Document:

Warrant to Purchase Common Stock

 EXHIBIT 10.10 
  
 NEITHER THIS WARRANT NOR THE SHARES OF STOCK ISSUABLE UPON EXERCISE HEREOF, HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED. NO SALE, TRANSFER OR OTHER DISPOSITION OF THIS WARRANT OR SAID SHARES MAY BE EFFECTED WITHOUT (i) AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (ii) AN OPINION OF COUNSEL FOR THE HOLDER, REASONABLY SATISFACTORY OR (iii) RECEIPT OF A
NO-ACTION LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION TO THE EFFECT THAT REGISTRATION UNDER THE ACT IS NOT REQUIRED. 
  
 Shares Issuable Upon Exercise: Up to 323,850 
  
 WARRANT TO PURCHASE COMMON STOCK 
 OF

 NANOGEN, INC. 
  
 Expires June 6, 2008 
  
 THIS CERTIFIES THAT, for value received, Aventis Pharma Deutschland GmbH, a German limited liability company (“Aventis”) or its
registered assigns (Aventis or its registered assigns shall hereinafter be referred to as “Holder”), is entitled, subject to the terms and conditions set forth below, to subscribe for and purchase up to 323,850 shares (as adjusted
pursuant to the provisions hereof, the “Shares”) of the fully paid and nonassessable common stock (“Common Stock”), par value $.001 per share, of Nanogen, Inc., a Delaware corporation (the
“Company”) at an exercise price per share of $5.618 (such price and such other price as shall result, from time to time, from adjustments specified herein is referred to as the “Exercise Price”). The term
“Warrant” as used herein shall mean this Warrant, and any warrants delivered in substitution or exchange therefor as provided herein. This Warrant is being issued pursuant to the Cooperation and Shareholders’ Agreement among
Aventis Research and Technologies Verwaltungs GmbH & Co. KG, Nanogen, Inc., a Delaware corporation and Nanogen Recognomics GmbH, a German limited liability company, dated June 30, 2001 (the “Shareholders’ Agreement”)

  
 1.    Term. Subject to the terms
and conditions set forth herein, this Warrant is exercisable, in whole or in part, at any time and from time to time from and after June 6, 2003 (the “Grant Date”) and prior to 5:00 p.m., Pacific Standard Time on the date above that
is the fifth anniversary of the Grant Date (the “Exercise Period”) and shall be void thereafter. 
  
 2.    Method of Exercise; Net Issue Exercise. 
  
 (a)    Method of Exercise; Payment; Issuance of New Warrant. This Warrant may be exercised by the
Holder, by either, at the election of the Holder, (i) the surrender of this Warrant to the Company (with the Notice of Exercise attached hereto as Exhibit A-1 duly completed and executed on behalf of the Holder), at the principal office of the
Company and by payment to the 

  

 -1- 

 
Company, for the account of the Company, by check or wire transfer of immediately available funds to a bank account specified by the Company, of an amount
equal to the Exercise Price multiplied by the number of Shares then being purchased as specified in the Exercise Form in lawful money of the United States of America or (ii) if in connection with a registered public offering of the Company’s
securities, the surrender of this Warrant (with the Notice of Exercise attached hereto as Exhibit A-2 duly completed and executed on behalf of Holder) at the principal office of the Company and by payment to the Company, for the account of the
Company, by check, wire transfer of immediately available funds to a bank account specified by the Company or from the proceeds of the sale of Shares to be sold by the Holder in such public offering of an amount equal to the Exercise Price
multiplied by the number of Shares then being purchased as specified in the Exercise Form in lawful money of the United States of America. The Company agrees that such Shares shall be deemed to be issued to the Holder as the record holder of such
Shares as of the close of business on the date on which this Warrant shall have been surrendered and payment made for the Shares as aforesaid (the “Exercise Date”). A stock certificate or certificates for the Shares specified in the
Notice of Exercise shall be delivered to the Holder as soon as practicable, and in any event within 30 days thereafter. If this Warrant shall have been exercised only in part, the Company shall, at the time of delivery of the stock certificate or
certificates, deliver to the Holder a new Warrant evidencing the rights to purchase the remaining Shares, which new Warrant shall in all other respects be identical with this Warrant. No adjustments shall be made on Shares issuable on the exercise
of this Warrant for any cash dividends paid or payable to holders of record of common stock prior to the date as of which the Holder shall be deemed to be the record holder of such Shares. However, the number of Shares shall be adjusted to reflect
any stock dividend, stock split or other conversion of the number of shares of the Company into a different number of shares, however denominated, as described in Section 3. 
  
