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                                                                EXHIBIT 3.(i)2

                           CERTIFICATE OF DESIGNATION

                    OF SERIES A PARTICIPATING PREFERRED STOCK

                                       OF

                                  NANOGEN, INC.



         We, Howard C. Birndorf, the Chief Executive Officer, and Harry J. 
Leonhardt, the Secretary, of Nanogen, Inc., a corporation organized and 
existing under the General Corporation Law of the State of Delaware, DO 
HEREBY CERTIFY:

         That pursuant to the authority conferred upon the Board of Directors 
by the Certificate of Incorporation of the Corporation, the said Board of 
Directors on November 17, 1998, adopted the following resolution creating a 
series of 100,000 shares of Preferred Stock designated as Series A 
Participating Preferred Stock:

         RESOLVED, that pursuant to the authority vested in the Board of 
Directors of the Corporation in accordance with the provisions of its 
Certificate of Incorporation, a series of Preferred Stock of the Corporation 
be and it hereby is created, and that the designation and amount thereof and 
the powers, preferences and relative, participating, optional and other 
special rights of the shares of such series, and the qualifications, 
limitations or restrictions thereof are as follows:

         1.   DESIGNATION AND AMOUNT. The shares of such series shall be 
designated as "Series A Participating Preferred Stock," $0.001 par value per 
share, and the number of shares constituting such series shall be 100,000. 
Such number of shares may be increased or decreased by resolution of the 
Board of Directors; provided, that no decrease shall reduce the number of 
shares of Series A Participating Preferred Stock to a number less than that 
of the shares then outstanding plus the number of shares issuable upon 
exercise of outstanding rights, options or warrants or upon conversion of 
outstanding securities issued by the Corporation.

         2.   DIVIDENDS AND DISTRIBUTIONS.

         (A) Subject to the prior and superior rights of the holders of any 
shares of any series of Preferred Stock ranking prior and superior to the 
shares of Series A Participating Preferred Stock with respect to dividends, 
the holders of shares of Series A Participating Preferred Stock in preference 
to the holders of shares of Common Stock, par value $0.001 per share (the 
"Common Stock"), of the Corporation and any other junior stock, shall be 
entitled to receive, when, as and if declared by the Board of Directors out 
of funds legally available for the purpose, quarterly dividends payable in 
cash on the first day of March, June, September and December in each year 
(each such date being referred to herein as a "Quarterly Dividend Payment 
Date"), commencing on the first Quarterly Dividend Payment Date after the 
first issuance of a share or fraction of a share of Series A Participating 
Preferred Stock in an amount per share (rounded to the nearest cent) equal to 
the greater of (a) $100.00, or (b) subject to the provision for adjustment 
hereinafter set forth, 1,000 times the aggregate per share amount of all cash 
dividends, and 1,000 times the aggregate per share amount (payable in kind) 
of all non-cash dividends or other distributions other than a dividend 
payable in shares of Common Stock or a subdivision of the outstanding shares 
of Common Stock (by reclassification or otherwise), declared on the Common 
Stock, since the immediately preceding Quarterly Dividend Payment Date, or, 
with respect to the first 

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Quarterly Dividend Payment Date, since the first issuance of any share or 
fraction of a share of Series A Participating Preferred Stock. In the event 
the Corporation shall at any time after the close of business on November 17, 
1998 (the "Rights Declaration Date") (i) declare any dividend on Common Stock 
payable in shares of Common Stock, (ii) subdivide the outstanding Common 
Stock, or (iii) combine the outstanding Common Stock into a smaller number of 
shares, by reclassification or otherwise, then in each such case the amount 
to which holders of shares of Series A Participating Preferred Stock were 
entitled immediately prior to such event under clause (b) of the preceding 
sentence shall be adjusted by multiplying such amount by a fraction the 
numerator of which is the number of shares of Common Stock outstanding 
immediately after such event and the denominator of which is the number of 
shares of Common Stock that were outstanding immediately prior to such event.

