leasehold interest free of any liens, claims, or
encumbrances, subject to clauses (i)-(v) above.

          4.13  Financial Statements and Preliminary Financial Statements. The
                ----------------------------------------------------------
Company has delivered to the Purchaser its audited financial statements (balance
sheet and profit and loss statement, statement of stockholders' equity and
statement of cash flows including notes thereto) at December 31, 1994, 1995 and
1996 for the fiscal years then ended and its unaudited financial statements for
the nine-month period ended September 30, 1997 (the "Financial Statements"). The
Financial Statements have been prepared in accordance with generally accepted
accounting principles applied on a consistent basis throughout the periods
indicated and with each other. The Financial Statements fairly present the
financial condition and operating results of the Company as of the dates, and
for the periods, indicated therein. Except as set forth in the Financial
Statements, the Company has no material liabilities, contingent or otherwise,
other than (i) liabilities incurred in the ordinary course of business
subsequent to September 30, 1997 and (ii) obligations under contracts and
commitments incurred in the ordinary course of business and not required under

                                       8
<PAGE>
 
generally accepted accounting principles to be reflected in the Financial
Statements, which, in both cases, individually do not exceed $125,000, and in
the aggregate do not exceed $800,000, other than commitments set forth on
Schedule 4.13 . Except as disclosed in the Financial Statements, the Company is
- -------------
not a guarantor or indemnitor of any indebtedness of any other person, firm, or
corporation. The Company maintains and will continue to maintain a standard
system of accounting established and administered in accordance with generally
accepted accounting principles.

          4.14  Changes. To the best of the Company's knowledge, since September
                --------
30, 1997, there has not been:

     a)  any change in the assets, liabilities, financial condition, business
prospects or operating results of the Company from that reflected in the
Financial Statements, except changes in the ordinary course of business that
have not been, in the aggregate, materially adverse;

     (b) any damage, destruction or loss, whether or not covered by insurance,
materially and adversely affecting the business, properties, prospects, or
financial condition of the Company (as such business is presently conducted and
as it is proposed to be conducted);

     (c) any waiver or compromise by the Company of a valuable right or of a
material debt owed to it;

     (d) any satisfaction or discharge of any lien, claim, or encumbrance or
payment of any obligation by the Company, except in the ordinary course of
business and that is not material to the business, properties, prospects, or
financial condition of the Company (as such business is presently conducted and
as it is proposed to be conducted);

     (e) any material change to a material contract or arrangement by which the
Company or any of its assets is bound or subject;

     (f) any material change in any compensation arrangement or agreement with
any employee, officer, director or stockholder;

     (g) any sale, assignment, or transfer of any patents, trademarks,
copyrights, trade secrets, or other intangible assets;

     (h) any resignation or termination of employment of any key officer of the
Company; and the Company, to the best of its knowledge, does not know of the
impending resignation of termination of employment of any such officer;

     (i) receipt of notice that there has been a loss of, or material order
cancellation by, any major customer of the Company;

                                       9
<PAGE>
 
     (j) any mortgage, pledge, transfer of a security interest in, or lien,
created by the Company, with respect to any of its material properties or
assets, except liens for taxes not yet due or payable;

     (k) any loans or guarantees made by the Company to or for the benefit of
its employees, officers, or directors, or any members of their immediate
families, other than travel advances and other advances made in the ordinary
course of its business;

     (l) any declaration, setting aside, or payment or other distribution in
respect of any of the Company's capital stock, or any direct or indirect
redemption, purchase, or other acquisition of any of such stock by the Company;

     (m) to the best of the Company's knowledge, any other event or condition of
any character that might materially and adversely affect the business,
properties, prospects, or financial condition of the Company (as such business
is presently conducted and as it is proposed to be conducted); or

     (n) any agreement or commitment by the Company to do any of the things
described in this paragraph 4.14.

          4.15  Patents and Trademarks. The Company owns or possesses sufficient
                -----------------------
legal rights to all patents, trademarks, service marks, trade names, copyrights,
trade secrets, licenses, information, and proprietary rights and processes
presently used by the Company in its business (the "CuraGen Intellectual
Property Rights"). To the best knowledge of the Company, the CuraGen
Intellectual Property Rights are the only intellectual property rights necessary
for its business as now conducted and as proposed to be conducted and, to the
best knowledge of the Company, do not conflict with, or infringe the rights of
others. The Company has provided to Purchaser a complete list of patents and
pending patent applications of the Company. Except for agreements with its own
employees or consultants, substantially in the form referenced in paragraph 4.18
below, there are no outstanding options, licenses, or agreements of any kind
relating to the foregoing, nor is the Company bound by or a party to any
options, licenses, or agreements of any kind with respect to the patents,
trademarks, service marks, trade names, copyrights, trade secrets, licenses,
information, and proprietary rights and processes of any other person or entity.
The Company has not received any communications alleging that the Company has
violated or, by conducting its business as proposed, would violate any of the
patents, trademarks, service marks, trade names, copyrights, trade secrets, or
other proprietary rights or processes of any other person or entity. The Company
is not aware that any of its employees is obligated under any contract
(including licenses, covenants, or commitments of any nature) or other
agreement, or subject to any judgment, decree, or order of any court or
administrative agency, that would interfere with the use

                                      10
<PAGE>
 
of such employee's best efforts to promote the interests of the Company or that
would conflict with the Company's business as proposed to be conducted. Neither
the execution nor delivery of this Agreement, nor the carrying on of the
Company's business by the employees of the Company, nor the conduct of the
Company's business as proposed, will, to the best of the Company's knowledge,
conflict with or result in a breach of the terms, conditions, or provisions of,
or constitute a default under, any contract, covenant, or instrument under which
any of such employees is now obligated. The Company does not believe it is or
will be necessary to use any inventions of any of its employees (or persons it
currently intends to hire) made prior to their employment by the Company.

          4.16  Manufacturing and Marketing Rights. The Company has not granted
                -----------------------------------
rights to manufacture, produce, assemble, license, market, or sell its products
to any other person or entity and is not bound by any agreement that affects the
Company's exclusive right to develop, manufacture, assemble, distribute, market,
or sell its products.

          4.17  Employees: Employee Compensation.  To the best of the Company's
                ---------------------------------                              
knowledge, there is no strike, or labor dispute or union organization activities
pending or threatened between it and its employees.  None of the Company's
employees belongs to any union or collective bargaining unit.  To the best of
its knowledge, the Company has complied in all material respects with all
applicable state and federal equal opportunity and other laws related to
employment.  To the best of the Company's knowledge, no employee of the Company
is or will be in violation of any judgment, decree, or order, or any term of any
employment contract, patent disclosure agreement, or other contract or agreement
relating to the relationship of any such employee with the Company, or any other
party because of the nature of the business conducted or to be conducted by the
Company or to the use by the employee of his best efforts with respect to such
business.  The Company is not a party to or bound by any currently effective
employment contract, deferred compensation agreement, bonus plan, incentive
plan, profit sharing plan, retirement agreement, or other employee compensation
agreement.  The Company is not aware that any officer or key employee, or that
any group of key employees, intends to terminate their employment with the
Company, nor does the Company have a present intention to terminate the
employment of any of the foregoing.  Subject to general principles related to
wrongful termination of employees, the employment of each officer and employee
of the Company is terminable at the will of the Company.

