ILLUMINA INC
S-1/A, EX-2.1, 2000-07-03
LABORATORY ANALYTICAL INSTRUMENTS
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                                                                     Exhibit 2.1

                         AGREEMENT AND PLAN OF MERGER
                               OF ILLUMINA, INC.
                            A DELAWARE CORPORATION
                                      AND
                           A CALIFORNIA CORPORATION



          THIS AGREEMENT AND PLAN OF MERGER dated as of May __, 2000 (the
"Agreement") is between Illumina, Inc., a Delaware corporation ("Illumina
Delaware") and Illumina, Inc., a California corporation ("Illumina California").
Illumina Delaware and Illumina California are sometimes referred to herein as
the "Constituent Corporations."

                                R E C I T A L S
                                ---------------

          A.  Illumina Delaware is a corporation duly organized and existing
under the laws of the State of Delaware and has an authorized capital of
110,000,000 shares, 60,000,000 of which are designated "Common Stock," $0.01 par
value, and 50,000,000 of which are designated "Preferred Stock," $0.01 par
value.  Of such authorized shares of Preferred Stock, 2,500,000 shares are
designated "Series A Preferred Stock," 2,500,000 shares are designated Series A-
1 Preferred Stock ("Series A-1 Preferred"), 12,000,000 shares are designated
Series B Preferred Stock ("Series B Preferred'), 12,000,000 are designed Series
B-1 Preferred Stock ("Series B-1 Preferred"), 7,000,000 shares are designated
Series C Preferred Stock ("Series C Preferred'), and 7,000,000 shares are
designated Series C-1 Preferred Stock ("Series C-1 Preferred"). As of the date
of this Agreement of Merger, 100 shares of Common Stock were issued and
outstanding, all of which were held by Illumina California.  No shares of
Preferred Stock were outstanding.

          B.  llumina California is a corporation duly organized and existing
under the laws of the State of California and has an authorized capital of
110,000,000 shares, 60,000,000 of which are designated "Common Stock," $0.01 par
value, and 50,000,000 of which are designated "Preferred Stock," $0.01 par
value.  Of such authorized shares of Preferred Stock, 2,500,000 shares are
designated "Series A Preferred Stock," 2,500,000 shares are designated Series A-
1 Preferred Stock ("Series A-1 Preferred"), 12,000,000 shares are designated
Series B Preferred Stock ("Series B Preferred'), 12,000,000 are designed Series
B-1 Preferred Stock ("Series B-1 Preferred"), 7,000,000 shares are designated
Series C Preferred Stock ("Series C Preferred'), and 7,000,000 shares are
designated Series C-1 Preferred Stock ("Series C-1 Preferred"). As of the date
of this Agreement and Plan of Merger, 5,139,083 shares of Common Stock,
2,499,998 shares of Series A Preferred Stock, 9,336,299 shares of Series B
Preferred Stock, and 7,000,000 shares of Series C Preferred Stock were issued
and outstanding. No shares of Series A-1 Preferred Stock, Series B-1 Preferred
Stock, or Series C-1 Preferred stock were issued and outstanding.

          C.  The Board of Directors of Illumina California has determined that,
for the purpose of effecting the reincorporation of Illumina California in the
State of Delaware, it is advisable and in
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the best interests of Illumina California that Illumina California merge with
and into Illumina Delaware upon the terms and conditions herein provided.

          D.  The respective Boards of Directors of Illumina Delaware and
Illumina California have approved this Agreement and have directed that this
Agreement be submitted to a vote of their respective shareholders and executed
by the undersigned officers.

          NOW, THEREFORE, in consideration of the mutual agreements and
covenants set forth herein, Illumina Delaware and Illumina California hereby
agree, subject to the terms and conditions hereinafter set forth, as follows:

                                   I. MERGER

          1.1  Merger.  In accordance with the provisions of this Agreement, the
               ------
Delaware General Corporation Law and the California Corporations Code, Illumina
California shall be merged with and into Illumina Delaware (the "Merger"), the
separate existence of Illumina California shall cease and Illumina Delaware
shall be, and is herein sometimes referred to as, the "Surviving Corporation,"
and the name of the Surviving Corporation shall be Illumina, Inc.