         (B) The Corporation shall declare a dividend or distribution on the 
Series A Participating Preferred Stock as provided in paragraph (A) above 
immediately after it declares a dividend or distribution on the Common Stock 
(other than a dividend payable in shares of Common Stock); provided that, in 
the event no dividend or distribution shall have been declared on the Common 
Stock during the period between any Quarterly Dividend Payment Date and the 
next subsequent Quarterly Dividend Payment Date, a dividend of $100 per share 
on the Series A Participating Preferred Stock shall nevertheless be payable 
on such subsequent Quarterly Dividend Payment Date.

         (C) Dividends shall begin to accrue and be cumulative on outstanding 
shares of Series A Participating Preferred Stock from the Quarterly Dividend 
Payment Date next preceding the date of issue of such shares of Series A 
Participating Preferred Stock unless the date of issue of such shares is 
prior to the record date for the first Quarterly Dividend Payment Date, in 
which case dividends on such shares shall begin to accrue from the date of 
issue of such shares, or unless the date of issue is a Quarterly Dividend 
Payment Date or is a date after the record date for the determination of 
holders of shares of Series A Participating Preferred Stock entitled to 
receive a quarterly dividend and before such Quarterly Dividend Payment Date 
in either of which events such dividends shall begin to accrue and be 
cumulative from such Quarterly Dividend Payment Date. Accrued but unpaid 
dividends shall not bear interest. Dividends paid on the shares of Series A 
Participating Preferred Stock in an amount less than the total amount of such 
dividends at the time accrued and payable on such shares shall be allocated 
pro rata on a share-by-share basis among all such shares at the time 
outstanding. The Board of Directors may fix a record date for the 
determination of holders of shares of Series A Participating Preferred Stock 
entitled to receive payment of a dividend or distribution declared thereon, 
which record date shall be no more than 30 days prior to the date fixed for 
the payment thereof.

         3.   VOTING RIGHTS. The holders of shares of Series A Participating 
Preferred Stock shall have the following voting rights:

                  (A) Subject to the provision for adjustment hereinafter set
         forth, each share of Series A Participating Preferred Stock shall
         entitle the holder thereof to 1,000 votes on all matters submitted to a
         vote of the stockholders of the Corporation. In the event the
         Corporation shall at any time after the Rights Declaration Date (i)
         declare any dividend on Common Stock payable in shares of Common Stock,
         (ii) subdivide the outstanding Common Stock into a greater number of
         shares, or (iii) combine the outstanding Common Stock into a smaller
         number of shares, by reclassification or otherwise, then in each such
         case the number of votes per share to which holders of shares of Series
         A Participating Preferred Stock were entitled immediately prior to such
         event shall be adjusted by multiplying such number by a fraction the
         numerator of which is the number of shares of Common Stock outstanding
         immediately after such event and the denominator of which is the number
         of shares of Common Stock outstanding immediately prior to such event.

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                  (B) Except as otherwise provided herein or by law, the holders
         of shares of Series A Participating Preferred Stock and the holders of
         shares of Common Stock and any other capital stock of the Corporation
         having general voting rights shall vote together as one class on all
         matters submitted to a vote of stockholders of the Corporation.

                  (C) (i) If at any time dividends on any Series A Participating
         Preferred Stock shall be in arrears in an amount equal to six quarterly
         dividends thereon, the occurrence of such contingency shall mark the
         beginning of a period (herein called a "default period") which shall
         extend until such time when all accrued and unpaid dividends for all
         previous quarterly dividend periods and for the current quarterly
         dividend period on all shares of Series A Participating Preferred Stock
         then outstanding shall have been declared and paid or set apart for
         payment. During each default period, all holders of Preferred Stock
         (including holders of the Series A Participating Preferred Stock) with
         dividends in arrears in an amount equal to six quarterly dividends
         thereon, voting as a class, irrespective of series, shall have the
         right to elect two directors.