                                      11
<PAGE>
 
          4.18  Proprietary Information and Inventions Agreements. Each employee
                --------------------------------------------------
and officer of the Company has executed an Employee Confidential Information and
Invention Agreement substantially in the form or forms which have been delivered
to counsel for the Purchaser. Each scientific consultant of the Company has
executed a confidentiality agreement with the Company.

          4.19  Tax Returns, Payments, and Elections. The Company has filed all
                -------------------------------------
tax returns and reports as required by law. These returns and reports are true
and correct in all material respects. The Company has paid all taxes and other
assessments due, except those contested by it in good faith. The provision for
taxes of the Company as shown in the Financial Statements is adequate for taxes
due or accrued as of the date thereof. The Company has not elected pursuant to
the Internal Revenue Code of 1986, as amended ("Code"), to be treated as an S
corporation or a collapsible corporation pursuant to Section 1362(a) or Section
341(f) of the Code, nor has it made any other elections pursuant to the Code
(other than elections that relate solely to methods of accounting, depreciation,
or amortization) that would have a material effect on the business, properties,
prospects, or financial condition of the Company. The Company has never had any
tax deficiency proposed or assessed against it and has not executed any waiver
of any statute of limitations on the assessments or collection of any tax or
governmental charge. None of the Company's federal income tax returns and none
of its state income or franchise tax or sales or use tax returns has ever been
audited by governmental authorities. Since the date of the Financial Statements,
the Company has made adequate provisions on its books of account for all taxes,
assessments, and governmental charges with respect to its business, properties,
and operations for such period. The Company has withheld or collected from each
payment made to each of its employees, the amount of all taxes, including, but
not limited to, federal income taxes, Federal Insurance Contribution Act taxes
and Federal Unemployment Tax Act taxes required to be withheld or collected
therefrom, and has paid the same to the proper tax receiving officers or
authorized depositories.

          4.20  Insurance. The Company has in full force and effect fire and
                ----------
casualty insurance policies, with extended coverage, sufficient in amount
(subject to reasonable deductibles) to allow it to replace any of its properties
that might be damaged or destroyed. The Company has in full force and effect
term life insurance, payable to the Company, on the lives of each of Jonathan M.
Rothberg and Gregory T.Went in the amount of $1,000,000 each. The Company has in
full

                                      12
<PAGE>
 
force and effect products liability and errors and omissions insurance in
amounts customary for companies similarly situated.

          4.21  Environmental and Safety Laws. To the best of its knowledge, the
                ------------------------------
Company is not in violation of any applicable statute, law, or regulation
relating to the environment or occupational health and safety, and to the best
of its knowledge, no material expenditures are or will be required in order to
comply with any such existing statute, law, or regulation.

          4.22  Investigation. It shall be no defense to an action for breach of
                --------------
this Agreement that the Purchaser or its agents have (or have not) made
investigations into the affairs of the Company or that the Company could not
have known of the misrepresentation or breach of warranty.

          4.23  Disclosure. To the best of the Company's knowledge, neither this
                -----------
Agreement nor any other written statements or certificates made or delivered in
connection herewith contains any untrue statement of a material fact or omits to
state a material fact necessary to make the statements herein or therein not
misleading.

          SECTION 5. Representations, Warranties and Covenants of the Purchaser.
                     -----------------------------------------------------------

          5.1.  The Purchaser represents and warrants to, and covenants with,
the Company, as of the date hereof and as of the Closing Date, that: (i) the
Purchaser is an "accredited investor" as defined in Regulation D under the
United States Securities Act of 1933, as amended (the "Securities Act"); and
also is knowledgeable and experienced in making investments in private placement
transactions such as the purchase of the Shares; (ii) the Purchaser is acquiring
the Shares set forth above for its own account for investment and with no
present intention of distributing any of such Shares except pursuant to an
effective registration statement under the Securities Act covering the sale, and
no arrangement or understanding exists with any other person regarding the
distribution of any of such Shares; (iii) the Purchaser will not, directly or
indirectly, voluntarily offer, sell, pledge, transfer or otherwise dispose of
(or solicit any offers to buy, purchase or otherwise acquire or take a pledge
of) any of the Shares except (a) in the event of an effective registration
statement under the Securities Act, (b) upon delivery of an opinion of counsel
(which shall be in form and substance reasonably satisfactory to the Company)
that such registration is not required, (c) in connection with a sale, transfer
or other disposition made pursuant to Section 144 of the Securities Act or (d)
to a wholly owned subsidiary of the Purchaser, in the case of (a), (c) and (d)
above, no opinion of counsel shall be required; and (iv) the Purchaser has had
an opportunity to
                                      13
<PAGE>
 
ask questions and receive answers from the management of the Company regarding
the Company, its business and the offering of the Shares.

          5.2.  The Purchaser further represents and warrants to, and covenants
with, the Company that (i) the Purchaser has full right, power, authority and
capacity to enter into the Transaction Documents and to consummate the
transactions contemplated hereby and has taken all necessary action to authorize
the execution, delivery and performance of the Transaction Documents, and (ii)
upon the execution and delivery of the Transaction Documents, such Transaction
Documents shall constitute valid and binding obligations of the Purchaser
enforceable in accordance with their terms.

          5.3.  The Purchaser acknowledges and understands that the Purchaser
must bear the economic risk of its investment in the Shares for an indefinite
period of time because the Shares have not been registered under the Securities
Act and, therefore, cannot be sold unless subsequently registered under the
Securities Act or an exemption from such registration is available. The
certificates representing the Shares issued to Purchaser will bear a legend in
substantially the following form:

          THE SECURITIES EVIDENCED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED
          UNDER THE UNITED STATES SECURITIES ACT OF 1933, AS AMENDED (THE
          "SECURITIES ACT"). SUCH SECURITIES MAY NOT BE OFFERED, SOLD,
          TRANSFERRED, PLEDGED, HYPOTHECATED OR OTHERWISE DISPOSED OF, IN THE
          ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT UNDER SAID ACT OR AN
          OPINION OF COUNSEL (WHICH SHALL BE IN FORM AND SUBSTANCE REASONABLY
          SATISFACTORY TO THE COMPANY) REASONABLY SATISFACTORY TO THE COMPANY
          (WHICH MAY BE THE PURCHASER'S IN-HOUSE COUNSEL), THAT SUCH
          REGISTRATION IS NOT REQUIRED, UNLESS SUCH SALE, TRANSFER OR OTHER
          DISPOSITION IS MADE PURSUANT TO RULE 144 OF THE SECURITIES ACT, IN
          WHICH CASE SUCH SALE, TRANSFER OR OTHER DISPOSITION MAY BE MADE AND NO
          OPINION OF COUNSEL SHALL BE REQUIRED, OR EXCEPT AS OTHERWISE PERMITTED
          UNDER A CERTAIN COMMON STOCK PURCHASE AGREEMENT DATED NOVEMBER __ 1997
          BETWEEN THE COMPANY

                                      14
<PAGE>
 
          AND THE ORIGINAL HOLDER, A COPY OF WHICH IS AVAILABLE UPON REQUEST
          FROM THE COMPANY FOR INSPECTION.

