NANOGEN INC
S-8, 1998-04-15
LABORATORY ANALYTICAL INSTRUMENTS
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     As filed with the Securities and Exchange Commission on April 15, 1998.

                                                   Registration No. 333-
- --------------------------------------------------------------------------------

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


                                    FORM S-8

                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933


                                  NANOGEN, INC.
- --------------------------------------------------------------------------------
             (Exact name of registrant as specified in its charter)


             DELAWARE                                   33-0489621
- -----------------------------------       --------------------------------------
  (State or other jurisdiction of          (I.R.S. Employer Identification No.)
  incorporation or organization)

       10398 PACIFIC CENTER COURT
          SAN DIEGO, CALIFORNIA                          92121
- ----------------------------------------           -----------------
(Address of Principal Executive Offices)              (Zip Code)


                          EMPLOYEE STOCK PURCHASE PLAN
- --------------------------------------------------------------------------------
                            (Full title of the plans)


          HOWARD C. BIRNDORF                              Copy to:
Chairman of the Board, Chief Executive
  Officer and Chief Financial Officer               THOMAS E. SPARKS, JR.
             Nanogen, Inc.                      Pillsbury Madison & Sutro LLP
      10398 Pacific Center Court                        P.O. Box 7880
          San Diego, CA 92121                   San Francisco, CA 94120-7880
            (619) 546-7700                             (415) 983-1000
- -------------------------------------------   ----------------------------------
    (Name, address and telephone number,
 including area code, of agent for service)

<TABLE>

                         CALCULATION OF REGISTRATION FEE
<CAPTION>
=========================================================================================================================
                                                     PROPOSED MAXIMUM          PROPOSED MAXIMUM
  TITLE OF SECURITIES TO       AMOUNT TO BE         OFFERING PRICE PER        AGGREGATE OFFERING          AMOUNT OF
      BE REGISTERED             REGISTERED               SHARE(1)                  PRICE(1)           REGISTRATION FEE
- -------------------------------------------------------------------------------------------------------------------------
<S>                           <C>                         <C>                     <C>                       <C> 
Common Stock, par
value $0.001..............    300,000 shares              $11.00                  $3,300,000                $974
=========================================================================================================================

(1)      Estimated solely for the purpose of computing the registration fee.

</TABLE>

                                -----------------

         The Registration Statement shall become effective upon filing in
accordance with Rule 462 under the Securities Act of 1933.

- --------------------------------------------------------------------------------

<PAGE>

                                     PART I

              INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS


ITEM 1.    PLAN INFORMATION.*

ITEM 2.    REGISTRANT INFORMATION AND EMPLOYEE PLAN ANNUAL INFORMATION.*

*          Information required by Part I to be contained in the Section 10(a)
           prospectus is omitted from this Registration Statement in accordance
           with Rule 428 under the Securities Act of 1933 and the Note to Part I
           of Form S-8.


                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.    INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE.

           The following documents filed by Registrant with the Securities and
Exchange Commission are incorporated by reference in this registration
statement:

           (1) Registrant's prospectus dated April 13, 1998 filed pursuant to
Rule 424(b) under the Securities Act of 1933 (in connection with Registrant's
Registration Statement on Form S-1, File No. 333-42791 (the "Form S-1
Registration Statement")), which contains the balance sheets of the Registrant
as of December 31, 1996 and 1997, and the related statements of operations,
stockholders' equity, and cash flows for each of the three years in the period
ended December 31, 1997, together with the report thereon of Ernst & Young LLP,
independent public accountants; and

           (2) The description of Registrant's Common Stock contained in
Registrant's registration statement on Form 8-A, filed April 7, 1998.

           In addition, all documents subsequently filed by Registrant pursuant
to Sections 13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934,
prior to the filing of a post-effective amendment which indicates that all
securities offered have been sold or which deregisters all securities then
remaining unsold, shall be deemed to be incorporated by reference in this
registration statement and to be a part hereof from the date of filing of such
documents.

ITEM 4.    DESCRIPTION OF SECURITIES.

           Not applicable.

ITEM 5.    INTERESTS OF NAMED EXPERTS AND COUNSEL.

           Not applicable.

                                       -2-

<PAGE>

ITEM 6.    INDEMNIFICATION OF DIRECTORS AND OFFICERS.