                  (ii) During any default period, such voting right of the
         holders of Series A Participating Preferred Stock may be exercised
         initially at a special meeting called pursuant to subparagraph (iii) of
         this Section 3(C) or at any annual meeting of stockholders, and
         thereafter at annual meetings of stockholders, provided that neither
         such voting right nor the right of the holders of any other series of
         Preferred Stock, if any, to increase, in certain cases, the authorized
         number of directors shall be exercised unless the holders of ten
         percent (10%) in number of shares of Preferred Stock outstanding shall
         be present in person or by proxy. The absence of a quorum of the
         holders of Common Stock shall not affect the exercise by the holders of
         Preferred Stock of such voting right. At any meeting at which the
         holders of Preferred Stock shall exercise such voting right initially
         during an existing default period, they shall have the right, voting as
         a class, to elect directors to fill such vacancies, if any, in the
         Board of Directors as may then exist up to two directors or, if such
         right is exercised at an annual meeting, to elect two directors. If the
         number which may be so elected at any special meeting does not amount
         to the required number, the holders of the Preferred Stock shall have
         the right to make such increase in the number of directors as shall be
         necessary to permit the election by them of the required number. After
         the holders of the Preferred Stock shall have exercised their right to
         elect directors in any default period and during the continuance of
         such period, the number of directors shall not be increased or
         decreased except by vote of the holders of Preferred Stock as herein
         provided or pursuant to the rights of any equity securities ranking
         senior to or pari passu with the Series A Participating Preferred
         Stock.

                  (iii) Unless the holders of Preferred Stock shall, during an
         existing default period, have previously exercised their right to elect
         directors, the Board of Directors may order, or any stockholder or
         stockholders owning in the aggregate not less than ten percent (10%) of
         the total number of shares of Preferred Stock outstanding, irrespective
         of series, may request, the calling of a special meeting of the holders
         of Preferred Stock, which meeting shall thereupon be called by the
         President, a Vice President or the Secretary of the Corporation. Notice
         of such meeting and of any annual meeting at which holders of Preferred
         Stock are entitled to vote pursuant to this paragraph (C)(iii) shall be
         given to each holder of record of Preferred Stock by mailing a copy of
         such notice to such holder at such holder's last address as the same
         appears on the books of the Corporation. Such meeting shall be called
         for a time not earlier than ten days and not later than 60 days after
         such order or request or in default of the calling of such 

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         meeting within 60 days after such order or request, such meeting may 
         be called on similar notice by any stockholder or stockholders owning 
         in the aggregate not less than ten percent (10%) of the total number 
         of shares of Preferred Stock outstanding. Notwithstanding the 
         provisions of this paragraph (C)(iii), no such special meeting shall 
         be called during the period within 60 days immediately preceding the 
         date fixed for the next annual meeting of the stockholders.
         
                  (iv) In any default period, the holders of Common Stock, and
         other classes of stock of the Corporation, if applicable, shall
         continue to be entitled to elect the whole number of directors until
         the holders of Preferred Stock shall have exercised their right to
         elect two directors voting as a class, after the exercise of which
         right (x) the directors so elected by the holders of Preferred Stock
         shall continue in office until their successors shall have been elected
         by such holders or until the expiration of the default period, and (y)
         any vacancy in the Board of Directors may (except as provided in
         paragraph (C)(ii) of this Section 3) be filled by vote of a majority of
         the remaining directors theretofore elected by the holders of the class
         of stock which elected the director whose office shall have become
         vacant. References in this paragraph (C) to directors elected by the
         holders of a particular class of stock shall include directors elected
         by such directors to fill vacancies as provided in clause (y) of the
         foregoing sentence.

                  (v) Immediately upon the expiration of a default period, (x)
         the right of the holders of Preferred Stock as a class to elect
         directors shall cease, (y) the term of any directors elected by the
         holders of Preferred Stock as a class shall terminate, and (z) the
         number of directors shall be such number as may be provided for in, or
         pursuant to, the Certificate of Incorporation or Bylaws irrespective of
         any increase made pursuant to the provisions of paragraph (C)(ii) of
         this Section 3 (such number being subject, however, to change
         thereafter in any manner provided by law or in the Certificate of
         Incorporation or Bylaws). Any vacancies in the Board of Directors
         effected by the provisions of clauses (y) and (z) in the preceding
         sentence may be filled by a majority of the remaining directors, even
         though less than a quorum.

                  (D) Except as set forth herein, holders of Series A
         Participating Preferred Stock shall have no special voting rights and
         their consent shall not be required (except to the extent they are
         entitled to vote with holders of Common Stock as set forth herein) for
         taking any corporate action.