The Company agrees to remove such legend from the certificates representing the
Shares issued to Purchaser at such time as such Shares may be legally sold under
Rule 144 (or any successor rule) without registration under the Securities Act,
at the request of the Purchaser and upon receipt from the Purchaser of an
opinion, which shall be in form and substance reasonably satisfactory to the
Company, of counsel reasonably satisfactory to the Company (which may be the
Purchaser's in-house counsel), that such legend may be removed.

     The Purchaser agrees that any sale, transfer, pledge, hypothecation or
other disposition of the Shares shall be made in compliance with such legend.

     SECTION 6.  Survival of Representations, Warranties and Agreements.
                 ------------------------------------------------------- 
Notwithstanding any investigation made by any party to this Agreement, all
covenants, agreements, representations and warranties made by the Company and
the Purchaser herein shall survive the execution of this Agreement, the delivery
to the Purchaser of the Shares being purchased, and the payment therefor.

     SECTION 7.  No Fee.  The parties hereto hereby represent that there are no
                 -------                                                       
brokers or finders entitled to compensation in connection with the transactions
contemplated hereby.

     SECTION 8.  Notices. All notices, requests, consents and other
                 --------
communications hereunder shall be in writing, shall be addressed to the
receiving party's address set forth below or to such other address as a party
may designate by notice hereunder, and shall be either (i) delivered by hand,
(ii) made by telex, telecopy or facsimile transmission, (iii) sent by overnight
courier, or (iv) sent by registered or certified mail, return receipt requested,
postage prepaid:

          (a)  if to the Company, to:                              

               CuraGen Corporation                                 
               555 Long Wharf Drive, 11/th/ Floor                    
               New Haven, CT 06511                                 
               Attention: Vice President of Business Development   
                                                                   
               with a copy to:                                     
                                                                   
               Jeffrey M. Wiesen, Esq.                             
               Mintz, Levin, Cohn, Ferris,                         
               Glovsky and Popeo, P.C.                             
               One Financial Center                                
               Boston, Massachusetts 02110                          

                                      15
<PAGE>
 
          (b)  if to the Purchaser, to:
 
               Genentech, Inc.
               1 DNA Way
               South San Francisco, CA 94080
               Attn: Corporate Secretary


All notices, requests, consents and other communications hereunder shall be
deemed to have been given either (i) if by hand, at the time of the delivery
thereof to the receiving party at the address of such party set forth above,
(ii) if made by telex, telecopy or facsimile transmission, at the time that
receipt thereof has been acknowledged by electronic confirmation or otherwise,
(iii) if sent by overnight courier, on the next business day following the day
such notice is delivered to the courier service, or (iv) if sent by registered
or certified mail, on the 5th business day following the day such mailing is
made.

     SECTION 9.  Changes. Any term of this Agreement may be amended or
                 --------
compliance therewith waived only with the written consent of both parties
hereto.


     SECTION 10.  Assignment. The rights and obligations under this Agreement
                  -----------
may not be assigned by either party hereto without the prior written consent of
the other party.

     SECTION 11.  Benefit. All statements, representations, warranties,
                  --------
covenants and agreements in this Agreement shall be binding on the parties
hereto and shall inure to the benefit of the respective successors and permitted
assigns of each party hereto. Nothing in this Agreement shall be construed to
create any rights or obligations except among the parties hereto, and no person
or entity shall be regarded as a third-party beneficiary of this Agreement.

     SECTION 12.  Expenses. Each of the parties hereto shall pay its own fees
                  ---------
and expenses (including the fees of any attorneys, accountants, appraisers or
others engaged by such party) in connection with this Agreement and the
transactions contemplated hereby whether or not the transactions contemplated
hereby are consummated.

     SECTION 13.  No Waiver; Cumulative Remedies. No failure or delay on the
                  -------------------------------
part of any party to this Agreement in exercising any right, power or remedy
hereunder shall operate as a waiver thereof; nor shall any single or partial
exercise of any such right, power or remedy preclude 

                                      16
<PAGE>
 
any other or further exercise thereof or the exercise of any other right, power
or remedy hereunder. The remedies herein provided are cumulative and not
exclusive of any remedies provided by law.

     SECTION 14.  Headings. The headings of the various sections of this
                  ---------
Agreement have been inserted for convenience of reference only and shall not be
deemed to be part of this Agreement.

     SECTION 15.  Transfer Taxes.  CuraGen will reimburse the Purchaser for any
                  ---------------                                              
transfer taxes incurred in connection with the issuance of the Shares.

     SECTION 16.  Severability. In case any provision contained in this
                  -------------
Agreement should be invalid, illegal or unenforceable in any respect, the
validity, legality and enforceability of the remaining provisions contained
herein shall not in any way be affected or impaired thereby.

     SECTION 17.  Governing Law. This Agreement shall be governed by and
                  --------------
construed in accordance with (a) the internal laws of the State of Delaware
without giving effect to principles of conflicts of law, and (b) United States
federal law.

     SECTION 18.  Counterparts.  This Agreement may be executed in counterparts,
                  -------------                                                 
each of which shall constitute an original, but all of which, when taken
together, shall constitute but one instrument, and shall become effective when
one or more counterparts have been signed by each party hereto and delivered to
the other parties.

     SECTION 19.  Further Assurances. From and after the date of this Agreement,
                  -------------------
upon the request of the Purchaser or the Company, the Company and the Purchaser
shall execute and deliver such instruments, documents and other writings as may
be reasonably necessary or desirable to confirm and carry out and to effectuate
fully the intent and purposes of this Agreement and the Shares.

                                      17
<PAGE>
 
     IN WITNESS WHEREOF, the parties hereto have duly executed this Agreement as
of the __day of ________, 1997.


                                   GENENTECH, INC.                         
                                                                           
                                                                           
                                                                           
                                   By:_____________________________________
                                      Name:                                
                                      Title:                               
                                                                           
                                                                           
                                   CURAGEN CORPORATION                     
                                                                           
                                                                           
                                                                           
                                   By:____________________________________ 
                                      Name:                                
                                      Title:                                

                                      18
<PAGE>
 
                                                                       EXHIBIT 1
                                                                       ---------
                                        
                         REGISTRATION RIGHTS AGREEMENT
                                        
     This Registration Rights Agreement (this "Agreement") is made and entered
into as of ______________, by and among CuraGen Corporation, a Delaware
corporation (the "Company") with principal offices at 555 Long Wharf Drive, 11th
Floor, New Haven, CT 06511 and Genentech, Inc., a Delaware corporation (the
"Stockholder") with principal offices at 1 DNA Way, South San Francisco, CA
94080.

