AFFYMETRIX INC
8-K, EX-3.1, 2000-06-13
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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                                                                     EXHIBIT 3.1


                      RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                                AFFYMETRIX, INC.

     Affymetrix, Inc., a Delaware corporation (the "Corporation"), hereby
certifies as follows:

     I.   The name of the corporation is Affymetrix, Inc. The date of filing of
its original certificate of incorporation with the Secretary of State was
May 5, 1998.

     II.  This restated certificate of incorporation amends, restates and
integrates the provisions of the certificate of incorporation of said
corporation and has been duly adopted in accordance with the provisions of
Sections 242 and 245 of the General Corporation Law of the State of Delaware by
the favorable vote of the holders of a majority of the outstanding stock
entitled to vote thereon.

     III. The text of the certificate of incorporation is hereby amended and
restated to read herein as set forth in full:

          FIRST: The name of the corporation is Affymetrix, Inc.

          SECOND: The address of the Corporation's registered office in the
     State of Delaware is 9 E. Loockerman Street, City of Dover, County of Kent.
     The name of the Corporation's registered agent at such address is National
     Corporate Research, Ltd.

          THIRD: The nature of the business or purposes to be conducted or
     promoted by the Corporation is to engage in any lawful act or activity for
     which corporations may be organized under the Delaware General Corporation
     Law.

          FOURTH: I. The Corporation is authorized to issue two classes of stock
     to be designated, respectively, Common Stock, par value $0.01 per share
     ("Common Stock"), and Preferred Stock, par value $0.01 per share
     ("Preferred Stock"). The total number of shares of all classes of stock
     which the Corporation shall have authority to issue is two hundred five
     million (205,000,000), consisting of two hundred million (200,000,000)
     shares of Common Stock and five million (5,000,000) shares of Preferred
     Stock.

          II.  The board of directors is authorized from time to time, subject
     to any limitations prescribed by law, to provide for the issuance of shares
     of Preferred Stock in one or more series, and in connection with the
     creation of any such series, by resolution or resolutions providing for the
     issuance of shares thereof, to establish from time to time the number of
     shares to be included in each such series, to determine and fix such voting
     powers, full or limited or no voting powers, and to fix the designation,
     preferences, and relative, participating, optional or other special rights
     of the shares of each such series, and any qualifications, limitations or
     restrictions thereof. The number of authorized shares of Preferred Stock
     may be increased or decreased (but not below the number of shares thereof
     then outstanding) by the affirmative vote of the holders of a majority of
     the Common Stock, without a vote of the holders of the Preferred Stock, or
     of any series thereof, unless a

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     vote of any such holders is required pursuant to the terms of any
     resolution or resolutions providing for the issue of such stock adopted by
     the board of directors of the Corporation.

          FIFTH: There shall be a series of Preferred Stock designated as
     "Series AA Preferred Stock" and the number of shares constituting such
     series shall be one million six hundred thirty-four thousand five hundred
     twenty-two (1,634,522) shares (the "Series AA Preferred Stock"). The
     rights, preferences, privileges, and restrictions granted to and imposed on
     the Series AA Preferred Stock are as set forth below:

     1.   DIVIDEND PROVISIONS.

               (a)  Subject to the rights of any series of Preferred Stock that
          may from time to time come into existence, the holders of shares of
          Series AA Preferred Stock shall be entitled to receive dividends
          payable in cash, out of any assets legally available therefor, prior
          and in preference to any declaration or payment of any dividend
          (payable other than in Common Stock or other securities and rights
          convertible into or entitling the holder thereof to receive, directly
          or indirectly, additional shares of Common Stock of this Corporation)
          on the Common Stock of this Corporation, at the rate per share per
          annum of $1.99 (as adjusted for any stock splits, stock dividends,
          combinations, recapitalizations or the like with respect to the Series
          AA Preferred Stock) payable in two equal installments on June 30 and
          December 31 of each year so long as such share of Series AA Preferred
          Stock is then outstanding. Such dividends shall accrue on each share
          from the Purchase Date (as defined below), and shall accrue from day
          to day, whether or not earned or declared. Such dividends shall be
          cumulative so that, except as provided below, if such dividends in
          respect of any previous or current dividend period, at the annual rate
          specified above, shall not have been paid, the deficiency shall first
          be fully paid before any dividend or other distribution shall be paid
          on or declared and set apart for the Common Stock. Cumulative
          dividends with respect to a share of Series AA Preferred Stock which
          are accrued, payable and/or in arrears shall, upon conversion of such
          share to Common Stock or redemption of such share, be paid to the
          extent assets are legally available therefor pursuant to the
          provisions of Section 2 and Section 3, respectively, and any amounts
          for which assets are not legally available shall be paid promptly as
          assets become legally available therefor; any partial payment will be
          made pro rata among the holders of such shares. The holders of the
          outstanding Series AA Preferred Stock can waive any dividend
          preference that such holders shall be entitled to receive under this
          Section 1 upon the affirmative vote or written consent of the holders
          of at least a majority of the Series AA Preferred Stock then
          outstanding.