         4.       CERTAIN RESTRICTIONS.

         (A) Whenever quarterly dividends or other dividends or distributions
payable on the Series A Participating Preferred Stock as provided in Section 2
are in arrears, thereafter and until all accrued and unpaid dividends and
distributions, whether or not declared, on shares of Series A Participating
Preferred Stock outstanding shall have been paid in full, the Corporation shall
not

                  (i) declare or pay dividends on, make any other distributions
         on, or redeem or purchase or otherwise acquire for consideration any
         shares of stock ranking junior (either as to dividends or upon
         liquidation, dissolution or winding up) to the Series A Participating
         Preferred Stock;

                  (ii) declare or pay dividends on or make any other
         distributions on any shares of stock ranking on a parity (either as to
         dividends or upon liquidation, dissolution or winding up) with the
         Series A Participating Preferred Stock except dividends paid ratably on
         the Series A Participating Preferred Stock and all such parity stock on
         which 

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         dividends are payable or in arrears in proportion to the total
         amounts to which the holders of all such shares are then entitled;

                  (iii) redeem or purchase or otherwise acquire for
         consideration shares of any stock ranking on a parity (either as to
         dividends or upon liquidation, dissolution or winding up) with the
         Series A Participating Preferred Stock provided that the Corporation
         may at any time redeem, purchase or otherwise acquire shares of any
         such parity stock in exchange for shares of any stock of the
         Corporation ranking junior (either as to dividends or upon dissolution,
         liquidation or winding up) to the Series A Participating Preferred
         Stock; or

                  (iv) purchase or otherwise acquire for consideration any
         shares of Series A Participating Preferred Stock or any shares of stock
         ranking on a parity with the Series A Participating Preferred Stock
         except in accordance with a purchase offer made in writing or by
         publication (as determined by the Board of Directors) to all holders of
         such shares upon such terms as the Board of Directors, after
         consideration of the respective annual dividend rates and other
         relative rights and preferences of the respective series and classes,
         shall determine in good faith will result in fair and equitable
         treatment among the respective series or classes.

         (B) The Corporation shall not permit any subsidiary of the 
Corporation to purchase or otherwise acquire for consideration any shares of 
stock of the Corporation unless the Corporation could, under paragraph (A) of 
this Section 4, purchase or otherwise acquire such shares at such time and in 
such manner.

         5.   REACQUIRED SHARES. Any shares of Series A Participating 
Preferred Stock purchased or otherwise acquired by the Corporation in any 
manner whatsoever shall be retired and cancelled promptly after the 
acquisition thereof. All such shares shall upon their cancellation become 
authorized but unissued shares of Preferred Stock and may be reissued as part 
of a new series of Preferred Stock to be created by resolution or resolutions 
of the Board of Directors, subject to the conditions and restrictions on 
issuance set forth herein.

         6.   LIQUIDATION, DISSOLUTION OR WINDING UP.

         (A) Upon any liquidation (voluntary or otherwise), dissolution or 
winding up of the Corporation, no distribution shall be made to the holders 
of shares of stock ranking junior (either as to dividends or upon 
liquidation, dissolution or winding up) to the Series A Participating 
Preferred Stock unless, prior thereto, the holders of shares of Series A 
Participating Preferred Stock shall have received per share, the greater of 
1,000 times $1.00 or 1,000 times the payment made per share of Common Stock, 
plus an amount equal to accrued and unpaid dividends and distributions 
thereon, whether or not declared, to the date of such payment (the "Series A 
Liquidation Preference"). Following the payment of the full amount of the 
Series A Liquidation Preference, no additional distributions shall be made to 
the holders of shares of Series A Participating Preferred Stock unless, prior 
thereto, the holders of shares of Common Stock shall have received an amount 
per share (the "Common Adjustment") equal to the quotient obtained by 
dividing (i) the Series A Liquidation Preference by (ii) 1,000 (as 
appropriately adjusted as set forth in subparagraph (C) below to reflect such 
events as stock splits, stock dividends and recapitalization with respect to 
the Common Stock) (such number in clause (ii), the "Adjustment Number"). 
Following the payment of the full amount of the Series A Liquidation 
Preference and the Common Adjustment in respect of all outstanding shares of 
Series A Participating Preferred Stock and Common Stock, respectively, 
holders of Series A Participating Preferred Stock and holders of shares of 
Common Stock shall receive their ratable and proportionate share of the 
remaining assets to be distributed in the ratio of the Adjustment Number to 1 
with respect to such Preferred Stock and Common 

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Stock, on a per share basis, respectively.