                                    RECITALS
                                        
     WHEREAS, the Company has issued to the Stockholder _____________ shares of
its Common Stock, $.01 par value per share (the "Common Stock"), pursuant to a
Stock Purchase Agreement dated as of even date herewith (the "Purchase
Agreement"); and

     WHEREAS, the Stockholder has agreed to advance to the Company a loan in the
aggregate principal amount of up to $26,000,000 which loan is evidenced by a
Promissory Note, dated ________________, (the "Note") and which may be repaid,
at the Company's option, in shares of Non-Voting Common Stock or which, under
certain circumstances, may be converted to shares of Series F Preferred Stock;
and

     WHEREAS, among the conditions to the consummation of the transactions
contemplated by the Purchase Agreement is the execution and delivery of a
Registration Rights Agreement providing for the registration rights described
herein.

     NOW THEREFORE, in consideration of the foregoing and the mutual promises
herein contained the parties agree as follows:

                                   AGREEMENT
                                        
1.   RESTRICTIONS ON TRANSFERABILITY OF SECURITIES; REGISTRATION RIGHTS

     1.1  CERTAIN DEFINITIONS
          -------------------

     As used in this Agreement, the following terms shall have the meanings set
forth below:

     (a)  "Commission" shall mean the Securities and Exchange Commission or any
other federal agency at the time administering the Securities Act.

     (b)  "Exchange Act" shall mean the Securities Exchange Act of 1934, as
amended, or any similar successor federal statute and the rules and regulations
thereunder, all as the same shall be in effect from time to time.
<PAGE>
 
     (c) "Holder" shall mean the Stockholder and any transferee to whom the
registration rights conferred by this Agreement have been transferred in
compliance with Section 1.2 and Section 1.8 hereof.

     (d) "Non Voting Common Stock" shall the shares of Non-Voting Common Stock
$.01 par value per share, of the Company issued to the Stockholder pursuant to
the terms of the Note.

     (e) "Registrable Securities" shall mean (i) shares of Common Stock, (ii)
shares of Common Stock issued or issuable upon conversion of the Non-Voting
Common Stock or Series F Preferred Stock, and (iii) any shares of Common Stock
issued as a dividend or other distribution with respect to or in exchange for or
in replacement of the shares referenced in (i) or (ii) above; provided however,
that Registrable Securities shall not include any shares of Common Stock (i)
which have previously been registered or which have been sold to the public, or
which have been sold in a private transaction in which the transferor's rights
under this Agreement are not assigned, or (ii) with respect to which the
registration rights under this Agreement have terminated under Section 1.15 of
this Agreement.

     (f) The terms "register," "registered" and "registration" shall refer to a
registration effected by preparing and filing a registration statement in
compliance with the Securities Act and the declaration or ordering of the
effectiveness of such registration statement.

     (g) "Registration Expenses" shall mean all expenses incurred in effecting
any registration pursuant to this Agreement, including, without limitation, all
registration, qualification, and filing fees, printing expenses, escrow fees,
fees and disbursements of counsel for the Company, blue sky fees and expenses,
and expenses of any regular or special audits incident to or required by any
such registration, but shall not include Selling Expenses.

     (h) "Restricted Securities" shall mean any Registrable Securities required
to bear the legends set forth in Section 1.2(b) hereof.

     (i) "Rule 144" shall mean Rule 144 as promulgated by the Commission under
the Securities Act, as such Rule may be amended from time to time, or any
similar successor rule that may be promulgated by the Commission.

     (j) "Rule 145" shall mean Rule 145 as promulgated by the Commission under
the Securities Act as such Rule may be amended from time to time, or any similar
successor rule that may be promulgated by the Commission.

     (k) "Securities Act" shall mean the Securities Act of 1933, as amended, or
any similar successor federal statute and the rules and regulations thereunder,
all as the same shall be in effect from time to time.

     (l) "Selling Expenses" shall mean all underwriting discounts, selling
commissions and stock transfer taxes applicable to the sale of Registrable
Securities and fees 

                                       2
<PAGE>
 
and disbursements of counsel for any Holder (other than the fees and
disbursements of counsel included in Registration Expenses).

     (m) "Series F Preferred Stock" shall mean shares of the Series F Non-Voting
Convertible Preferred Stock, $.01 par value per share, of the Company issued to
the Stockholder pursuant to the terms of the Note.


1.2  RESTRICTIONS ON TRANSFER
     ------------------------
 
     (a) Each Holder agrees not to make any disposition of all or any portion of
the Registrable Securities unless and until (i) there is then in effect a
registration statement under the Securities Act covering such proposed
disposition and such disposition is made in accordance with such registration
statement, (ii) the transferee has agreed in writing for the benefit of the
Company prior to such transfer, and as a condition thereof, delivers to the
Company a written instrument by which such transferee agrees to be bound by this
Section 1.2, provided and to the extent such Section is then applicable, and (A)
such Holder shall have notified the Company of the proposed disposition and
shall have furnished the Company with a detailed statement of the circumstances
surrounding the proposed disposition, and (B) if requested by the Company, such
Holder shall have furnished the Company with an opinion of counsel, reasonably
satisfactory to the Company, that such disposition will not require registration
of such shares under the Securities Act or (iii) the disposition is made
pursuant to Rule 144.  It is agreed that the Company will not require opinions
of counsel for transactions made pursuant to Rule 144.

     Notwithstanding the provisions of 1.2(i), (ii) and (iii) above, no such
registration statement or opinion of counsel shall be necessary for a transfer
by a Holder which is (A) a partnership to its partners or retired partners (who
retire after the date hereof) in accordance with partnership interests, of (B)
to the Holder's family member or trust for the benefit of an individual Holder,
provided such transfer is without consideration and the transferee will be
subject to the terms of this Section 1.2 to the same extent as if he were an
original Holder hereunder.

     (b) Each certificate representing Registrable Securities shall (unless
otherwise permitted by the provisions of this Agreement) be stamped or otherwise
imprinted with legends substantially similar to the following (in addition to
any legend required under applicable state securities laws):

THE SECURITIES EVIDENCED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE
UNITED STATES SECURITIES ACT OF 1933, AS AMENDED (THE "SECURITIES ACT").  SUCH
SECURITIES MAY NOT BE OFFERED, SOLD, TRANSFERRED, PLEDGED, HYPOTHECATED OR
OTHERWISE DISPOSED OF, IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT
UNDER SAID ACT OR AN OPINION OF COUNSEL (WHICH SHALL BE IN FORM AND SUBSTANCE
REASONABLY SATISFACTORY TO THE COMPANY) REASONABLY SATISFACTORY TO THE COMPANY,
THAT SUCH REGISTRATION IS NOT REQUIRED, UNLESS SUCH SALE, 

                                       3
<PAGE>
 
TRANSFER OR OTHER DISPOSITION IS MADE PURSUANT TO RULE 144 OF THE SECURITIES
ACT, IN WHICH CASE NO OPINION OF COUNSEL SHALL BE REQUIRED, OR EXCEPT AS
OTHERWISE PERMITTED UNDER A CERTAIN STOCK PURCHASE AGREEMENT DATED NOVEMBER__,
1997 AMONG THE COMPANY, THE ORIGINAL HOLDER AND OTHERS, A COPY OF WHICH IS
AVAILABLE UPON REQUEST FROM THE COMPANY FOR INSPECTION.