           Section 145 of the Delaware General Corporation Law provides for the
indemnification of officers, directors, and other corporate agents in terms
sufficiently broad to indemnify such persons under certain circumstances for
liabilities (including reimbursement for expenses incurred) arising under the
Securities Act of 1933, as amended (the "Act"). Article XI of the Registrant's
Restated Certificate of Incorporation (Exhibit 3.(i)3 to the Form S-1
Registration Agreement) and Article VI of the Registrant's Bylaws (Exhibit
3.(ii)2 to the Form S-1 Registration Agreement) provide for indemnification of
the Registrant's directors, officers, employees and other agents to the extent
and under the circumstances permitted by the Delaware General Corporation Law.
The Registrant has also entered into agreements with its directors and officers
that will require the Registrant, among other things, to indemnify them against
certain liabilities that may arise by reason of their status or service as
directors or officers to the fullest extent not prohibited by law (Exhibit 10.7
to the Form S-1 Registration Statement).

           The Underwriting Agreement (Exhibit 1.1 to the Form S-1 Registration
Statement) provides for indemnification by the Underwriters of the Registrant,
its directors and officers, and by the Registrant of the Underwriters, for
certain liabilities, including liabilities arising under the Act, and affords
certain rights of contribution with respect thereto.

ITEM 7.    EXEMPTION FROM REGISTRATION CLAIMED.

           Not applicable.

ITEM 8.    EXHIBITS.

           See Index to Exhibits.

ITEM 9.    UNDERTAKINGS.

           (a)  The undersigned Registrant hereby undertakes:

                    (1) To file, during any period in which offers or sales are
           being made, a post-effective amendment to this registration
           statement:

                             (i) To include any prospectus required by section
                    10(a)(3) of the Securities Act of 1933;

                             (ii) To reflect in the prospectus any facts or
                    events arising after the effective date of the registration
                    statement (or the most recent post-effective amendment
                    thereof) which, individually or in the aggregate, represent
                    a fundamental change in the information set forth in the
                    registration statement;

                             (iii) To include any material information with
                    respect to the plan of distribution not previously disclosed
                    in the registration statement or any material change to such
                    information in the registration statement;

           provided, however, that paragraphs (a)(1)(i) and (a)(1)(ii) do not
           apply if the registration statement is on Form S-3 or Form S-8, and
           the information required to be included in a post-effective amendment
           by those paragraphs is contained in periodic

                                       -3-

<PAGE>

           reports filed by the Registrant pursuant to section 13 or section
           15(d) of the Securities Exchange Act of 1934 that are incorporated by
           reference in the registration statement.

                    (2) That, for the purpose of determining any liability under
           the Securities Act of 1933, each such post-effective amendment 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.

                    (3) To remove from registration by means of a post-effective
           amendment any of the securities being registered which remain unsold
           at the termination of the offering.

           (b) The undersigned Registrant hereby further undertakes that, for
purposes of determining any liability under the Securities Act of 1933, each
filing of the Registrant's annual report pursuant to section 13(a) or section
15(d) of the Securities Exchange Act of 1934 that is incorporated by reference
in the registration statement 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.

           (c) Insofar as indemnification for liabilities arising under the
Securities Act of 1933 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 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 Act and will
be governed by the final adjudication of such issue.

                                       -4-

<PAGE>

                                   SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, the
Registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-8, and has duly caused this
registration statement to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of San Diego, State of California, on April 14,
1998.

                                   NANOGEN, INC.



                                   By            /S/ HOWARD C. BIRNDORF
                                      ------------------------------------------
                                                   Howard C. Birndorf
                                         Chairman of the Board, Chief Executive
                                           Officer and Chief Financial Officer



                                POWER OF ATTORNEY

           KNOW ALL MEN BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Howard C. Birndorf, Tina S. Nova, Ph.D.
and Harry J. Leonhardt, and each of them his true and lawful attorneys-in-fact
and agents, each with full power of substitution and resubstitution, for him and
in his name, place and stead, in any and all capacities, to sign any and all
amendments, including post-effective amendments, to this registration statement,
and to file the same, with exhibits thereto and other documents in connection
therewith, with the Securities and Exchange Commission, granting unto said
attorneys-in-fact and agents, full power and authority to do and perform each
and every act and thing requisite and necessary to be done, as fully to all
intents and purposes as he might or could do in person, hereby ratifying and
confirming all that said attorneys-in-fact and agents, or his substitute or
substitutes, may do or cause to be done by virtue hereof.