 (b)    Net Issue Exercise. In lieu of exercising this Warrant pursuant to Section 2(a), the
Holder may elect to receive, without payment by the Holder of any additional consideration, shares equal to the value of this Warrant or any portion hereof by the surrender of this Warrant or such portion to the Company (with the Notice of Exercise
attached hereto as Exhibit A-1 hereto duly completed and executed) at the principal office of the Company. Thereupon, the Company shall issue to the Holder such number of fully paid and nonassessable shares of Common Stock as is computed using the
following formula: 
  
 X = Y (A-B) 
         A 
  
 where 
  
 X = the number of shares to be issued to the Holder 
        pursuant to this Section 2(b). 
  
 Y = the number of shares of common stock otherwise 
        issuable under this Warrant (as adjusted to the date 
        of such calculation). 
  
 A = the closing stock price of one share of the 
        Company’s common stock as reported by the 
  

 -2- 

 Nasdaq National Market the business day 
 immediately prior to the Exercise. 
  
 B = the Exercise Price in effect under this Warrant at the 
 time the net issue election is made pursuant to this 
 Section 2(b). 
  
 3.    Adjustment of Warrant Price and Number of Shares. The number and kind of securities purchasable upon the exercise of the
Warrant and the Warrant Price shall be subject to adjustment from time to time upon the occurrence of certain events, as follows: 
  
 (a)    Reclassification or Merger. In case of any reclassification, change or conversion of securities of the class issuable
upon exercise of this Warrant (other than a change in par value, or from par value top no par value, or from no par value to par value, or as a result of a subdivision or combination), or in case of any merger of the Company with or into another
corporation (other than a merger with another corporation in which the Company is a continuing corporation and which does not result in any reclassification or change of outstanding securities issuable upon exercise of this Warrant), or in case of
any sale of all or substantially all of the assets of the Company, the Company, or such successor or purchasing corporation, as the case may be, shall execute a new Warrant) providing that the Holder of this Warrant shall have the right to exercise
such new Warrant and upon such exercise to receive, in lieu of each share of Common Stock theretofore issuable upon exercise of this Warrant, the kind and amount of shares of stock, other securities, money and property receivable upon such
reclassification, change or merger by a holder of one share of Common Stock. Such new Warrant shall provide for adjustments that shall be as nearly equivalent as may be practicable to the adjustments provided for in this Section 3. The provisions of
this Section 3(a) shall similarly apply to successive reclassification, changes, mergers and transfers. 
  
 (b)    Subdivisions or Combination of Shares. If the Company at any time while this Warrant remains outstanding and unexpired
shall subdivide or combine its Common Stock, the Warrant Price and the number of shares issuable upon exercise hereof shall be proportionately adjusted. 
  
 (c)    Stock Dividends. If the Company at any time while this Warrant is outstanding and unexpired shall pay a dividend payable
in shares of Common Stock (except any distribution specifically provided for in Sections 3 (a) and (b)), then the Warrant Price shall be adjusted, from and after the date of determination of stockholders entitled to receive such dividend or
distribution, to that price determined by multiplying the Warrant Price in effect immediately prior to such date of determination by a fraction (i) the numerator of which shall be the total number of shares of Common Stock outstanding immediately
prior to such dividend or distribution, and (ii) the denominator of which shall immediately after such dividend or distribution and the number of Shares subject to this Warrant against impairment. 
  
 (d)    No Impairment. The Company will not, by
amendment of its Certificate 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 

  

 -3- 

 
avoid the observance or performance of any of the terms to be observed or performed hereunder by the Company, but will at all times in good faith assist in
the carrying out of all the provisions of this Section 3 and in the taking of all such actions as may be necessary or appropriate in order to protect the rights of the holder of this warrant against impairment. 
  