          1.2  Filing and Effectiveness.  The Merger shall become effective when
               ------------------------
the following actions shall have been completed:

               (a) This Agreement and Merger shall have been adopted and
approved by the shareholders of each Constituent Corporation in accordance with
the requirements of the Delaware General Corporation Law and the California
Corporations Code;

               (b) All of the conditions precedent to the consummation of the
Merger specified in this Agreement shall have been satisfied or duly waived by
the party entitled to satisfaction thereof; and

               (c) An executed Agreement and Plan of Merger meeting the
requirements of the Delaware General Corporation Law shall have been filed with
the Secretary of State of the State of Delaware.

          The date and time when the Merger shall become effective, as
aforesaid, is herein called the "Effective Date of the Merger."

          1.3  Effect of the Merger.  Upon the Effective Date of the Merger, the
               --------------------
separate existence of Illumina California shall cease and Illumina Delaware, as
the Surviving Corporation, (i) shall continue to possess all of its assets,
rights, powers and property as constituted immediately prior to the Effective
Date of the Merger, (ii) shall be subject to all actions previously taken by its
and Illumina California's Board of Directors, (iii) shall succeed, without other
transfer, to all of the assets, rights, powers and property of Illumina
California in the manner more fully set forth in Section 259 of the Delaware
General Corporation Law, (iv) shall continue to be subject to all of the

                                      -2-
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debts, liabilities and obligations of Illumina Delaware as constituted
immediately prior to the Effective Date of the Merger, and (v) shall succeed,
without other transfer, to all of the debts, liabilities and obligations of
Illumina California in the same manner as if Illumina Delaware had itself
incurred them, all as more fully provided under the applicable provisions of the
Delaware General Corporation Law and the California Corporations Code.

                II.   CHARTER DOCUMENTS, DIRECTORS AND OFFICERS

          2.1  Certificate of Incorporation.  The Certificate of Incorporation
               ----------------------------
of Illumina Delaware as in effect immediately prior to the Effective Date of the
Merger shall continue in full force and effect as the Certificate of
Incorporation of the Surviving Corporation until duly amended in accordance with
the provisions thereof and applicable law.

          2.2  Bylaws.  The Bylaws of Illumina Delaware as in effect immediately
               ------
prior to the Effective Date of the Merger shall continue in full force and
effect as the Bylaws of the Surviving Corporation until duly amended in
accordance with the provisions thereof and applicable law.

          2.3  Directors and Officers.  The directors and officers of Illumina
               ----------------------
California immediately prior to the Effective Date of the Merger shall be the
directors and officers of the Surviving Corporation until their successors shall
have been duly elected and qualified or as otherwise provided by law, the
Certificate of Incorporation of the Surviving Corporation or the Bylaws of the
Surviving Corporation.

                     III.   MANNER OF CONVERSION OF STOCK

          3.1  Illumina California Common Shares.  Upon the Effective Date of
               ---------------------------------
the Merger, each share of Illumina California Common Stock, $0.01 par value,
issued and outstanding immediately prior thereto shall, by virtue of the Merger,
and without any action by the Constituent Corporations, by the holder of such
shares or by any other person, be converted into and exchanged for one fully
paid and nonassessable share of Common Stock, $0.01 par value, of the Surviving
Corporation.  No fractional share interests of Surviving Corporation Common
Stock shall be issued.  In lieu thereof, any fractional share interests to which
a holder would otherwise be entitled shall be aggregated.

          3.2  Illumina California Preferred Shares.
               ------------------------------------

               (a) Upon the Effective Date of the Merger, each share of Series A
Preferred Stock, Series A-1 Preferred Stock, Series B Preferred Stock, Series B-
1 Preferred Stock, Series C Preferred Stock, and Series C-1 Preferred Stock of
Illumina California, $0.01 par value, issued and outstanding immediately prior
to the Merger, which shares are convertible into such number of shares of
Illumina California Common Stock as set forth in the Illumina California
Articles of Incorporation, as amended, shall, by virtue of the Merger, and
without any action by the Constituent Corporations, by the holder of such shares
or by any other person, be converted into or exchanged for one fully paid and
nonassessable share of Series A Preferred Stock, Series A-1 Preferred Stock,
Series B Preferred Stock, Series B-1 Preferred Stock, Series C Preferred Stock,
or Series C-1 Preferred Stock, $0.01 par value, of the Surviving Corporation,
respectively, having such rights,

                                      -3-
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preferences and privileges as set forth in the Certificate of Incorporation of
the Surviving Corporation, which share of Preferred Stock shall be convertible
into the same number of shares of the Surviving Corporation's Common Stock,
$0.01 par value, as such share of Illumina California Preferred Stock was so
convertible into immediately prior to the Effective Date of the Merger, subject
to adjustment pursuant to the terms of the Certificate of Incorporation of the
Surviving Corporation.