           Pursuant to the requirements of the Securities Act of 1933, this
registration statement has been signed by the following persons in the
capacities and on the date indicated:

<TABLE>
<CAPTION>
                        NAME                                             TITLE                              DATE

<S>                                                   <C>                                            <C> 
               /S/ HOWARD C. BIRNDORF                 Chairman of the Board, Chief                   April 14, 1998
- ----------------------------------------------------  Executive Officer and Chief
                 Howard C. Birndorf                   Financial Officer (Principal
                                                      Executive Officer and Principal
                                                      Financial Officer)


                /S/ DANA A. KRZYSTON                  Controller (Principal Accounting               April 14, 1998
- ----------------------------------------------------
                  Dana A. Krzyston                    Officer)

                                       -5-

<PAGE>

                        NAME                                             TITLE                              DATE


               /S/ TINA S. NOVA, PH.D.                President and Chief Operating                  April 14, 1998
- ----------------------------------------------------
                 Tina S. Nova, Ph.D.                  Officer, Director


                 /S/ BROOK H. BYERS                   Director                                       April 14, 1998
- ----------------------------------------------------
                   Brook H. Byers


             /S/ ROBERT E. CURRY, PH.D.               Director                                       April 14, 1998
- ----------------------------------------------------
               Robert E. Curry, Ph.D.


                  /S/ CAM L. GARNER                   Director                                       April 14, 1998
- ----------------------------------------------------
                    Cam L. Garner


                 /S/ DAVID LUDVIGSON                  Director                                       April 9, 1998
                   David Ludvigson


                 /S/ THOMAS G. LYNCH                  Director                                       April 14, 1998
- ----------------------------------------------------
                   Thomas G. Lynch


             /S/ ANDREW E. SENYEI, M.D.               Director                                       April 14, 1998
- ----------------------------------------------------
               Andrew E. Senyei, M.D.

</TABLE>

                                       -6-

<PAGE>

                                INDEX TO EXHIBITS



Exhibit
Number                              Exhibit
- --------   ---------------------------------------------------------------------


  4.1*     Form of Common Stock Certificate.


  5.1      Opinion regarding legality of securities to be offered.


 10.1      Nanogen, Inc. Employee Stock Purchase Plan


 23.1      Consent of Ernst & Young LLP, Independent Auditors.


 23.2      Consent of Pillsbury Madison & Sutro LLP (included in Exhibit 5.1).


 24.1      Power of Attorney (see page 5).


- -------------------

* Incorporated by reference to Exhibit 4.1 to Registrant's Registration
  Statement on Form S-1, No. 333-42791.

                                       -7-

                                                                     EXHIBIT 5.1
                                                                     -----------

                   [PILLSBURY MADISON & SUTRO LLP LETTERHEAD]



                                 April 14, 1998



Nanogen, Inc.
10398 Pacific Center Court
San Diego, CA 92121

         Re:      Registration Statement on Form S-8


Ladies and Gentlemen:

         With reference to the Registration Statement on Form S-8 to be filed by
Nanogen, Inc., a Delaware corporation (the "Company"), with the Securities and
Exchange Commission under the Securities Act of 1933, relating to 300,000 shares
of the Company's Common Stock issuable pursuant to the Employee Stock Purchase
Plan of the Company (the "ESPP"), it is our opinion that such shares of the
Common Stock of the Company, when issued and sold in accordance with the ESPP
will be legally issued, fully paid and nonassessable.

         We hereby consent to the filing of this opinion with the Securities and
Exchange Commission as Exhibit 5.1 to the Registration Statement.

                                        Very truly yours,

                                        /s/ Pillsbury Madison & Sutro LLP



                                                                    EXHIBIT 10.1
                                                                    ------------

                                  NANOGEN, INC.

                          EMPLOYEE STOCK PURCHASE PLAN


SECTION 1.  PURPOSE OF THE PLAN.

         The Plan was adopted by the Company's Board of Directors on November
21, 1997, and amended by the Board of Directors effective as of April 3, 1998,
subject to approval of the Company's stockholders. The Plan effective date is
the effective date of the Company's initial underwritten public offering.

         The purpose of the Plan is to provide Eligible Employees with an
opportunity to increase their proprietary interest in the success of the Company
by purchasing Stock from the Company on favorable terms and to pay for such
purchases through payroll deductions. The Plan is intended to qualify under
section 423 of the Internal Revenue Code of 1986, as amended.