               (b)  Subject to the rights of any shares of Preferred Stock that
          may from time to time come into existence and in addition to the
          amounts paid pursuant to subsection 1(a) above, the holders of shares
          of Series AA Preferred Stock shall be entitled to receive an amount
          equal to any dividend paid (other than dividends paid in Common Stock
          or other securities and rights convertible into or entitling the
          holder thereof to receive, directly or indirectly, additional shares
          of Common Stock of this Corporation) on the Common Stock of this
          Corporation (as determined on a per annum basis and on as a converted
          basis for the Series AA Preferred Stock), payable when, as and if
          declared by the Board of Directors. Such dividends shall not be
          cumulative.

     2.   LIQUIDATION PREFERENCE.

               (a)  In the event of any liquidation, dissolution or winding up
          of this Corporation, either voluntary or involuntary, subject to the
          rights of series of Preferred Stock that may from time to time come
          into existence, the holders of Series AA Preferred Stock shall be
          entitled to receive, prior and in preference to any distribution of
          any of the assets of this Corporation to the holders of Common Stock
          by reason of their ownership thereof, an amount per share equal to the
          sum of (i) $30.59 for each outstanding share of Series AA Preferred
          Stock (the "Original Series AA Issue Price") (subject to adjustment of
          such fixed dollar amounts for any stock splits, stock dividends,

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          combinations, recapitalizations or the like with respect to the Series
          AA Preferred Stock), (ii) accrued but unpaid dividends on such share,
          and (iii) a per share amount equal to the difference obtained by
          subtracting (A) the product of ten percent of the annual per share
          dividend multiplied by a fraction, the numerator of which is the
          number of days elapsed since the date upon which the first share of
          Series AA Preferred Stock was first issued (the "Purchase Date") and
          the denominator of which is 365, from (B) the annual per share
          dividend. The sum obtained by adding the amounts described in clauses
          (i), (ii) and (iii) of the preceding sentence is referred to herein as
          the "Series AA Liquidation Preference". If upon the occurrence of such
          event, the assets and funds thus distributed among the holders of the
          Series AA Preferred Stock shall be insufficient to permit the payment
          to such holders of the full aforesaid preferential amounts, then,
          subject to the rights of series of Preferred Stock that may from time
          to time come into existence, the entire assets and funds of this
          Corporation legally available for distribution shall be distributed
          ratably among the holders of the Series AA Preferred Stock in
          proportion to the amount of such stock owned by each such holder.

               (b)  Upon the completion of the distribution required by
          subparagraph (a) of this Section 2 and any other distribution that may
          be required with respect to series of Preferred Stock that may from
          time to time come into existence, if assets remain in this
          Corporation, the holders of the Common Stock of this Corporation,
          shall receive an amount per share of Common Stock equal to the
          quotient obtained by dividing (i) the Series AA Liquidation
          Preference, by (ii) the number of shares of Common Stock into which
          one (1) share of Series AA Preferred Stock could then be converted
          pursuant to Section 4 hereof. If upon the occurrence of such event,
          the assets and funds thus distributed among the holders of the Common
          Stock shall be insufficient to permit the payment to such holders of
          the full aforesaid preferential amount, then, subject to the rights of
          series of Preferred Stock that may from time to time come into
          existence, the entire remaining assets and funds of this Corporation
          legally available for distribution shall be distributed ratably among
          the holders of the Common Stock in proportion to the amount of such
          stock owned by each such holder.

               (c)  After the distributions described in subsection (a) and (b)
          above have been paid, subject to the rights of series of Preferred
          Stock that may from time to time come into existence, the remaining
          assets of this Corporation available for distribution to stockholders
          shall be distributed among the holders of Series AA Preferred Stock
          and Common Stock pro rata based on the number of shares of Common
          Stock held by each (assuming full conversion of all such Series AA
          Preferred Stock).