         (B) In the event there are not sufficient assets available to permit 
payment in full of the Series A Liquidation Preference and the liquidation 
preferences of all other series of Preferred Stock, if any, which rank on a 
parity with the Series A Participating Preferred Stock then such remaining 
assets shall be distributed ratably to the holders of such parity shares in 
proportion to their respective liquidation preferences. In the event there 
are not sufficient assets available to permit payment in full of the Common 
Adjustment, then such remaining assets shall be distributed ratably to the 
holders of Common Stock.

         (C) In the event the Corporation shall at any time after the Rights 
Declaration Date (i) declare any dividend on Common Stock payable in shares 
of Common Stock, (ii) subdivide the outstanding Common Stock, or (iii) 
combine the outstanding Common Stock into a smaller number of shares, by 
reclassification or otherwise, then in each such case the Adjustment Number 
in effect immediately prior to such event shall be adjusted by multiplying 
such Adjustment Number by a fraction the numerator of which is the number of 
shares of Common Stock outstanding immediately after such event and the 
denominator of which is the number of shares of Common Stock that were 
outstanding immediately prior to such event.

         7.   CONSOLIDATION, MERGER, ETC. In case the Corporation shall enter 
into any consolidation, merger, combination or other transaction in which the 
shares of Common Stock are exchanged for or changed into other stock or 
securities, cash and/or any other property, then in any such case the shares 
of Series A Participating Preferred Stock shall at the same time be similarly 
exchanged or changed in an amount per share (subject to the provision for 
adjustment hereinafter set forth) equal to 1,000 times the aggregate amount 
of stock, securities, cash and/or any other property (payable in kind), as 
the case may be, into which or for which each share of Common Stock is 
changed or exchanged. In the event the Corporation shall at any time after 
the Rights Declaration Date (i) declare any dividend on Common Stock payable 
in shares of Common Stock, (ii) subdivide the outstanding Common Stock, or 
(iii) combine the outstanding Common Stock into a smaller number of shares, 
then in each such case the amount set forth in the preceding sentence with 
respect to the exchange or change of shares of Series A Participating 
Preferred Stock shall be adjusted by multiplying such amount by a fraction 
the numerator of which is the number of shares of Common Stock outstanding 
immediately after such event and the denominator of which is the number of 
shares of Common Stock that are outstanding immediately prior to such event.

         8.   REDEMPTION. The shares of Series A Participating Preferred 
Stock shall not be redeemable.

         9.   RANKING. The Series A Participating Preferred Stock shall rank 
junior to all other series of the Corporation's Preferred Stock as to the 
payment of dividends and the distribution of assets, unless the terms of any 
such series shall provide otherwise.

         10.  AMENDMENT. The Certificate of Incorporation and the Bylaws of 
the Corporation shall not be further amended in any manner which would 
materially alter or change the powers, preferences or special rights of the 
Series A Participating Preferred Stock so as to affect them adversely without 
the affirmative vote of the holders of at least 66-2/3% of the outstanding 
shares of Series A Participating Preferred Stock voting separately as a class.

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         11.  FRACTIONAL SHARES. Series A Participating Preferred Stock may 
be issued in fractions of a share which shall entitle the holder, in 
proportion to such holder's fractional shares, to exercise voting rights, 
receive dividends, participate in distributions and to have the benefit of 
all other rights of holders of Series A Participating Preferred Stock.

         IN WITNESS WHEREOF, we have executed and subscribed this Certificate 
and do affirm the foregoing as true under the penalties of perjury this 17th 
day of November, 1998.



                                         /s/ Howard C. Birndorf           
                                        ------------------------------------
                                        Howard C. Birndorf,
                                        Chief Executive Officer 


                                        Attest:


                                         /s/ Harry J. Leonhardt          
                                        ------------------------------------
                                        Harry J. Leonhardt, Secretary


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