SECTION 2. ADMINISTRATION OF THE PLAN.

         (a) THE COMMITTEE. The Plan shall be administered by the Committee. The
interpretation and construction by the Committee of any provision of the Plan or
of any right to purchase Stock granted under the Plan shall be conclusive and
binding on all persons.

         (b) RULES AND FORMS. The Committee may adopt such rules and forms under
the Plan as it considers appropriate.

SECTION 3.  ENROLLMENT AND PARTICIPATION.

         (a) OFFERING PERIODS. While the Plan is in effect, two overlapping
Offering Periods shall commence in each calendar year. Except for the first
Offering Period, Offering Periods shall consist of the twenty-four (24) month
periods commencing on each January 1 and July 1. The first Offering Period shall
commence on the effective date of the Company's initial public offering and end
on December 31, 1999.

         (b) ACCUMULATION PERIODS. While the Plan is in effect, two Accumulation
Periods shall commence in each calendar year. Except for the first Accumulation
Period, Accumulation Periods shall consist of the six (6) month periods
commencing on each January 1 and July 1. The first Accumulation Period shall
commence on the effective date of the Company's initial public offering and end
on June 30, 1998.

         (c) ENROLLMENT. Any individual who, on the day preceding the first day
of an Offering Period, qualifies as an Eligible Employee may elect to become a
Participant in the

                                       -1-

<PAGE>

Plan for such Offering Period by executing the enrollment form prescribed for
this purpose by the Committee.

         (d) DURATION OF PARTICIPATION. Once enrolled in the Plan, a Participant
shall continue to participate until he or she ceases to be an Eligible Employee,
withdraws from the Plan or reaches the end of the Accumulation Period in which
he or she discontinued contributions. A Participant who discontinued
contributions under Section 4(d) or withdrew from the Plan under Section 5(a)
may again become a Participant, if he or she then is an Eligible Employee, by
following the procedure described in Subsection (c) above.

         (e) APPLICABLE OFFERING PERIOD. For purposes of calculating the
Purchase Price under Section 7(b), the applicable Offering Period shall be
determined as follows:

                  (i) Once a Participant is enrolled in the Plan for an Offering
         Period, such Offering Period shall continue to apply to him or her
         until the earliest of (A) the end of such Offering Period, (B) the end
         of his or her participation under Subsection (d) above or (C)
         re-enrollment in a subsequent Offering Period under Paragraph (ii)
         below.

                  (ii) In the event that the Fair Market Value of Stock on the
         last trading day before the commencement of the Offering Period in
         which the Participant is enrolled is higher than on the last trading
         day before the commencement of any subsequent Offering Period, the
         Participant shall automatically be re-enrolled for such subsequent
         Offering Period.

                  (iii) When a Participant reaches the end of an Offering Period
         but his or her participation is to continue, then such Participant
         shall automatically be re-enrolled for the Offering Period that
         commences immediately after the end of the prior Offering Period.

SECTION 4.  EMPLOYEE CONTRIBUTIONS.

         (a) FREQUENCY OF PAYROLL DEDUCTIONS. A Participant may purchase shares
of Stock under the Plan solely by means of payroll deductions. Payroll
deductions, as designated by the Participant pursuant to Subsection (b) below,
shall occur on each payday during participation in the Plan.

         (b) AMOUNT OF PAYROLL DEDUCTIONS. An Eligible Employee shall designate
on the enrollment form the portion of his or her Compensation that he or she
elects to have withheld for the purchase of Stock. Such portion shall be a whole
percentage of the Eligible Employee's Compensation, but not less than one
percent (1%) nor more than fifteen percent (15%).

         (c) CHANGING WITHHOLDING RATE. If a Participant wishes to change the
rate of payroll withholding, he or she may do so by filing a new enrollment form
with the Company not

                                       -2-

<PAGE>

later than one week prior to the last working day prior to the commencement of
the Accumulation Period for which such change is to be effective.

         (d) DISCONTINUING PAYROLL DEDUCTIONS. If a Participant wishes to
discontinue employee contributions entirely, he or she may do so by filing a new
enrollment form at any time. Payroll withholding shall cease as soon as
reasonably practicable after such form has been received by the Company.

SECTION 5.  WITHDRAWAL FROM THE PLAN.