               (d)(i) The following events shall be deemed to be a liquidation,
          dissolution or winding up within the meaning of this Section 2: (A) a
          consolidation or merger of this Corporation with or into any other
          corporation or corporations as a result of which the holders of voting
          stock of this Corporation immediately prior to such transaction do not
          own, directly or indirectly, more than 50% of the voting power of the
          surviving corporation or its parent corporation immediately after such
          transaction, or (B) a sale, conveyance or disposition of all or
          substantially all of the assets of this Corporation.

                    (ii) In any of such events, the value of the assets
               distributed to the stockholders of this Corporation shall be
               determined as set forth herein. If the assets distributed to the
               stockholders of this Corporation consist of other than cash or
               securities, the value of such assets shall be the fair market
               value thereof, as determined by this Corporation and the holders
               of at least a majority of the voting power of all the then
               outstanding shares of Preferred Stock. If the assets distributed
               to the stockholders of this Corporation consist of securities,
               such securities shall be valued as follows:

               A.   Securities not subject to investment letter or other similar
          restrictions on free marketability covered by (B) below:

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                    (1)  If traded on a securities exchange or through the
               Nasdaq National Market, the value shall be deemed to be the
               average of the closing prices of the securities on such exchange
               or system over the twenty (20) trading day period ending three
               (3) trading days prior to the closing;

                    (2)  If actively traded over-the-counter, the value shall be
               deemed to be the average of the closing bid or sale prices
               (whichever is applicable) over the twenty (20) trading day period
               ending three (3) trading days prior to the closing; and

                    (3)  If there is no active public market, the value shall be
               the fair market value thereof, as mutually determined by this
               Corporation and the holders of at least a majority of the voting
               power of all then outstanding shares of Preferred Stock.

               B.   The method of valuation of securities subject to investment

          letter or other restrictions on free marketability (other than
          restrictions arising solely by virtue of a stockholder's status as
          an affiliate or former affiliate) shall be to make an appropriate
          discount from the market value determined as above in (A) (1), (2)
          or (3) to reflect the approximate fair market value thereof, as
          mutually determined by this Corporation and the holders of at least
          a majority of the voting power of all then outstanding shares of
          such Preferred Stock.

     3.   REDEMPTION.

               (a)  REDEMPTION AT THE OPTION OF THIS CORPORATION.

                    (i)  Subject to the rights of series of Preferred Stock
               that may from time to time come into existence, at any time on
               or prior to March 9, 2001, this Corporation may at any time it
               may lawfully do so, at the option of the Board of Directors,
               redeem in whole or in part the Series AA Preferred Stock by
               paying in cash therefor a sum equal to (A) the Original Series
               AA Issue Price (subject to adjustment of such fixed dollar
               amount for any stock splits, stock dividends, combinations,
               recapitalizations or the like with respect to the Series AA
               Preferred Stock), plus (B) accrued but unpaid dividends on
               such share (the "Early Redemption Price"); provided that the
               closing sale price of this Corporation's Common Stock on the
               Nasdaq National Market (or such other national securities
               exchange on which the Common Stock is then listed) has been at
               or above $52.00 (subject to adjustment of such fixed dollar
               amount for any stock splits, stock dividends, combinations,
               recapitalizations or the like with respect to the Common
               Stock) for twenty (20) of thirty (30) consecutive trading days
               prior to the applicable Corporation Redemption Date (as
               defined below), which thirty (30) day period shall have ended
               not more than ten (10) trading days prior to the date of the
               Corporation Redemption Notice (as defined below). Any
               redemption effected pursuant to this subsection 3(a)(i) shall
               be made on a pro rata basis among the holders of the Series AA
               Preferred Stock in proportion to the number of shares of
               Series AA Preferred Stock then held by them.

                    (ii) Subject to the rights of series of Preferred Stock that
               may from time to time come into existence, at any time after
               March 9, 2001, this Corporation may at any time it may
               lawfully do so, at the option of the Board of Directors,
               redeem in whole or in part the Series AA Preferred Stock by
               paying in cash therefor a sum equal to the Series AA
               Liquidation Preference (the "Late Redemption Price"). Any
               redemption effected pursuant to this subsection 3(a)(ii) shall
               be made on a pro rata basis among the holders of the Series AA
               Preferred Stock in proportion to the number of shares of
               Series AA Preferred Stock then held by them.