          3.3  Illumina California Options, Stock Purchase Rights and
               ------------------------------------------------------
Convertible Securities.
----------------------

               (a) Upon the Effective Date of the Merger, the Surviving
Corporation shall assume the obligations of Illumina California under, and
continue, the option plans (including without limitation Illumina California's
1998 Incentive Stock Plan) and all other employee benefit plans of Illumina
California. Each outstanding and unexercised option, other right to purchase, or
security convertible into Illumina California Common Stock or Illumina
California Preferred Stock (a "Right") shall become, subject to the provisions
in paragraph (c) hereof, an option, right to purchase or a security convertible
into the Surviving Corporation's Common Stock or Preferred Stock, respectively,
on the basis of one share of the Surviving Corporation's Common Stock or
Preferred Stock, as the case may be, for each one share of Illumina California
Common Stock or Preferred Stock, as the case may be, issuable pursuant to any
such Right, on the same terms and conditions and at an exercise price equal to
the exercise price applicable to any such Illumina California Right at the
Effective Date of the Merger. This paragraph 3.3(a) shall not apply to Illumina
California Common Stock or Preferred Stock. Such Common Stock and Preferred
Stock are subject to paragraph 3.1 and 3.2, respectively, hereof.

               (b) A number of shares of the Surviving Corporation's Common
Stock and Preferred Stock shall be reserved for issuance upon the exercise of
options, stock purchase rights and convertible securities equal to the number of
shares of Illumina California Common Stock and Illumina California Preferred
Stock so reserved immediately prior to the Effective Date of the Merger.

               (c) The assumed Rights shall not entitle any holder thereof to a
fractional share upon exercise or conversion (unless the holder was entitled to
a fractional interest immediately prior to the Merger).  In lieu thereof, any
fractional share interests to which a holder of an assumed Right (other than an
option issued pursuant to Illumina California's 1998 Incentive Stock Plan) would
otherwise be entitled upon exercise or conversion shall be aggregated (but only
with other similar Rights which have the same per share terms).  To the extent
that after such aggregation, the holder would still be entitled to a fractional
share with respect thereto upon exercise or conversion, the holder shall be
entitled upon the exercise or conversion of all such assumed Rights pursuant to
their terms (as modified herein), to one full share of Common Stock or Preferred
Stock in lieu of such fractional share.  With respect to each class of such
similar Rights, no holder will be entitled to more than one full share in lieu
of a fractional share upon exercise or conversion.

          Notwithstanding the foregoing, with respect to options issued under
the Illumina California 1998 Incentive Stock Plan that are assumed in the
Merger, the number of shares of Common Stock

                                      -4-
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to which the holder would be otherwise entitled upon exercise of each such
assumed option following the Merger shall be rounded down to the nearest whole
number and the exercise price shall be rounded up to the nearest whole cent. In
addition, no "additional benefits" (within the meaning of Section 424(a)(2) of
the Internal Revenue Code of 1986, as amended) shall be accorded to the
optionees pursuant to the assumption of their options.

          3.4  Illumina Delaware Common Stock.  Upon the Effective Date of the
               ------------------------------
Merger, each share of Common Stock, $0.01 par value, of Illumina Delaware issued
and outstanding immediately prior thereto shall, by virtue of the Merger, and
without any action by Illumina Delaware, the holder of such shares or any other
person, be canceled and returned to the status of authorized but unissued
shares.