         (a) WITHDRAWAL. A Participant may elect to withdraw from the Plan by
filing the prescribed form with the Company at any time before the last day of
an Accumulation Period. As soon as reasonably practicable thereafter, payroll
deductions shall cease and the entire amount credited to the Participant's Plan
Account shall be refunded to him or her in cash, without interest. No partial
withdrawals shall be permitted.

         (b) RE-ENROLLMENT AFTER WITHDRAWAL. A former Participant who has
withdrawn from the Plan shall not be a Participant until he or she re-enrolls in
the Plan under Section 3(b).

SECTION 6.  TERMINATION OF EMPLOYMENT OR DEATH.

         (a) TERMINATION OF EMPLOYMENT. Termination of employment as an Eligible
Employee for any reason, including death, shall be treated as an automatic
withdrawal from the Plan under Section 5(a). (A transfer from one Participating
Company to another shall not be treated as a termination of employment.)

         (b) DEATH. In the event of the Participant's death, the amount credited
to his or her Plan Account shall be paid to a beneficiary designated by him or
her for this purpose on the prescribed form or, if none, to the Participant's
estate. Such form shall be valid only if it was filed with the Company before
the Participant's death.

SECTION 7.  PLAN ACCOUNTS AND PURCHASE OF SHARES.

         (a) PLAN ACCOUNTS. The Company shall maintain a Plan Account on its
books in the name of each Participant. Whenever an amount is deducted from the
Participant's Compensation under the Plan, such amount shall be credited to the
Participant's Plan Account. No interest shall be credited to Plan Accounts.

         (b) PURCHASE PRICE. The Purchase Price for each share of Stock
purchased at the close of an Accumulation Period shall be the lower of:

                  (i) Eighty-five percent (85%) of the Fair Market Value of such
         share on the last trading day before the commencement of the applicable
         Offering Period (as determined under Section 3(e)); or

                                       -3-

<PAGE>

                  (ii) Eighty-five percent (85%) of the Fair Market Value of
         such share on the last trading day in such Accumulation Period.

         (c) NUMBER OF SHARES PURCHASED. As of the last day of each Accumulation
Period, each Participant shall be deemed to have elected to purchase the number
of shares of Stock calculated in accordance with this Subsection (c), unless the
Participant has previously elected to withdraw from the Plan in accordance with
Section 5(a). The amount then in the Participant's Plan Account shall be divided
by the Purchase Price, and the number of shares that results shall be purchased
from the Company with the funds in the Participant's Plan Account. The foregoing
notwithstanding, no Participant shall purchase more than a maximum of 2,500
shares of Stock with respect to any Accumulation Period nor shares of Stock in
excess of the amounts set forth in Sections 8 and 12(a). The Committee may
determine with respect to all Participants that any fractional share, as
calculated under this Subsection (c), shall be rounded down to the next lower
whole share.

         (d) AVAILABLE SHARES INSUFFICIENT. In the event that the aggregate
number of shares that all Participants elect to purchase during an Accumulation
Period exceeds the maximum number of shares remaining available for issuance
under Section 12(a), then the number of shares to which each Participant is
entitled shall be determined by multiplying the number of shares available for
issuance by a fraction, the numerator of which is the number of shares that such
Participant has elected to purchase and the denominator of which is the number
of shares that all Participants have elected to purchase.

         (e) ISSUANCE OF STOCK. Certificates representing the shares of Stock
purchased by a Participant under the Plan shall be issued to him or her as soon
as reasonably practicable after the close of the applicable Accumulation Period,
except that the Committee may determine that such shares shall be held for each
Participant's benefit by a broker designated by the Committee (unless the
Participant has elected that certificates be issued to him or her). Shares may
be registered in the name of the Participant or jointly in the name of the
Participant and his or her spouse as joint tenants with right of survivorship or
as community property.

         (f) UNUSED CASH BALANCES. An amount remaining in the Participant's Plan
Account that represents the Purchase Price for any fractional share shall be
carried over in the Participant's Plan Account to the next Accumulation Period.
Any amount remaining in the Participant's Plan Account that represents the
Purchase Price for whole shares that could not be purchased by reason of
Subsection (c) above or Section 12(a) shall be refunded to the Participant in
cash, without interest.

         (g) FAILURE OF SHAREHOLDERS TO APPROVE PLAN. In the event shareholders
of the Company do not approve this Plan, the Participant's Plan Account shall be
repaid to the Participant in cash and no Company shares will be purchased for
the Participant under this Plan.