THE SHARES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO THE REGISTRATION
RIGHTS AGREEMENT DATED NOVEMBER__, 1997, AS AMENDED, A COPY OF WHICH IS
AVAILABLE FOR INSPECTION AT THE OFFICES OF THE COMPANY OR MAY BE AVAILABLE UPON
REQUEST.

     (c) The Company shall be obligated to reissue promptly unlegended
Registrable Securities at the request of any Holder thereof if the Holder shall
have obtained an opinion of counsel (which counsel may be counsel to the
Company) reasonably acceptable to the Company to the effect that the Registrable
Securities proposed to be disposed of may lawfully be so disposed of without
registration, qualification or legend.

     (d) Any legend endorsed on any Registrable Securities pursuant to
applicable state securities laws and any stop-transfer instructions with respect
to any Registrable Securities shall be removed upon receipt by the Company of an
order of the appropriate blue sky authority authorizing such removal.

1.3  REGISTRATION ON FORM S-3
     ------------------------

     (a) After the effective date of the Company's initial public offering (the
"Offering Effective Date"), the Company shall use its best efforts to qualify
for registration on Form S-3 or any comparable or successor form or forms.
After the Company has qualified for the use of Form S-3, the Holder of
Registrable Securities shall have the right, at any time on or after the first
anniversary of the Offering Effective Date, to request registrations on Form S-3
(such request shall be in writing and shall state the number of shares of
Registrable Securities to be disposed of and the intended methods of disposition
of such shares by such Holder); provided, however, that the Company shall not be
                                --------  -------                               
obligated to effect any such registration if (i) the Holder, together with the
holders of any other securities of the Company entitled to inclusion in such
registration, propose to sell Registrable Securities and such other securities
(if any) on Form S-3 at an aggregate price to the public of less than $500,000;
(ii) in a given twelve-month period, the Company has effected two (2) such
registrations, (iii) it is to be effected more than ten (10) years after the
Offering Effective Date; or (iv) the Company shall have furnished to such Holder
a certificate signed by the President of the Company stating that in the good
faith judgment of the Board of Directors of the Company, it would be materially
detrimental to the Company for such registration statement to be filed in the
near future and that it has, therefore, determined to defer the filing of such
registration statement, in which case the Company shall have the right to defer
such filing for a period of not more than one hundred eighty (180) days after
receipt of the request of the Holder; provided, that the Company shall not defer
                                      --------                                  
its obligation in this manner more than once in any twelve-month period.

                                       4
<PAGE>
 
     (b) The Company shall not be obligated to effect, or to take any action to
effect, any such registration pursuant to this Section 1.3:

               (i)   In any particular jurisdiction in which the Company would
         be required to execute a general consent to service of process in
         effecting such registration, qualification or compliance, unless the
         Company is already subject to service in such jurisdiction and except
         as may be required by the Securities Act;

               (ii)  After the Company has initiated ten (10) such registrations
         for the Holder pursuant to this Section 1.3 (counting for these
         purposes only registrations which have been declared or ordered
         effective and pursuant to which securities have been sold and
         registrations which have been withdrawn by the Holder as to which the
         Holder have not elected to bear the Registration Expenses pursuant to
         Section 1.5 hereof and would, absent such election, have been required
         to bear such expenses);

               (iii) During the period starting with the date sixty (60) days
         prior to the Company's good faith estimate of the date of filing of and
         ending on a date one hundred eighty (180) days after the effective date
         of, a Company-initiated registration, including a demand registration
         initiated by the Company on behalf of any holder of demand registration
         rights; provided that the Company is actively employing in good faith
         all reasonable efforts to cause such registration statement to become
         effective; or

               (iv)  If the Company shall have effected a registration pursuant
         to Section 1.3(a) within one hundred eighty (180) days preceding the
         Company's receipt of the Holder's request.

     (c) Subject to the foregoing, upon delivery by the Holder of the notice
described in Section 1.3(a) above, the Company shall (i) promptly give written
notice of the proposed registration to all other Holders (if any) and (ii) as
soon as practicable, use its best efforts to effect such registration
(including, without limitation, filing post-effective amendments, appropriate
qualifications under applicable blue sky or other state securities laws and
appropriate compliance with the Securities Act) as would permit or facilitate
the sale and distribution of all or such portion of such Registrable Securities
as are specified in such request, together with all or such portion of the
Registrable Securities of any other Holder joining in such request as are
specified in a written request received by the Company within twenty (20) days
after such written notice from the Company is mailed or delivered.  The
registration statement filed pursuant to the request of the Holder may, subject
to the provisions of Sections 1.3(b) and 1.10 hereof, include other securities
of the Company with respect to which registration rights have been granted, and
may include securities of the Company being sold for the account of the Company.

                                       5
<PAGE>
 
     (d) All Registration Expenses incurred in connection with any registration,
qualification or compliance pursuant to Section 1.3 hereof shall be borne by the
Company.

     (e) If the registration requested pursuant to Section 1.3 is underwritten,
the rights of the Holder to registration pursuant to Section 1.3 shall be
conditioned upon such Holder's participation in such underwriting and the
inclusion of such Holder's Registrable Securities in the underwriting to the
extent provided herein.  The Holder may elect to include in such underwriting
all or a part of its Registrable Securities.  Notwithstanding the foregoing, the
Company shall not be obligated to register the Registrable Securities of any
Holder who fails promptly to provide to the Company such information as the
Company may reasonably request at the time to enable the Company to comply with
applicable laws or regulations or to facilitate preparation of the registration
statement.

     (f) If the Company shall request inclusion in any registration pursuant to
Section 1.3 of securities being sold for its own account, or if other persons
shall request inclusion in any registration pursuant to Section 1.3, the Holder
shall offer to include such securities in the underwriting and may condition
such offer on their acceptance of the further applicable provisions of this
Section 1 (including Section 1.10).  The Company shall (together with the Holder
and other persons proposing to distribute their securities through such
underwriting) enter into an underwriting agreement in customary form with the
representative of the underwriter or underwriters.  Notwithstanding any other
provision of this Section 1.3, if the representative of the underwriters advises
the Holder in writing that marketing factors require a limitation on the number
of shares to be underwritten, the number of shares to be included in the
underwriting or registration shall be allocated as set forth in Section 1.10
hereof.  If a person who has requested inclusion in such registration as
provided above does not agree to the terms of any such underwriting, such person
shall be excluded therefrom by written notice from the Company, the underwriter
or the Holder.  Any Registrable Securities or other securities excluded shall
also be withdrawn from such registration.  If shares are so withdrawn from the
registration and if the number of shares to be included in such registration was
previously reduced as a result of marketing factors pursuant to this Section
1.3(f), then the Company shall offer to all persons who have retained rights to
include securities in the registration the right to include additional
securities in the registration in an aggregate amount equal to the number of
shares so withdrawn, with such shares to be allocated among such persons
requesting additional inclusion in accordance with Section 1.10.