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                    (iii) Subject to the rights of series of Preferred Stock
               that may from time to time come into existence, at least
               twenty (20) but no more than thirty (30) days prior to the
               date on which this Corporation proposes to redeem any shares
               of Series AA Preferred Stock (each a "Corporation Redemption
               Date"), written notice shall be personally delivered, sent by
               reliable international courier, or sent by confirmed facsimile
               to each holder of record (at the close of business on the
               business day next preceding the day on which notice is given)
               of the Series AA Preferred Stock to be redeemed, at the
               address last shown on the records of this Corporation for such
               holder, notifying such holder of the redemption to be effected
               on the applicable Corporation Redemption Date, specifying the
               number of shares to be redeemed from such holder, the
               applicable Corporation Redemption Date, the Early or Late
               Redemption Price, as applicable, the place at which payment
               may be obtained and calling upon such holder to surrender to
               this Corporation, in the manner and at the place designated,
               his, her or its certificate or certificates representing the
               shares to be redeemed (the "Corporation Redemption Notice").
               Except as provided in subsection 3(a)(iv) or 3(a)(v), on or
               after each Corporation Redemption Date, each holder of Series
               AA Preferred Stock to be redeemed on such Corporation
               Redemption Date shall surrender to this Corporation the
               certificate or certificates representing such shares, in the
               manner and at the place designated in the Corporation
               Redemption Notice, and thereupon the Early or Late Redemption
               Price, as applicable, of such shares shall be payable to the
               order of the person whose name appears on such certificate or
               certificates as the owner thereof and each surrendered
               certificate shall be cancelled. In the event less than all the
               shares represented by any such certificate are redeemed, a new
               certificate shall be issued representing the unredeemed
               shares. Any shares of Series AA Preferred Stock that are not
               redeemed shall remain subject to redemption by this
               Corporation pursuant to this Section 3(a).

                    (iv) Each holder of Series AA Preferred Stock may, at
               anytime up to two (2) trading days prior to the applicable
               Corporation Redemption Date, elect to convert all shares of
               Series AA Preferred Stock designated for redemption in the
               Corporation Redemption Notice into shares of Common Stock
               pursuant to Section 4 below.

                    (v)  From and after each Corporation Redemption Date,
               unless there shall have been a default in payment of the Early
               or Late Redemption Price, as applicable, all rights of the
               holders of shares of Series AA Preferred Stock designated for
               redemption on such Corporation Redemption Date in the
               Corporation Redemption Notice as holders of Series AA
               Preferred Stock (except the right to receive the Early or Late
               Redemption Price, as applicable, without interest upon
               surrender of their certificate or certificates) shall cease
               with respect to such shares, and such shares shall not
               thereafter be transferred on the books of this Corporation or
               be deemed to be outstanding for any purpose whatsoever.
               Subject to the rights of series of Preferred Stock that may
               from time to time come into existence, if the funds of this
               Corporation legally available for redemption of shares of
               Series AA Preferred Stock on any Corporation Redemption Date
               are insufficient to redeem the total number of shares of
               Series AA Preferred Stock to be redeemed on such date, those
               funds that are legally available will be used to redeem the
               maximum possible number of such shares ratably among the
               holder(s) of such shares to be redeemed such that an equal
               percentage of the number of shares held by each holder of
               Series AA Preferred Stock is redeemed (provided that this
               Corporation shall have no obligation to issue or redeem any
               fractional shares). The shares of Series AA Preferred Stock
               not redeemed shall remain outstanding and entitled to all the
               rights and preferences provided herein. Subject to the rights
               of series of Preferred Stock that may from time to time come
               into

<PAGE>

               existence, at any time thereafter when additional funds of
               this Corporation are legally available for the redemption of
               shares of Series AA Preferred Stock, such funds will
               immediately be used to redeem the balance of the shares that
               this Corporation has become obliged to redeem on any
               Corporation Redemption Date but that it has not redeemed.

               (b)  REDEMPTION AT OPTION OF STOCKHOLDERS.