                                       -4-

<PAGE>

SECTION 8.  LIMITATIONS ON STOCK OWNERSHIP.

         Any other provision of the Plan notwithstanding, no Participant shall
be granted a right to purchase Stock under the Plan if:

         (a) Such Participant, immediately after his or her election to purchase
such Stock, would own stock possessing more than five percent (5%) of the total
combined voting power or value of all classes of stock of the Company or any
parent or Subsidiary of the Company; or

         (b) Under the terms of the Plan, such Participant's rights to purchase
stock under this and all other qualified employee stock purchase plans of the
Company or any parent or Subsidiary of the Company would accrue at a rate that
exceeds $25,000 of the fair market value of such stock (determined at the time
when such right is granted) for each calendar year for which such right or
option is outstanding at any time.

         Ownership of stock shall be determined after applying the attribution
rules of section 424(d) of the Internal Revenue Code of 1986, as amended. For
purposes of this Section 8, each Participant shall be considered to own any
stock that he or she has a right or option to purchase under this or any other
plan, and each Participant shall be considered to have the right to purchase
2,500 shares of Stock under this Plan with respect to each Accumulation Period.

SECTION 9.  RIGHTS NOT TRANSFERABLE.

         The rights of any Participant under the Plan, or any Participant's
interest in any Stock or moneys to which he or she may be entitled under the
Plan, shall not be transferable by voluntary or involuntary assignment or by
operation of law, or in any other manner other than by beneficiary designation
or the laws of descent and distribution. If a Participant in any manner attempts
to transfer, assign or otherwise encumber his or her rights or interest under
the Plan, other than by beneficiary designation or the laws of descent and
distribution, then such act shall be treated as an election by the Participant
to withdraw from the Plan under Section 5(a).

SECTION 10.  NO RIGHTS AS AN EMPLOYEE.

         Nothing in the Plan shall be construed to give any person the right to
remain in the employ of a Participating Company. Each Participating Company
reserves the right to terminate the employment of any person at any time, with
or without cause.

SECTION 11.  NO RIGHTS AS A STOCKHOLDER.

         A Participant shall have no rights as a stockholder with respect to any
shares that he or she has purchased, or may have a right to purchase, under the
Plan until the date of issuance of a stock certificate for such shares.

                                       -5-

<PAGE>

SECTION 12.  STOCK OFFERED UNDER THE PLAN.

         (a) AUTHORIZED SHARES. The aggregate number of shares of Stock
available for purchase under the Plan shall be 300,000 (after giving effect to
the 2-for-3 reverse split of the Company's capital stock) subject to adjustment
pursuant to this Section 12.

         (b) ANTI-DILUTION ADJUSTMENTS. The aggregate number of shares of Stock
offered under the Plan, the 2,500-share limitation described in Section 7(c) and
the price of shares that any Participant has elected to purchase shall be
adjusted proportionately by the Committee for any increase or decrease in the
number of outstanding shares of Stock resulting from a subdivision or
consolidation of shares, the payment of a stock dividend, any other increase or
decrease in such shares effected without receipt or payment of consideration by
the Company or the distribution of the shares of a Subsidiary to the Company's
stockholders.

         (c) REORGANIZATIONS. In the event of a dissolution or liquidation of
the Company, or a merger or consolidation to which the Company is a constituent
corporation, the Plan shall terminate unless the plan of merger, consolidation
or reorganization provides otherwise, and all amounts that have been withheld
but not yet applied to purchase Stock hereunder shall be refunded, without
interest. The Plan shall in no event be construed to restrict in any way the
Company's right to undertake a dissolution, liquidation, merger, consolidation
or other reorganization.

SECTION 13.  AMENDMENT OR DISCONTINUANCE.

         The Board of Directors shall have the right to amend, suspend or
terminate the Plan at any time and without notice. Except as provided in Section
12, any increase in the aggregate number of shares of Stock to be issued under
the Plan shall be subject to approval by a vote of the stockholders of the
Company. In addition, any other amendment of the Plan shall be subject to
approval by a vote of the stockholders of the Company to the extent required by
an applicable law or regulation.

SECTION 14.  DEFINITIONS.

         (a) "ACCUMULATION PERIOD" means a six (6) month period during which
contributions may be made toward the purchase of Stock under the Plan, as
determined pursuant to Section 3(b).

         (b) "BOARD OF DIRECTORS" means the Board of Directors of the Company,
as constituted from time to time.