1.4  REGISTRATION PROCEDURES
     -----------------------

     In the case of each registration effected by the Company pursuant to
Section 1.3, the Company will keep each Holder advised in writing as to the
initiation of each registration and as to the completion thereof. At its
expense, the Company will use its best efforts to:

     (a) Keep such registration effective for a period of one hundred eighty
(180) days or until the Holder has completed the distribution described in the
registration statement relating thereto, whichever first occurs; provided,
                                                                 -------- 
however, that such 180-day period shall be extended, if necessary, to keep the
- -------                                                                       
registration statement effective until all such Registrable Securities are 

                                       6
<PAGE>
 
sold, provided that Rule 145, or any successor rule under the Securities Act,
permits an offering on a continuous or delayed basis, and provided further that
applicable rules under the Securities Act governing the obligation to file a
post-effective amendment permit, in lieu of filing a post-effective amendment
that (I) includes any prospectus required by Section 10(a)(3) of the Securities
Act or (II) reflects facts or events representing a material or fundamental
change in the information set forth in the registration statement, the
incorporation by reference of information required to be included in (I) and
(II) above to be contained in periodic reports filed pursuant to Section 13 or
15(d) of the Exchange Act in the registration statement;

     (b) Prepare and file with the Commission such amendments and supplements to
such registration statement and the prospectus used in connection with such
registration statement as may be necessary to comply with the provisions of the
Securities Act with respect to the disposition of all securities covered by such
registration statement;

     (c) Furnish such number of prospectuses and other documents incident
thereto, including any amendment of or supplement to the prospectus, as the
Holder from time to time may reasonably request;

     (d) Notify each seller of Registrable Securities covered by such
registration statement at any time when a prospectus relating thereto is
required to be delivered under the Securities Act of the happening of any event
as a result of which the prospectus included in such registration statement as
then in effect, includes an untrue statement of a material fact or omits to
state a material fact required to be stated therein or necessary to make the
statements therein not misleading or incomplete in the light of the
circumstances then existing, and at the request of any such seller prepare and
furnish to such seller a reasonable number of copies of a supplement to or an
amendment of such prospectus as may be necessary so that as thereafter delivered
to the purchasers of such shares such prospectus shall not include an untrue
statement of a material fact or omit to state a material fact required to be
stated therein or necessary to make the statements therein not misleading or
incomplete in the light of the circumstances then existing;

     (e) Cause all such Registrable Securities registered pursuant hereunder to
be listed on each securities exchange on which similar securities issued by the
Company are then listed;

     (f) Provide a transfer agent and registrar for all Registrable Securities
registered pursuant to such registration statement and a CUSIP number for all
such Registrable Securities, in each case not later than the effective date of
such registration; and

     (g) Otherwise use its best efforts to comply with all applicable rules and
regulations of the Commission, and make available to its security holders, as
soon as reasonably practicable an earnings statement covering the period of at
least twelve months, but not more than eighteen months, beginning with the first
month after the effective date of the Registration Statement, which earnings
statement shall satisfy the provisions of Section 11(a) of the Securities Act.

                                       7
<PAGE>
 
1.5  INDEMNIFICATION
     ---------------

     (a) The Company will indemnify each Holder, each of its officers, directors
and partners, legal counsel and accountants and each person controlling such
Holder within the meaning of Section 15 of the Securities Act, with respect to
which registration, qualification, or compliance has been effected pursuant to
this Section 1, and each underwriter, if any, and each person who controls
within the meaning of Section 15 of the Securities Act any underwriter, against
all expenses, claims, losses, damages, and liabilities (or actions, proceedings,
or settlements in respect thereof) arising out of or based on any untrue
statement (or alleged untrue statement) of a material fact contained in any
prospectus, offering circular, or other document (including any related
registration statement, notification, or the like) incident to any such
registration, qualification, or compliance or based on any omission (or alleged
omission) to state therein a material fact required to be stated therein or
necessary to make the statements therein not misleading, or any violation by the
Company of the Securities Act or any rule or regulation thereunder applicable to
the Company and relating to action or inaction required of the Company in
connection with any such registration, qualification, or compliance, and will
reimburse each such Holder, each of its officers, directors, partners, legal
counsel, and accountants and each person controlling such Holder, each such
underwriter, and each person who controls any such underwriter for any legal and
any other expenses reasonably incurred in connection with investigating and
defending or settling any such claim, loss, damage, liability or action,
provided that the Company will not be liable in any such case to the extent that
any such claim, loss, damage, liability or expense arises out of or is based on
any untrue statement or omission based upon written information furnished to the
Company by such Holder or underwriter specifically for use in the preparation
thereof. It is agreed that the indemnity agreement contained in this Section
1.5(a) shall not apply to amounts paid in settlement of any such loss, claim,
damage, liability or action if such settlement is effected without the consent
of the Company (which consent shall not be unreasonably withheld).

     (b) Each Holder will, if Registrable Securities held by him are included in
the securities as to which such registration, qualification, or compliance is
being effected, indemnify the Company, each of its directors, officers, legal
counsel, and accountants and each underwriter, if any, of the Company's
securities covered by such a registration statement, each person who controls
the Company or such underwriter within the meaning of Section 15 of the
Securities Act, each other such Holder, and each of their officers, directors,
and partners, and each person controlling such Holder, against all expenses,
claims, losses, damages and liabilities (or actions, proceedings, or settlements
in respect thereof) arising out of or based on any untrue statement (or alleged
untrue statement) of a material fact contained in any prospectus, offering
circular, or other document (including any related registration statement,
notification, or the like) incident to any such registration, qualification, or
compliance, or based on any omission (or alleged omission) to state therein a
material fact required to be stated therein or necessary to make the statements
therein not misleading, and will reimburse the Company and such Holder,
directors, officers, partners, legal counsel, and accountants, persons,
underwriters, or control persons for any legal or any other expenses reasonably
incurred in connection with investigating and defending or settling any such
claim, loss, damage, liability, or action, in each case to the extent, but only
to the extent, that such untrue statement (or alleged untrue statement) or
omission (or 

                                       8
<PAGE>
 
alleged omission) is made in such registration statement, prospectus, offering
circular, or other document in reliance upon and in conformity with written
information furnished to the Company by such Holder specifically for use in the
preparation thereof; provided, however, that the obligations of such Holder
hereunder shall not apply to amounts paid in settlement of any such claims,
losses, damages, or liabilities (or actions in respect thereof) if such
settlement is effected without the consent of such Holder (which consent shall
not be unreasonably withheld); and provided that in no event shall any indemnity
under this Section 1.5 exceed the net proceeds from the offering received by
such Holder.

     (c) Each party entitled to indemnification under this Section 1.5 (the
"Indemnified Party") shall give notice to the party required to provide
indemnification (the "Indemnifying Party") promptly after such Indemnified Party
has actual knowledge of any claim as to which indemnity may be sought, and shall
permit the Indemnifying Party to assume the defense of such claim or any
litigation resulting therefrom, provided that counsel for the Indemnifying
Party, who shall conduct the defense of such claim or any litigation resulting
therefrom, shall be approved by the Indemnified Party (whose approval shall not
unreasonably be withheld), and the Indemnified Party may participate in such
defense at such party's expense, and provided further that the failure of any
Indemnified Party to give notice as provided herein shall not relieve the
Indemnifying Party of its obligations under this Section 1.5 to the extent such
failure is not prejudicial. No Indemnifying Party in the defense of any such
claim or litigation shall, except with the consent of each Indemnified Party,
consent to entry of any judgment or enter into any settlement that does not
include as an unconditional term thereof, the giving by the claimant or
plaintiff to such Indemnified Party of a release from all liability in respect
to such claim or litigation and no Indemnified Party shall consent to entry of
any judgment or settle such claim or litigation without the prior written
consent of the Indemnifying Party. Each Indemnified Party shall furnish such
information regarding itself or the claim in question as an Indemnifying Party
may reasonably request in writing and as shall be reasonably required in
connection with defense of such claim and litigation resulting therefrom.