 (e)    Notices of Record Date. In any event in any
taking of the Company of a record of its stockholders for the purpose of determining stockholders who are entitled to receive payment of any dividend (other than cash dividend) or other distribution, any right to subscribe for, purchase or otherwise
acquire any share of any class or any other securities or property, or to receive any other right, or for the purpose of determining stockholders who are entitled to vote in connection with any proposed merger or consolidation of the Company with or
into any other corporation, or any proposed sale, lease or conveyance of all or substantially all of the assets of the Company, or any proposed liquidation, dissolution or winding up of the Company, the Company shall mail to the Holder of the
Warrant, at least 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. 
  
 4.    Notice of
Adjustments. Whenever the Warrant Price shall be adjusted pursuant to the provisions hereof, the Company shall within 20 days of such adjustment deliver a certificate signed by its chief financial officer to the registered holder(s) hereof
setting forth, in reasonable detail, the event requiring the adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and the Warrant Price after giving effect to such adjustment. 
  
 5.    No Fractional Shares or Scrip. No fractional
shares or scrip representing fractional shares shall be issued upon the exercise of this Warrant. In lieu of any fractional share to which the Holder would otherwise be entitled, the Company shall make a cash payment equal to the Exercise Price
multiplied by such fraction. 
  
 6.    Replacement of Warrant. On receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery
of an indemnity agreement reasonably satisfactory in form and substance to the Company or, in the case of mutilation, on surrender and cancellation of this Warrant, the Company at its expense shall execute and deliver, in lieu of this Warrant, a new
warrant of like tenor and amount. 
  
 7.    Rights of Stockholders. The Holder of this Warrant shall not be entitled to vote or receive dividends or be deemed the holder of common stock nor shall anything contained herein be construed to confer upon
the Holder, as such, any of the rights of a stockholder of the Company or any right to vote for the election of directors or upon any matter submitted to stockholders at any meeting thereof, or to give or withhold consent to any corporate action
(whether upon any recapitalization, issuance of stock, reclassification of stock, change of par value, or change of stock to no par value, consolidation, merger, conveyance, or otherwise) or to receive notice of meetings, or to receive dividends or
subscription rights or otherwise until the Warrant shall have been exercised as provided herein. 
  

 -4- 

 8.    Transfer of Warrant. 
  
 (a)    Warrant Register. The Company will maintain
a register (the “Warrant Register”) containing the names and addresses of the Holder or Holders. Any Holder of this Warrant or any portion thereof may change his address as shown on the Warrant Register by written notice to the
Company requesting such change. Any notice or written communication required or permitted to be given to the Holder may be delivered or given by mail to such Holder as shown on the Warrant Register and at the address shown on the Warrant Register.
Until this Warrant is transferred on the Warrant Register of the Company, the Company may treat the Holder as shown on the Warrant Register as the absolute owner of this Warrant for all purposes, notwithstanding any notice to the contrary.

  
 (b)    Warrant Agent. The Company
may, by written notice to the Holder, appoint an agent for the purpose of maintaining the Warrant Register referred to in Section 8(a) above, issuing the common stock, exchanging this Warrant, replacing this Warrant, or any or all of the foregoing.
Thereafter, any such registration, issuance, exchange, or replacement, as the case may be, shall be made at the office of such agent. 
  
 (c)    Transferability and Nonnegotiability of Warrant. This Warrant may not be transferred or assigned in whole or in part
without compliance with all applicable federal and state securities laws by the transferor and the transferee (including the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, if such are
requested by the Company). Notwithstanding the foregoing, no investment representation letter or opinion of counsel shall be required for any transfer of this Warrant (or any portion thereof) or any shares of common stock issued upon exercise hereof
(i) in compliance with Rule 144 or Rule 144A of the Act, or (ii) by gift, will or intestate succession by the Holder to his or her spouse or lineal descendants or ancestors or any trust for any of the foregoing; provided that in each of the
foregoing cases the transferee agrees in writing to be subject to the terms of this Section 8(c). In addition, if the holder of the Warrant (or any portion thereof) or any common stock issued upon exercise hereof delivers to the Company an
unqualified opinion of counsel that no subsequent transfer of such Warrant or common stock shall require registration under the Act, the Company shall, upon such contemplated transfer, promptly deliver new documents/certificates for such Warrant or
common stock that do not bear the legend set forth in Section 8(e)(ii) below. Subject to the provisions of this Warrant with respect to compliance with the Securities Act of 1933, as amended (the “Act”), title to this Warrant may be
transferred by endorsement (by the Holder executing the Assignment Form attached hereto as Exhibit B) and delivery in the same manner as a negotiable instrument transferable by endorsement and delivery. 
  