         (c) "COMMITTEE" means a committee of the Board of Directors, consisting
of one or more directors appointed by the Board of Directors.

         (d)  "COMPANY" means Nanogen, Inc., a Delaware corporation.

                                       -6-

<PAGE>

         (e) "COMPENSATION" means the total compensation paid in cash to a
Participant by a Participating Company, including salaries, wages, overtime pay
and commissions, but excluding bonuses, incentive compensation, moving or
relocation allowances, car allowances, imputed income attributable to cars or
life insurance, taxable fringe benefits and similar items, all as determined by
the Committee.

         (f)  "ELIGIBLE EMPLOYEE" means any employee of a Participating Company:

                  (i) Whose customary employment is for more than five (5)
         months per calendar year and for more than twenty (20) hours per week;
         and

                  (ii) Who has been an employee of a Participating Company for
         not less than one (1) month.

         (g) "FAIR MARKET VALUE" shall mean the market price of Stock,
determined by the Committee as follows:

                  (i) If Stock was traded over-the-counter on the date in
         question but was not traded on the Nasdaq Stock Market or the Nasdaq
         National Market, then the Fair Market Value shall be equal to the mean
         between the last reported representative bid and asked prices quoted
         for such date by the principal automated inter-dealer quotation system
         on which Stock is quoted or, if the Stock is not quoted on any such
         system, by the "Pink Sheets" published by the National Quotation
         Bureau, Inc.;

                  (ii) If Stock was traded over-the-counter on the date in
         question and was traded on the Nasdaq Stock Market or the Nasdaq
         National Market, then the Fair Market Value shall be equal to the
         last-transaction price quoted for such date by the Nasdaq Stock Market
         or the Nasdaq National Market;

                  (iii) If the Stock was traded on a stock exchange on the date
         in question, then the Fair Market Value shall be equal to the closing
         price reported by the applicable composite transactions report for such
         date; and

                  (iv) If none of the foregoing provisions is applicable, then
         the Fair Market Value shall be determined by the Committee in good
         faith on such basis as it deems appropriate.

Whenever possible, the determination of Fair Market Value by the Committee shall
be based on the prices reported in the Western Edition of THE WALL STREET
JOURNAL or as reported directly to the Company by Nasdaq or a comparable
exchange. Such determination shall be conclusive and binding on all persons.

         (h) "OFFERING PERIOD" means a twenty-four (24) month period with
respect to which the right to purchase Stock may be granted under the Plan, as
determined pursuant to Section 3(a).

                                       -7-

<PAGE>

         (i) "PARTICIPANT" means an Eligible Employee who elects to participate
in the Plan, as provided in Section 3(c).

         (j) "PARTICIPATING COMPANY" means the Company and each present or
future Subsidiary, except Subsidiaries excluded by the Committee.

         (k) "PLAN" means this Nanogen, Inc. Employee Stock Purchase Plan, as
amended from time to time.

         (l) "PLAN ACCOUNT" means the account established for each Participant
pursuant to Section 6(a).

         (m) "PURCHASE PRICE" means the price at which Participants may purchase
Stock under the Plan, as determined pursuant to Section 7(b).

         (n)  "STOCK" means the Common Stock of the Company.

         (o) "SUBSIDIARY" means a corporation, fifty percent (50%) or more of
the total combined voting power of all classes of stock of which is owned by the
Company or by another Subsidiary.

SECTION 15.  EXECUTION.

         To record the adoption of the Plan by the Board of Directors, the
Company has caused its duly authorized officer to affix the corporate name and
seal hereto.

                                  NANOGEN, INC.



                                          By /S/ HARRY J. LEONHARDT, ESQ.
                                             -----------------------------------

                                          Its  VICE PRESIDENT, GENERAL COUNSEL
                                              ----------------------------------
                                               AND SECRETARY
                                              ----------------------------------

                                       -8-


                                                                    EXHIBIT 23.1
                                                                    ------------


               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS


We consent to the incorporation by reference in the Registration Statement (Form
S-8) pertaining to the Employee Stock Purchase Plan of Nanogen, Inc. of our
report dated January 16, 1998, except for the last paragraph of Note 4 as to
which the date is January 29, 1998, included in the Registration Statement (Form
S-1 No. 333-42791) for the registration of 300,000 shares of its common stock.



                                          ERNST & YOUNG LLP

                                          /s/ ERNST & YOUNG LLP


San Diego, California
April 8, 1998



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