     (d) If the indemnification provided for in this Section 1.5 is held by a
court of competent jurisdiction to be unavailable to an Indemnified Party with
respect to any loss, liability, claim, damage, or expense referred to therein,
then the Indemnifying Party, in lieu to indemnifying such Indemnified Party
hereunder, shall contribute to the amount paid or payable by such Indemnified
Party as a result of such loss, liability, claim, damage, or expense in such
proportion as is appropriate to reflect the relative fault of the Indemnifying
Party on the one hand and of the Indemnified Party on the other in connection
with the statements or omissions that resulted in such loss, liability, claim,
damage, or expense, as well as any other relevant equitable considerations. The
relative fault of the Indemnifying Party and of the Indemnified Party shall be
determined by reference to, among other things, whether the untrue or alleged
untrue statement of a material fact or the omission to state a material fact
relates to information supplied by the Indemnifying Party or by the Indemnified
Party and the parties' relative intent, knowledge, access to information, and
opportunity to correct or prevent such statement or omission.

     (e) Notwithstanding the foregoing, to the extent that the provisions on
indemnification and contribution contained in the underwriting agreement entered
into in 

                                       9
<PAGE>
 
connection with the underwritten public offering are in conflict with the
foregoing provisions, the provisions in the underwriting agreement shall
control.

1.6  INFORMATION BY HOLDER
     ---------------------

     Each Holder of Registrable Securities shall furnish to the Company such
information regarding such Holder and the distribution proposed by such Holder
as the Company may reasonably request in writing and as shall be reasonably
required in connection with any registration, qualification, or compliance
referred to in this Section 1, except to the extent that the furnishing of such
information would violate any law or any contractual arrangement.  The Company
shall not be obligated to register the Registrable Securities of any Holder who
fails promptly to provide to the Company such information as the Company may
reasonably request at the time to enable the Company to comply with applicable
laws or regulations or to facilitate preparation of the registration statement,
including any information that the Holder fails to provide on the basis that
such information would violate any law or any contractual arrangement.


1.7  RULE 144 REPORTING
     ------------------

     With a view to making available the benefits of certain rules and
regulations of the Commission that may permit the sale of the Restricted
Securities to the public without registration, the Company agrees to use its
best efforts to:

     (a) Make and keep public information regarding the Company available as
those terms are understood and defined in Rule 144 under the Securities Act, at
all times from and after ninety (90) days following the effective date of the
first registration under the Securities Act filed by the Company for an offering
of its securities to the general public;

     (b) File with the Commission in a timely manner all reports and other
documents required of the Company under the Securities Act and the Exchange Act
at any time after it has become subject to such reporting requirements;

     (c) So long as a Holder owns any Restricted Securities, furnish to the
Holder forthwith upon written request a written statement by the Company as to
its compliance with the reporting requirements of Rule 144 (at any time from and
after ninety (90) days following the effective date of the first registration
statement filed by the Company for an offering of its securities to the general
public), and of the Securities Act and the Exchange Act (at any time after it
has become subject to such reporting requirements), a copy of the most recent
annual or quarterly report of the Company, and such other reports and documents
so filed as a Holder may reasonably request in availing itself of any rule or
regulation of the Commission allowing a Holder to sell any such securities
without registration.

                                      10
<PAGE>
 
1.8  TRANSFER OR ASSIGNMENT OF REGISTRATION RIGHTS
     ---------------------------------------------

     The rights to cause the Company to register securities granted to a Holder
by the Company under this Section 1 may be transferred or assigned by a Holder
only to a transferee or assignee of not less than 50,000 shares of Registrable
Securities (as presently constituted and subject to subsequent adjustments for
stock splits, stock dividends, reverse stock splits, and the like), provided
that the Company is given written notice at the time of said transfer or
assignment stating the name and address of the transferee or assignee and
identifying the securities with respect to which such registration rights are
being transferred or assigned, and, provided further, that the transferee or
assignee of such rights assumes the obligations of such Holder under this
Section 1 and prior to such transfer, as a condition thereof, delivers to the
Company a written instrument by which such transferee agrees to be bound by this
Agreement.

1.9  "MARKET STAND-OFF" AGREEMENT
     ----------------------------

     If requested by the Company and an underwriter of Common Stock (or other
securities) of the Company, a stockholder shall not sell or otherwise transfer
or dispose of any Common Stock (or other securities) of the Company held by such
stockholder (other than those included in the registration) during the one
hundred eighty (180) day period following the effective date of a registration
statement of the Company filed under the Securities Act, provided that:

     (a) if the stockholder is not an "affiliate" (as defined under Rule 144) of
the Company nor does it hold beneficially or of record 10% or more of the
outstanding equity securities of the Company at the time a registration
statement is filed, then such agreement shall only apply to the first such
registration statement of the Company, including securities to be sold on its
behalf to the public in an underwritten offering; and

     (b) all officers and directors of the Company enter into similar
agreements.

     The obligations described in this Section 1.9 shall not apply to a
registration relating solely to employee benefit plans on Form S-8 or similar
forms that may be promulgated in the future, or a registration relating solely
to a Commission Rule 145 transaction on Form S-4 or similar forms that may be
promulgated in the future. The Company may impose stop-transfer instructions
with respect to the shares (or securities) subject to the foregoing restriction
until the end of said one hundred eighty (180) day period.

1.10 LIMITATIONS ON SUBSEQUENT REGISTRATION RIGHTS.
     --------------------------------------------- 

     From and after the date of this Agreement, the Company shall not, without
the prior written consent of the Holders of a majority of the outstanding
Registrable Securities, enter into any agreement with any holder or prospective
holder of any securities of the Company which would allow such holder or
prospective holder to include such securities in any registration filed under
Section 1.3 hereof, unless under the terms of such agreement, such holder or
prospective holder may include such securities in any such registration only to
the extent that the inclusion of

                                      11
<PAGE>
 
such securities will not reduce the amount of the Registrable Securities of the
Holders which are included.

1.11 ALLOCATION OF REGISTRATION OPPORTUNITIES
     ----------------------------------------

     In any circumstance in which all of the Registrable Securities and other
shares of Common Stock of the Company (including shares of Common Stock issued
or issuable upon conversion of shares of any currently unissued series of
Preferred Stock of the Company) with registration rights (the "Other Shares")
requested to be included in a registration on behalf of the Holder or other
selling stockholders cannot be so included as a result of limitations of the
aggregate number of shares of Registrable Securities and Other Shares that may
be so included, the number of shares of Registrable Securities and Other Shares
that may be so included shall be allocated among the Holders requesting
inclusion of shares pro rata on the basis of the number of shares of Registrable
Securities and that would be held by such Holders, assuming conversion, that
such Holders had requested to be included in the registration.