 (d)    Exchange of Warrant Upon a Transfer. On
surrender of this Warrant for exchange, properly endorsed on the Assignment Form and subject to the provisions of this Warrant with respect to compliance with the Act and with the limitations on assignments and transfers and contained in this
Section 8, the Company shall issue to or on the order of the Holder a new warrant or warrants of like tenor, in the name of the Holder or as the Holder (on payment by the Holder of any applicable transfer taxes) may direct, for the number of shares
issuable upon exercise hereof. 
  

 -5- 

 (e)    Compliance with Securities Laws. 
  
 (i)    The Holder of this Warrant
represents and warrants to the Company that it is an accredited investor under the Act. The Holder represents and warrants to the Company that it has all of the information necessary for it to evaluate an investment in the Company’s securities.

  
 (ii)    The Holder of this
Warrant, by acceptance hereof, acknowledges that this Warrant and the shares of common stock to be issued upon exercise hereof are being acquired solely for the Holder’s own account and not as a nominee for any other party, and for investment,
and that the Holder will not offer, sell or otherwise dispose of this Warrant or any shares of common stock to be issued upon exercise hereof except under circumstances that will not result in a violation of the Act or any applicable state
securities laws. Upon the exercise of this Warrant, the Holder shall, if requested by the Company, confirm in writing, in a form satisfactory to the Company, that the shares of common stock so purchased are being acquired solely for the
Holder’s own account and not as a nominee for any other party, for investment, and not with a view toward distribution or resale. 
  
 (iii)    This Warrant and all shares of common stock issued upon exercise hereof shall be stamped or imprinted with a
legend in substantially the following form (in addition to any legend required by state securities laws): 
  
 “NEITHER THIS WARRANT NOR THE SHARES OF STOCK ISSUABLE UPON EXERCISE HEREOF, HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. NO
SALE, TRANSFER OR OTHER DISPOSITION OF THIS WARRANT OR SAID SHARES MAY BE EFFECTED WITHOUT (i) AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (ii) AN OPINION OF COUNSEL FOR THE HOLDER, REASONABLY SATISFACTORY OR (iii) RECEIPT OF A NO-ACTION
LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION TO THE EFFECT THAT REGISTRATION UNDER THE ACT IS NOT REQUIRED.” 
  
 (iv)    The Company agrees to remove promptly, upon the request of the holder of this Warrant and Securities issuable
upon exercise of the Warrant, the legend set forth in Section 8(e)(ii) above from the documents/certificates for such securities upon full compliance with this Agreement and Rules 144 and 144A. 
  
 9.    Reservation of Stock. The Company covenants
that, the Company will reserve from its authorized and unissued common stock a sufficient number of shares to provide for the issuance of common stock upon the exercise of this Warrant (including any adjustment in the number of Shares pursuant to
Section 2(a)). The Company further covenants that all shares that may be issued upon the exercise of rights represented by this Warrant and payment of the Exercise Price, all as set forth herein, will be free from all taxes, liens and charges in
respect of the issue thereof (other than taxes in respect of any transfer occurring contemporaneously or 

  

 -6- 

 
otherwise specified herein). The Company agrees that its issuance of this Warrant shall constitute full authority to its officers who are charged with the
duty of executing stock certificates to execute and issue the necessary certificates for shares of common stock upon the exercise of this Warrant. 
  