                    (i)  Subject to the rights of series of Preferred Stock
               that may from time to time come into existence, at any time on
               or after March 9, 2005, provided that this Corporation shall
               have received a written request from the holders of not less
               than a majority of the then outstanding Series AA Preferred
               Stock that a specified percentage of such holders' shares of
               Series AA Preferred Stock be redeemed, and concurrently with
               surrender by such holders of the certificates representing
               such shares, this Corporation shall, to the extent it may
               lawfully do so, redeem the shares specified in such request by
               paying in cash therefor a sum per share equal to (A) $30.59
               per share of Series AA Preferred Stock (as adjusted for any
               stock splits, stock dividends, recapitalizations or the like)
               plus (B) accrued but unpaid dividends on such share (the
               "Series AA Redemption Price"); provided, however, in no event
               shall this Corporation be required to redeem more than 817,261
               shares of Series AA Preferred Stock (as adjusted for any stock
               splits, stock dividends, recapitalizations or the like) during
               any twelve month period. Any request made pursuant to this
               subsection 3(b)(i) shall be delivered at least one hundred and
               eighty (180) days prior to the date on which the redemption is
               requested to occur (a "Stockholder Redemption Date"). Any
               redemption of Series AA Preferred Stock effected pursuant to
               this subsection 3(b)(i) shall be made on a pro rata basis
               among the holders of the Series AA Preferred Stock in
               proportion to the number of shares of Series AA Preferred
               Stock proposed to be redeemed by such holders.

                    (ii) Subject to the rights of series of Preferred Stock
               that may from time to time come into existence, at least
               twenty (20) but no more than thirty (30) days prior to a
               Stockholder Redemption Date, written notice shall be
               personally delivered, sent by reliable international courier,
               or sent by confirmed facsimile to each holder of record (at
               the close of business on the business day next preceding the
               day on which notice is given) of the Series AA Preferred Stock
               to be redeemed, at the address last shown on the records of
               this Corporation for such holder, notifying such holder of the
               redemption to be effected on the Stockholder Redemption Date,
               specifying the number of shares to be redeemed from such
               holder, the Stockholder Redemption Date, the Series AA
               Redemption Price, the place at which payment may be obtained
               and calling upon such holder to surrender to this Corporation,
               in the manner and at the place designated, his, her or its
               certificate or certificates representing the shares to be
               redeemed (the "Stockholder Redemption Notice"). Except as
               provided in subsection (3)(b)(iii), on or after the
               Stockholder Redemption Date, each holder of Series AA
               Preferred Stock to be redeemed on such Redemption Date shall
               surrender to this Corporation the certificate or certificates
               representing such shares, in the manner and at the place
               designated in the Stockholder Redemption Notice, and thereupon
               the Series AA Redemption Price for such shares shall be
               payable to the order of the person whose name appears on such
               certificate or certificates as the owner thereof and each
               surrendered certificate shall be cancelled. In the event less
               than all the shares represented by any such certificate are
               redeemed, a new certificate shall be issued representing the
               unredeemed shares.

                    (iii) From and after the Stockholder Redemption Date,
               unless there shall have been a default in payment of the
               Series AA Redemption Price, all rights of the holders of
               shares of

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               Series AA Preferred Stock designated for redemption on the
               Stockholder Redemption Date in the Stockholder Redemption
               Notice as holders of Series AA Preferred Stock (except the
               right to receive the Series AA Redemption Price without
               interest upon surrender of their certificate or certificates)
               shall cease with respect to such shares, and such shares shall
               not thereafter be transferred on the books of this Corporation
               or be deemed to be outstanding for any purpose whatsoever.
               Subject to the rights of series of Preferred Stock that may
               from time to time come into existence, if the funds of this
               Corporation legally available for redemption of shares of
               Series AA Preferred Stock on the Stockholder Redemption Date
               are insufficient to redeem the total number of shares of
               Series AA Preferred Stock to be redeemed on such date, those
               funds that are legally available will be used to redeem the
               maximum possible number of such shares ratably among the
               holders of such shares to be redeemed such that an equal
               percentage of the number of shares held by each holder of
               Series AA Preferred Stock is redeemed (provided that this
               Corporation shall have no obligation to issue or redeem any
               fractional shares). The shares of Series AA Preferred Stock
               not redeemed shall remain outstanding and entitled to all the
               rights and preferences provided herein. Subject to the rights
               of series of Preferred Stock that may from time to time come
               into existence, at any time thereafter when additional funds
               of this Corporation are legally available for the redemption
               of shares of Series AA Preferred Stock, such funds will
               immediately be used to redeem the balance of the shares that
               this Corporation has become obliged to redeem on the
               Stockholder Redemption Date but that it has not redeemed.