          3.5  Exchange of Certificates.  After the Effective Date of the
               ------------------------
Merger, each holder of an outstanding certificate representing shares of
Illumina California Common Stock or Preferred Stock may be asked to surrender
the same for cancellation to an exchange agent, whose name will be delivered to
holders prior to any requested exchange (the "Exchange Agent"), and each such
holder shall be entitled to receive in exchange therefor a certificate or
certificates representing the number of shares of the Surviving Corporation's
Common Stock or Preferred Stock, as the case may be, into which the surrendered
shares were converted as herein provided.  Until so surrendered, each
outstanding certificate theretofore representing shares of Illumina California
Common Stock or Preferred Stock shall be deemed for all purposes to represent
the number of shares of the Surviving Corporation's Common Stock or Preferred
Stock, respectively, into which such shares of Illumina California Common Stock
or Preferred Stock, as the case may be, were converted in the Merger.

          The registered owner on the books and records of the Surviving
Corporation or the Exchange Agent of any such outstanding certificate shall,
until such certificate shall have been surrendered for transfer or conversion or
otherwise accounted for to the Surviving Corporation or the Exchange Agent, have
and be entitled to exercise any voting and other rights with respect to and to
receive dividends and other distributions upon the shares of Common Stock or
Preferred Stock of the Surviving Corporation represented by such outstanding
certificate as provided above.

          Each certificate representing Common Stock or Preferred Stock of the
Surviving Corporation so issued in the Merger shall bear the same legends, if
any, with respect to the restrictions on transferability as the certificates of
Illumina California so converted and given in exchange therefore, unless
otherwise determined by the Board of Directors of the Surviving Corporation in
compliance with applicable laws.

          If any certificate for shares of the Surviving Corporation's stock is
to be issued in a name other than that in which the certificate surrendered in
exchange therefor is registered, it shall be a condition of issuance thereof
that the certificate so surrendered shall be properly endorsed and otherwise in
proper form for transfer, that such transfer otherwise be proper and comply with
applicable securities laws and that the person requesting such transfer pay to
the Exchange Agent any transfer or other taxes payable by reason of issuance of
such new certificate in a name other than

                                      -5-
<PAGE>

that of the registered holder of the certificate surrendered or establish to the
satisfaction of the Surviving Corporation that such tax has been paid or is not
payable.

                                IV.    GENERAL

          4.1  Covenants of Illumina Delaware. Illumina Delaware covenants and
               ------------------------------
agrees that it will, on or before the Effective Date of the Merger:

               (a) Qualify to do business as a foreign corporation in the State
of California and, in connection therewith, irrevocably appoint an agent for
service of process as required under the provisions of Section 2105 of the
California Corporations Code.

               (b) File any and all documents with the California Franchise Tax
Board necessary for the assumption by Illumina Delaware of all of the franchise
tax liabilities of Illumina California.

               (c) Take such other actions as may be required by the California
Corporations Code.

          4.2  Further Assurances.  From time to time, as and when required by
               ------------------
Illumina Delaware or by its successors or assigns, there shall be executed and
delivered on behalf of Illumina California such deeds and other instruments, and
there shall be taken or caused to be taken by it such further and other actions
as shall be appropriate or necessary in order to vest or perfect in or conform
of record or otherwise by Illumina Delaware the title to and possession of all
the property, interests, assets, rights, privileges, immunities, powers,
franchises and authority of Illumina California and otherwise to carry out the
purposes of this Agreement, and the officers and directors of Illumina Delaware
are fully authorized in the name and on behalf of Illumina California or
otherwise to take any and all such action and to execute and deliver any and all
such deeds and other instruments.

          4.3  Abandonment.  At any time before the Effective Date of the
               -----------
Merger, this Agreement may be terminated and the Merger may be abandoned for any
reason whatsoever by the Board of Directors of either Illumina California or of
Illumina Delaware, or of both, notwithstanding the approval of this Agreement by
the shareholders of Illumina California or by the sole stockholder of Illumina
Delaware, or by both.

          4.4  Amendment.  The Boards of Directors of the Constituent
               ---------
Corporations may amend this Agreement at any time prior to the filing of this
Agreement (or certificate in lieu thereof) with the Secretary of State of the
State of Delaware, provided that an amendment made subsequent to the adoption of
this Agreement by the stockholders of either Constituent Corporation shall not:
(a) alter or change the amount or kind of shares, securities, cash, property
and/or rights to be received in exchange for or on conversion of all or any of
the shares of any class or series thereof of such Constituent Corporation, (b)
alter or change any term of the Certificate of Incorporation of the Surviving
Corporation to be effected by the Merger, or (c) alter or change any of the
terms and conditions of this Agreement if such alteration or change would
adversely affect the holders of any class or series of capital stock of either
Constituent Corporation.