 10.    Registration on Form S-3. 
  
 (a)    The Company shall use its best efforts to qualify for registration on Form S-3 or any comparable or successor form or forms.
After the Company has qualified for the use of Form S-3, Holder shall have the right to request one or more registrations on Form S-3 (such requests shall be in writing and shall state the number of Shares to be disposed of and the intended methods
of disposition of such shares by Holder), provided, however, that the Company shall not be obligated to effect any such registration if (i) Holder proposes to sell Shares on Form S-3 at an aggregate price to the public of less than $3,000,000, or
(ii) in the event the Company shall furnish the certification described in Section 10(d)(ii) (but subject to the limitations set forth therein), or (iii) the Company has, within the one year period preceding the date of such request already effected
one registration on Form S-3 for the Holders pursuant to this Section 10. 
  
 (b)    If a request complying with the requirements of Section 10(a) hereof is delivered to the Company, the provisions of Sections 10(a)(i) and (ii) and Section 10(c) hereof shall apply to such
registration. If the registration is for an underwritten offering, the provisions of Sections 10(b) hereof shall apply to such registration. 
  
 (c)    The Company shall not be obligated to effect, or to take any action to effect, any such registration pursuant to this Section
10: 
  
 (i)    In any
particular jurisdiction in which the Company would be required to execute a general consent to service of process in effecting such registration, qualification, or compliance, unless the Company is already subject to service in such jurisdiction and
except as may be required by the Act; 
  
 (ii)    During the period starting with the date 60 days prior to the Company’s good faith estimate of the date of filing of, and ending on a date 180 days after the effective date of, a Company-initiated
registration; provided that the Company is actively employing in good faith all reasonable efforts to cause such registration statement to become effective; 
  
 (d)    Subject to the foregoing clauses (i) and (ii), the Company shall file a registration statement covering the Shares so requested
to be registered as soon as practicable after receipt of the request of Holder; provided, however, that if (i) in the good faith judgment of the Board of Directors of the Company, such registration would be seriously detrimental to the Company and
the Board of Directors of the Company concludes, as a result, that it is essential to defer the filing of such registration statement at such time, and (ii) the Company shall furnish to Holder a certificate signed by the President of the Company
stating that in the good faith judgment of the Board of Directors of the Company, it would be seriously detrimental to the Company for such registration statement to be filed in the near future and that it is, therefore, essential to defer the
filing of such registration statement, then the Company shall have the right to defer such filing 

  

 -7- 

 
for the period during which such disclosure would be seriously detrimental, provided that (except as provided in clause (c) above) the Company may not defer
the filing for a period of more than 180 days after receipt of the request of Holder, and, provided further, that the Company shall not defer its obligation in this manner more than once in any twelve month period. 
  
 11.    Expenses of Registration. All Registration
Expenses (as defined herein) incurred in connection with any registration, qualification or compliance pursuant to Section 10 hereof and reasonable fees of one counsel for Holder shall be borne by the Company. All Selling Expenses (as defined
herein) relating to securities so registered shall be borne by the holders of such securities pro rata on the basis of the number of shares of securities so registered on their behalf. “Registration Expenses” shall mean all
expenses incurred in effecting any registration pursuant to this Warrant, including, without limitation, all registration, qualification, and filing fees, printing expenses, escrow fees, fees and disbursements of counsel for the Company, fees and
disbursements of one special counsel for the selling stockholders, blue sky fees and expenses, accounting fees and expenses of any regular or special audits incident to or required by any such registration, but shall not include Selling Expenses and
fees and disbursements of additional counsel for the stockholders. Registration Expenses do not include the compensation of regular employees of the Company, which shall be paid in any event by the Company. “Selling Expenses” shall
mean all underwriting discounts and selling commissions applicable to the sale of Shares and fees and disbursements of counsel for any Holder (other than the fees and disbursements of counsel included in Registration Expenses). 
  
 12.    Amendments. This Warrant and any term
hereof may be changed, waived, discharged or terminated only by an instrument in writing signed by the party against which enforcement of such change, waiver, discharge or termination is sought. 
  
 13.    Miscellaneous. 
  
 (a)    Governing Law. This Warrant shall
constitute a contract under the laws of the State of California and for all purposes shall be construed in accordance with and governed by the laws of said state, without regard to the conflicts of law provisions thereof. 
  