     4.   CONVERSION. The holders of the Series AA Preferred Stock shall have
conversion rights as follows (the "Conversion Rights"):

               (a)  RIGHT TO CONVERT. Each share of Series AA Preferred Stock
          shall be convertible, at the option of the holder thereof, at any
          time after the Purchase Date of such share and on or prior to the
          second trading day prior to the Redemption Date, if any, as may
          have been fixed in any Redemption Notice with respect to such share
          of the Series AA Preferred Stock, at the office of this Corporation
          or any transfer agent for such stock, into such number of fully
          paid and nonassessable shares of Common Stock as is determined by
          dividing the Original Series AA Issue Price by the Conversion Price
          applicable to such share, determined as hereafter provided, in
          effect on the date the certificate is surrendered for conversion
          (the "Conversion Ratio"). The initial Conversion Price per share
          for shares of Series AA Preferred Stock shall be $39.77 per share;
          provided, however, that the Conversion Price for the Series AA
          Preferred Stock shall be subject to adjustment as set forth in
          subsection 4(d).

               (b)  AUTOMATIC CONVERSION. Each share of Series AA Preferred
          Stock shall automatically be converted into shares of Common Stock
          at the Conversion Ratio at the time in effect for such Series AA
          Preferred Stock immediately upon the date specified by written
          consent or agreement of the holders of a majority of the then
          outstanding shares of Series AA Preferred Stock.

               (c)  MECHANICS OF CONVERSION. Before any holder of Series AA
          Preferred Stock shall be entitled to convert the same into shares
          of Common Stock, he or she shall surrender the certificate or
          certificates therefor, duly endorsed, at the office of this
          Corporation or of any transfer agent for the Series AA Preferred
          Stock, and shall give written notice to this Corporation at its
          principal corporate office, of the election to convert the same and
          shall state therein the name or names in which the certificate or
          certificates for shares of Common Stock are to be issued. This
          Corporation shall, as soon as practicable thereafter, issue and
          deliver at such office to such holder of Series AA Preferred Stock,
          or to the nominee or nominees of such holder, a certificate or
          certificates for the number of shares of Common Stock to which such
          holder shall be entitled as aforesaid. Such conversion shall be
          deemed to have been made immediately prior to the close of business
          on the date of such surrender of the shares of Series AA Preferred

<PAGE>


          Stock to be converted, and the person or persons entitled to
          receive the shares of Common Stock issuable upon such conversion
          shall be treated for all purposes as the record holder or holders
          of such shares of Common Stock as of such date. If the conversion
          is in connection with an underwritten offering of securities
          registered pursuant to the Securities Act of 1933, the conversion
          may, at the option of any holder tendering Series AA Preferred
          Stock for conversion, be conditioned upon the closing with the
          underwriters of the sale of securities pursuant to such offering,
          in which event the persons entitled to receive the Common Stock
          upon conversion of the Series AA Preferred Stock shall not be
          deemed to have converted such Series AA Preferred Stock until
          immediately prior to the closing of such sale of securities.

               (d)  CONVERSION PRICE ADJUSTMENTS OF PREFERRED STOCK FOR SPLITS,
          STOCK DIVIDENDS, COMBINATIONS AND THE LIKE. The Conversion Price of
          the Series AA Preferred Stock shall be subject to adjustment from
          time to time as follows:

                    (i)  In the event this Corporation should at any time or
               from time to time after the Purchase Date fix a record date
               for the effectuation of a split or subdivision of the
               outstanding shares of Common Stock or the determination of
               holders of Common Stock entitled to receive a dividend or
               other distribution payable in additional shares of Common
               Stock or other securities or rights convertible into, or
               entitling the holder thereof to receive directly or
               indirectly, additional shares of Common Stock (hereinafter
               referred to as "Common Stock Equivalents") without payment of
               any consideration by such holder for the additional shares of
               Common Stock or the Common Stock Equivalents (including the
               additional shares of Common Stock issuable upon conversion or
               exercise thereof), then, as of such record date (or the date
               of such dividend distribution, split or subdivision if no
               record date is fixed), the Conversion Price of the Series AA
               Preferred Stock shall be appropriately decreased so that the
               number of shares of Common Stock issuable on conversion of
               each share of such series shall be increased in proportion to
               such increase of the aggregate of shares of Common Stock
               outstanding and those issuable with respect to such Common
               Stock Equivalents.

                    (ii) If the number of shares of Common Stock outstanding at
               any time after the Purchase Date is decreased by a combination
               of the outstanding shares of Common Stock, then, following the
               record date of such combination, the Conversion Price for the
               Series AA Preferred Stock shall be appropriately increased so
               that the number of shares of Common Stock issuable on
               conversion of each share of such series shall be decreased in
               proportion to such decrease in outstanding shares.