     No Holder shall have any right to take any action to restrain, enjoin, or
otherwise delay any registration as the result of any controversy that might
arise with respect to the interpretation or implementation of this Section 1.

1.12 TERMINATION OF REGISTRATION RIGHTS
     ----------------------------------

     The right of any Holder to request registration or inclusion in any
registration pursuant to Section 1.3 shall terminate on such date after the
Offering Effective Date as all shares of Registrable Securities held or entitled
to be held upon conversion by such Holder may immediately be sold under Rule 144
during any ninety (90) day period.

2.   MISCELLANEOUS

2.1  GOVERNING LAW
     -------------

     This Agreement shall be governed in all respects by the laws of the State
of Delaware, as if entered into by and between Delaware residents exclusively
for performance entirely within Delaware, and excluding that body of laws
pertaining to conflicts of laws.

2.2  SUCCESSORS AND ASSIGNS
     ----------------------

     Except as otherwise expressly provided herein, the provisions hereof shall
inure to the benefit of and be binding upon the successors, assigns, heirs,
executors and administrators of the parties hereto.

2.3  ENTIRE AGREEMENT; AMENDMENT; WAIVER
     -----------------------------------

     This Agreement (including the Exhibits hereto) constitutes the full and
entire understanding and agreement between the parties with regard to the
subjects hereof and thereof.

                                      12
<PAGE>
 
This Agreement supersedes any and all prior understandings as to the subject
matter of this Agreement.  Neither this Agreement nor any term hereof may be
amended, waived, discharged or terminated, except by a written instrument signed
by the Company and the Holders of at least fifty percent (50%) of the
Registrable Securities.  Any such amendment, waiver, discharge or termination
shall be binding on all the Holders, but in no event shall the obligation of any
Holder hereunder be materially increased, except upon the written consent of
such Holder.

2.4  NOTICES, ETC.
     -------------

     All notices and other communications required or permitted hereunder shall
be in writing and shall be mailed by United States first class mail, postage
prepaid, or delivered personally by hand or nationally recognized courier
addressed (a) if to the Stockholder, at the address set forth on the first page
of this Agreement, or at such other address as such holder or permitted assignee
shall have furnished to the Company in writing, or (b) if to the Company, at 555
Long Wharf Drive, 11th Floor, New Haven CT 06511, or at such other address as
the Company shall have furnished to each holder in writing. All such notices and
other written communications shall be effective on the date of mailing or
delivery.

2.5  DELAYS OR OMISSIONS
     -------------------

     No delay or omission to exercise any right, power or remedy accruing to any
Holder, upon any breach or default of the Company under this Agreement shall
impair any such right, power or remedy of such Holder nor shall it be construed
to be a waiver of any such breach or default, or an acquiescence therein, or of
or in any similar breach or default thereafter occurring; nor shall any waiver
of any single breach or default be deemed a waiver of any other breach or
default therefore or thereafter occurring. Any waiver, permit, consent or
approval of any kind or character on the part of any Holder of any breach or
default under this Agreement or any waiver on the part of any Holder of any
provisions or conditions of this Agreement must be made in writing and shall be
effective only to the extent specifically set forth in such writing. All
remedies, either under this Agreement or by law or otherwise afforded to any
Holder, shall be cumulative and not alternative.

2.6  RIGHTS; SEPARABILITY
     --------------------

     Unless otherwise expressly provided herein, a Holder's rights hereunder are
several rights, not rights jointly held with any of the other Holders. In case
any provision of the Agreement shall be invalid, illegal or unenforceable, the
validity, legality and enforceability of the remaining provisions shall not in
any way be affected or impaired thereby.

2.7  CONFIDENTIAL INFORMATION
     ------------------------

     Each Holder acknowledges that the information received by them pursuant
hereto may be confidential and for its use only, and it will not use such
confidential information in violation of the Exchange Act or reproduce, disclose
or disseminate such information to any other person (other than its employees or
agents having a need to know the contents of such information, and

                                      13
<PAGE>
 
its attorneys), except in connection with the exercise of rights under this
Agreement, unless the Company has made such information available to the public
generally or such Holder is required to disclose such information by a
governmental body.

2.8  TITLES AND SUBTITLES
     --------------------

     The titles of the paragraphs and subparagraphs of this Agreement are for
convenience of reference only and are not to be considered in construing this
Agreement.

2.9  COUNTERPARTS
     ------------

     This Agreement may be executed in any number of counterparts, each of which
shall be an original, but all of which together shall constitute one instrument.


IN WITNESS WHEREOF, the parties hereto have executed this Registration Rights
Agreement effective as of the day and year first above written.

CURAGEN CORPORATION


By _____________________________
   Name:
   Title:


GENENTECH, INC.


By _____________________________
   Name:
   Title:

                                      14

<TABLE> <S> <C>

<PAGE>
 
<ARTICLE> 5
<LEGEND>
THIS SCHEDULE CONTAINS SUMMARY FINANCIAL INFORMATION EXTRACTED FROM THE CURAGEN
CORPORATION DECEMBER 31, 1997 FINANCIAL STATEMENTS AND IS QUALIFIED IN ITS
ENTIRETY BY REFERENCE TO SUCH FINANCIAL STATEMENTS.
</LEGEND>
       
<S>                                               <C>
<PERIOD-TYPE>                                     12-MOS
<FISCAL-YEAR-END>                                      DEC-31-1997
<PERIOD-START>                                         JAN-01-1997
<PERIOD-END>                                           DEC-31-1997
<CASH>                                                  17,417,161
<SECURITIES>                                                     0
<RECEIVABLES>                                              588,314
<ALLOWANCES>                                                     0
<INVENTORY>                                                      0
<CURRENT-ASSETS>                                        19,260,089
<PP&E>                                                   8,656,032
<DEPRECIATION>                                         (1,735,836)
<TOTAL-ASSETS>                                          26,519,029
<CURRENT-LIABILITIES>                                    4,521,417
<BONDS>                                                          0
                                            0
                                              1,459,196
<COMMON>                                                    85,801
<OTHER-SE>                                              12,137,178
<TOTAL-LIABILITY-AND-EQUITY>                            26,519,029
<SALES>                                                          0
<TOTAL-REVENUES>                                         5,896,543
<CGS>                                                            0
<TOTAL-COSTS>                                                    0
<OTHER-EXPENSES>                                         9,742,546
<LOSS-PROVISION>                                                 0
<INTEREST-EXPENSE>                                         684,537
<INCOME-PRETAX>                                        (7,222,010)
<INCOME-TAX>                                                     0
<INCOME-CONTINUING>                                    (7,222,010)
<DISCONTINUED>                                                   0
<EXTRAORDINARY>                                                  0
<CHANGES>                                                        0
<NET-INCOME>                                           (7,222,010)
<EPS-PRIMARY>                                                (.92)
<EPS-DILUTED>                                                (.92)
        

</TABLE>


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