 (b)    Attorneys’ Fees; Litigation Expenses.
In the event of a dispute with regard to the interpretation of this Warrant, the prevailing party may collect the cost of attorney’s fees, litigation expenses or such other expenses as may be incurred in the enforcement of the prevailing
party’s rights hereunder. 
  
 (c)    Transfer Restrictions. The rights to cause the Company to register securities granted to a Holder by the Company under Section 10 may be transferred or assigned by Holder only to a transferee or assignee of
not less than 100,000 Shares, provided that the Company is given written notice at the time of or within a reasonable time after such transfer or assignment, stating the name and address of the transferee or assignee and identifying the securities
with respect to which such registration rights are being transferred or assigned, and, provided further, that the transferee or assignee of such rights assumes the obligations of such Holder under this Warrant. 
  

 -8- 

 (d)    Expiration Date. This Warrant shall be exercisable as provided for
herein, except that in the event that the expiration date of this Warrant shall fall on a Saturday, Sunday or United States federally recognized Holiday, this expiration date for this Warrant shall be extended to 5:00 p.m. Pacific standard time on
the business day following such Saturday, Sunday or recognized Holiday. 
  
 IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by its one of its officers thereunto duly authorized. 
  
 Dated: June 6, 2003 
  
  
  

			
	NANOGEN, INC., a Delaware corporation
		
	By	 	/s/ HOWARD BIRNDORG
	 	 	

	 	 	 Howard C. Birndorf
 Chief Executive
Officer

  

 -9- 

 EXHIBIT A-1 
 NOTICE OF EXERCISE 
  

	To:	Nanogen, Inc.
                                        
                                        
                                        
                                Date:
                     

 10398 Pacific Center Court 
 San Diego, CA 92121 
 Attn: General Counsel 
  
 Dear Sir: 
  
 (1)    The undersigned hereby elects to purchase shares
of common stock of Nanogen, Inc. (the “Company”) either (check box): 
  
  ̈    pursuant to the terms of Section 2(a) of the attached Warrant, and tenders herewith
payment of the purchase price for such shares in full or 
  
  ̈    pursuant to the net issue provisions of Section 2(b) of the Warrant and surrenders the right to purchase
             shares of Common Stock pursuant to the Warrant. 
  
 (2)    In exercising this Warrant, the undersigned hereby confirms and acknowledges that the shares of common stock to be issued upon
conversion thereof are being acquired solely for the account of the undersigned and not as a nominee for any other party, or for investment, and that the undersigned will not offer, sell or otherwise dispose of any such shares of common stock except
under circumstances that will not result in a violation of the Securities Act of 1933, as amended, or any applicable state securities laws. 
  
 (3)    Please issue a certificate or certificates representing said shares of common stock in the name of the undersigned or in such
other name as is specified below: 
  

			
	 
		
	 	 	 
	 	 	

	 	 	(Name)

  

 -10- 

 (4)    Please issue a new Warrant for the unexercised portion of the attached Warrant
in the name of the undersigned or in such other name as is specified below: 
  

	
	 
	
	 
	

	(Name)

  

	
	 
	
	 
	

	Signature

  

			
	 
		
	Address:	 	 
	 	 	

	 	 	 
	 	 	

  

 -11- 

 EXHIBIT A-2 
 NOTICE OF EXERCISE 
 (PURSUANT TO REGISTRATION) 

	To:	Nanogen, Inc.
                                        
                                        
                                        
                                Date:
                     

 10398 Pacific Center Court 
 San Diego, CA 92121 
 Attn: General Counsel 
  
 Dear Sir: 
  
 (1)    Contingent upon and effective immediately prior to
the closing (the “Closing”) of the Company’s public offering contemplated by the Registration Statement on Form S-3, filed with the Securities and Exchange Commission on
                                , 20    , the
undersigned hereby elects to purchase
                                        
shares of Common Stock of the Company (or such lesser number of shares as may be sold on behalf of the undersigned at the Closing) pursuant to the terms of the attached Warrant. 
  
 (2)    Please deliver to the custodian for the selling stockholders a stock certificate representing
such              shares. 
  