               (e)  OTHER DISTRIBUTIONS. In the event this Corporation shall
          declare a distribution payable in securities of other persons,
          evidences of indebtedness issued by this Corporation or other
          persons, assets (excluding cash dividends) or other options or
          rights not referred to in subsection 4(d)(i), then, in each such
          case for the purpose of this Subsection 4(e), the holders of the
          Series AA Preferred Stock shall be entitled to a proportionate
          share of any such distribution as though they were the holders of
          the number of shares of Common Stock of this Corporation into which
          their shares of Series AA Preferred Stock are convertible as of the
          record date fixed for the determination of the holders of Common
          Stock of this Corporation entitled to receive such distribution.

               (f)  RECAPITALIZATIONS. If at any time or from time to time there
          shall be a recapitalization of the Common Stock (other than a
          subdivision, combination or merger or sale of assets transaction
          provided for elsewhere in this Section 4 or Section 2) provision
          shall be made so that the holders of the Series AA Preferred Stock
          shall thereafter be entitled to receive upon conversion of the
          Series AA Preferred Stock the number of shares of stock or other
          securities or property of this Corporation or otherwise, to which a
          holder of Common Stock deliverable upon conversion would have been
          entitled on such

<PAGE>

          recapitalization. In any such case, appropriate adjustment shall be
          made in the application of the provisions of this Section 4 with
          respect to the rights of the holders of the Series AA Preferred
          Stock after the recapitalization to the end that the provisions of
          this Section 4 (including adjustment of the Conversion Price then
          in effect and the number of shares purchasable upon conversion of
          the Series AA Preferred Stock) shall be applicable after that event
          as nearly equivalent as may be practicable.

               (g)  NO IMPAIRMENT. This Corporation will not, by amendment of
          its Amended and Restated Articles of Incorporation or through any
          reorganization, recapitalization, 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 this Corporation, but will at all times in good faith
          assist in the carrying out of all the provisions of this Section 4
          and in the taking of all such action as may be necessary or
          appropriate in order to protect the Conversion Rights of the
          holders of the Series AA Preferred Stock against impairment.

               (h)  NO FRACTIONAL SHARES AND CERTIFICATE AS TO ADJUSTMENTS.

                    (i)  No fractional shares shall be issued upon the
               conversion of any share or shares of the Series AA Preferred
               Stock, and the number of shares of Common Stock to be issued
               shall be rounded down to the nearest whole share. This
               Corporation shall provide the holder of any fractional
               interest with an amount of cash equal to the fair market value
               of one share of this Corporation's Common Stock multiplied by
               such fractional interest. Whether or not fractional shares are
               issuable upon such conversion shall be determined on the basis
               of the total number of shares of Series AA Preferred Stock the
               holder is at the time converting into Common Stock and the
               number of shares of Common Stock issuable upon such aggregate
               conversion.

                    (ii) Upon the occurrence of each adjustment or readjustment
               of the Conversion Price of Series AA Preferred Stock pursuant
               to this Section 4, this Corporation, at its expense, shall
               promptly compute such adjustment or readjustment in accordance
               with the terms hereof and prepare and furnish to each holder
               of Series AA Preferred Stock a certificate setting forth such
               adjustment or readjustment and showing in detail the facts
               upon which such adjustment or readjustment is based. This
               Corporation shall, upon the written request at any time of any
               holder of Series AA Preferred Stock, furnish or cause to be
               furnished to such holder a like certificate setting forth (A)
               such adjustment and readjustment, (B) the Conversion Price for
               such series of Preferred Stock at the time in effect, and (C)
               the number of shares of Common Stock and the amount, if any,
               of other property that at the time would be received upon the
               conversion of a share of Series AA Preferred Stock.

               (i)  NOTICES OF RECORD DATE. In the event of any taking by this
          Corporation of a record of the holders of any class of securities
          for the purpose of determining the holders thereof who are entitled
          to receive any dividend (other than a cash dividend) or other
          distribution, any right to subscribe for, purchase or otherwise
          acquire any shares of stock of any class or any other securities or
          property, or to receive any other right, this Corporation shall
          mail to each holder of Series AA Preferred Stock, at least twenty
          (20) days prior to the date specified therein, a notice specifying
          the date on which any such record is to be taken for the purpose of
          such dividend, distribution or right, and the amount and character
          of such dividend, distribution or right.