                                      -6-
<PAGE>

          4.5  Registered Office.  The registered office of the Surviving
               -----------------
Corporation in the State of Delaware is 1209 Orange Street, Wilmington, County
of New Castle, Delaware 19801 and The Corporation Trust Company is the
registered agent of the Surviving Corporation at such address.

          4.6  Agreement.  Executed copies of this Agreement will be on file at
               ---------
the principal place of business of the Surviving Corporation at 9390 Towne
Centre Drive, Suite 200, San Diego, CA 92121, and copies thereof will be
furnished to any shareholder of either Constituent Corporation, upon request and
without cost.

          4.7  Governing Law.  This Agreement shall in all respects be
               -------------
construed, interpreted and enforced in accordance with and governed by the laws
of the State of Delaware and, so far as applicable, the merger provisions of the
California Corporations Code.

          4.8  FIRPTA Notification.  (a) On the Effective Date of the Merger,
               -------------------
Illumina California shall deliver to Illumina Delaware, as agent for the
shareholders of Illumina California, a properly executed statement (the
"Statement") substantially in the form attached hereto as Exhibit A.  Illumina
Delaware shall retain the Statement for a period of not less than seven years
and shall, upon request, provide a copy thereof to any person that was a
shareholder of Illumina California immediately prior to the Merger.  In
consequence of the approval of the Merger by the shareholders of Illumina
California, (i) such shareholders shall be considered to have requested that the
Statement be delivered to Illumina Delaware as their agent and (ii) Illumina
Delaware shall be considered to have received a copy of the Statement at the
request of the Illumina California shareholders for purposes of satisfying
Illumina Delaware's obligations under Treasury Regulation Section 1.1445-
2(c)(3).

               (b) Illumina California shall deliver to the Internal Revenue
Service a notice regarding the Statement in accordance with the requirements of
Treasury Regulation Section 1.897-2(h)(2).

                                      -7-
<PAGE>

          IN WITNESS WHEREOF, this Agreement having first been approved by the
Boards of Directors of Illumina Delaware and Illumina California is hereby
executed on behalf of each of such two corporations and attested by their
respective officers thereunto duly authorized.

                                       ILLUMINA, INC.
                                       a Delaware corporation


                                       By: ___________________________________
                                           Jay T. Flatley, President and Chief
                                           Executive Officer

ATTEST:


__________________________
Michael J. O'Donnell
Secretary

                                       ILLUMINA, INC.
                                       a California corporation


                                       By:___________________________________
                                          Jay T. Flatley, President and Chief
                                          Executive Officer

ATTEST:


__________________________
Michael J. O'Donnell
Secretary




ILLUMINA, INC.
AGREEMENT & PLAN OF MERGER
<PAGE>

                                   Exhibit A
                                   ---------

                                                                   May ___, 2000
TO THE SHAREHOLDERS OF ILLUMINA, INC.:

     In connection with the reincorporation (the "Reincorporation") in Delaware
of Illumina, Inc., a California corporation (the "Company"), pursuant to the
Agreement and Plan of Merger (the "Agreement") dated as of May __, 2000 between
the Company and Illumina, Inc., a Delaware corporation and wholly-owned
subsidiary of the Company ("Illumina Delaware"), your shares of Company stock
will be replaced by shares of stock in Illumina Delaware.

     In order to establish that (i) you will not be subject to tax under Section
897 of the Internal Revenue Code of 1986, as amended (the "Code"), in
consequence of the Reincorporation and (ii) Illumina Delaware will not be
required under Section 1445 of the Code to withhold taxes from the Illumina
Delaware stock that you will receive in connection therewith, the Company hereby
represents to you that, as of the date of this letter, shares of Company stock
do not constitute a "United States real property interest" within the meaning of
Section 897(c) of the Code and the regulations issued thereunder.

     A copy of this letter will be delivered to Illumina Delaware pursuant to
Section 4.8 of the Agreement.

     Under penalties of perjury, the undersigned officer of the Company hereby
declares that, to the best knowledge and belief of the undersigned, the facts
set forth herein are true and correct.

                                             Sincerely,


                                             ________________________________
                                             Jay T. Flatley, Chief Executive
                                             Officer and President


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