               (j)  RESERVATION OF STOCK ISSUABLE UPON CONVERSION. This
          Corporation shall at all times reserve and keep available out of
          its authorized but unissued shares of Common Stock, solely for the
          purpose of effecting the conversion of the shares of the Series AA
          Preferred

<PAGE>

          Stock, such number of its shares of Common Stock as shall from time
          to time be sufficient to effect the conversion of all outstanding
          shares of the Series AA Preferred Stock; and if at any time the
          number of authorized but unissued shares of Common Stock shall not
          be sufficient to effect the conversion of all then outstanding
          shares of the Series AA Preferred Stock, in addition to such other
          remedies as shall be available to the holder of such Preferred
          Stock, this Corporation will take such corporate action as may, in
          the opinion of its counsel, be necessary to increase its authorized
          but unissued shares of Common Stock to such number of shares as
          shall be sufficient for such purposes, including, without
          limitation, engaging in best efforts to obtain the requisite
          stockholder approval of any necessary amendment to this Certificate
          of Designation or the Amended and Restated Articles of
          Incorporation.

               (k)  NOTICES. Any notice required by the provisions of this
          Section 4 to be given to the holders of shares of Series AA
          Preferred Stock shall be deemed given if deposited in the United
          States mail, postage prepaid, and addressed to each holder of
          record at his address appearing on the books of this Corporation.

          5.   VOTING RIGHTS. The holder of each share of Series AA Preferred
     Stock shall have the right to one vote for each share of Common Stock into
     which such Series AA Preferred Stock could then be converted at the
     record date for determination of the stockholders entitled to vote
     thereon, and with respect to such vote, such holder shall have full
     voting rights and powers equal to the voting rights and powers of the
     holders of Common Stock, and shall be entitled, notwithstanding any
     provision hereof, to notice of any stockholders' meeting in accordance
     with the bylaws of this Corporation, and shall be entitled to vote,
     together with holders of Common Stock, with respect to any question upon
     which holders of Common Stock have the right to vote and otherwise as
     required by law. Fractional votes shall not, however, be permitted and
     any fractional voting rights available on an as-converted basis (after
     aggregating all shares into which shares of Series AA Preferred Stock
     held by each holder could be converted) shall be rounded to the nearest
     whole number (with one-half be in grounded upward).

          SIXTH: The following provisions are inserted for the management of the
     business and for 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 Certificate of Incorporation or the Bylaws of the
          Corporation, 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 Bylaws of the Corporation so provide.
          Directors need not be stockholders.

               C.   Any action required or permitted to be taken by the
          stockholders of the Corporation must be effected at a duly called
          annual or special meeting of stockholders of the Corporation and
          may not be effected by any consent in writing by such stockholders.

               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 Bylaws of the Corporation.

               E.   Special meetings of stockholders of the Corporation may be
          called nly by the Chairman of the Board or the President or by the
          board of directors acting pursuant to a resolution adopted by a
          majority of the entire board of directors. For purposes of this
          Certificate of Incorporation, the term "entire board of directors"
          shall mean the total number of authorized directors whether or not
          there exist any vacancies in previously authorized directorships.

<PAGE>


          SEVENTH: The board of directors is expressly empowered to adopt,
     alter, amend or repeal Bylaws of the Corporation. Any adoption, alteration,
     amend mentor repeal of the Bylaws of the Corporation by the board of
     directors shall require the approval of a majority of the entire board of
     directors. The stockholders shall also have power to adopt, amend or repeal
     the Bylaws of the Corporation; provided, however, 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 Certificate of Incorporation, the affirmative
     vote of the holders of at least a majority 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 adopt, alter, amend or repeal any
     provision of the Bylaws of the Corporation.

          EIGHTH: The corporation reserves the right to amend and repeal any
     provision contained in this Certificate of Incorporation in the manner from
     time to time prescribed by the laws of the State of Delaware. All rights
     herein conferred are granted subject to this reservation.

          NINTH: To the fullest extent permitted by Delaware General Corporation
     Law, a director of the corporation shall not be personally liable to the
     corporation or its stockholders for monetary damages for breach of
     fiduciary duty as a director, except for liability (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 Section 174 of the
     Delaware General Corporation Law, or (iv) for any transaction from which
     the director derived an improper personal benefit. 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. Any repeal or modification of this provision shall not
     adversely affect any right or protection of a director of the corporation
     existing at the time of such repeal or modification.

     IN WITNESS WHEREOF, the Corporation has caused this Certificate to be
executed by Stephen P.A. Fodor, its Chairman and Chief Executive Officer, on the
12th day of June, 2000.

                                         AFFYMETRIX, INC.


                                         By:  /s/ STEPHEN P.A. FODOR
                                            ------------------------
                                                 Stephen P.A. Fodor



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