 (3)    The undersigned has instructed the custodian for the selling stockholders to deliver to the Company
$                                 or, if less, the net proceeds due the
undersigned from the sale of shares in the aforesaid public offering. If such net proceeds are less than the purchase price for such shares, the undersigned agrees to deliver the difference to the Company prior to the Closing. 
  
 (4)    Please issue a certificate or certificates
representing said shares of common stock in the name of the undersigned or in such other name as is specified below: 
  

			
	 
		
	 	 	 
	 	 	

	 	 	(Name)

  

 -12- 

 (5)    Please issue a new Warrant for the unexercised portion of the attached Warrant
in the name of the undersigned or in such other name as is specified below: 
  

	
	 
	
	 
	

	(Name)

  

	
	 
	
	 
	

	Signature

  

			
	 
		
	Address:	 	 
	 	 	

	 	 	 
	 	 	

  

 -13- 

 EXHIBIT B 
 ASSIGNMENT FORM 

	To:	Nanogen, Inc.
                                        
                                        
                                        
                                Date:
                     

 10398 Pacific Center Court 
 San Diego, CA 92121 
 Attn: General Counsel 
  
 Dear Sir: 
  
 FOR VALUE RECEIVED, the undersigned registered owner of this Warrant hereby
sells, assigns and transfers unto the Assignee named below all of the rights of the undersigned under the within Warrant, with respect to the number of shares of common stock set forth below: 
  

					
	 Name of Assignee
	 	Address	 	No. of Shares
	
	 	
	 	

	 	 	 	 	 
	 	 	 	 	 
	 	 	 	 	 

  
 and does hereby irrevocably constitute
and appoint the General Counsel of Nanogen, Inc. (the “Company”) to make such transfer on the books of the Company, maintained for the purpose, with full power of substitution in the premises. 
  
 The undersigned also represents that, by assignment hereof, the Assignee
acknowledges that this Warrant and the shares of stock to be issued upon exercise hereof or conversion thereof are being acquired for investment and that the Assignee will not offer, sell or otherwise dispose of this Warrant or any shares of stock
to be issued upon exercise hereof or conversion thereof except under circumstances which will not result in a violation of the Securities Act of 1933, as amended, or any applicable state securities laws. Further, the Assignee has acknowledged that
upon exercise of this Warrant, the Assignee shall, if requested by the Company, confirm in writing, in a form satisfactory to the Company, that the shares of stock so purchased are being acquired for investment and not with a view toward
distribution or resale. 

	
	 
	
	 
	

	Signature (of Holder)

  

			
	 
		
	Address:	 	 
	 	 	

	 	 	 
	 	 	

  

 -14-Separation Agreement and Release of Claims - Ira Marks

 CONFIDENTIAL 
 EXHIBIT 10.25 
  
 SEPARATION AGREEMENT AND RELEASE OF CLAIMS 
  
 THIS SEPARATION AND RELEASE AGREEMENT (the “Agreement”), dated August 15, 2003 is entered into by IRA MARKS (“Executive”) and NANOGEN, INC., a Delaware corporation (the “Company”). 
  
 WHEREAS, Executive and the Company have had a business relationship wherein
Executive has been an officer, and employee of the Company; and 
  
 WHEREAS, Executive and the Company wish to end their relationship with all actual and potential disputes between them completely and amicably resolved: 
  

NOW, THEREFORE, in consideration of the mutual covenants contained herein, and in consideration of the amounts to be paid by the Company to Executive
under this Agreement, amounts which Executive is not otherwise entitled to receive, Executive and the Company hereby agree as follows: 
  
 1.    Resignation from Company. Until September 5, 2003 Executive shall continue to be an employee of the Company and be
entitled the all of the benefits and obligations connected therewith. Executive shall resign as an officer of the Company effective September 5, 2003 and shall no longer be employed as an employee of the Company effective September 5, 2003
(“Severance Date”). Executive agrees that at all times he is employed with the Company, he will fully and faithfully discharge the duties and responsibilities of his position with the Company, as requested by the Company’s President.
The Executive agrees that from and after the Severance Date, for a period of up to two (2) months (as requested by the Company’s President) the Executive shall assist the Company in transitioning his responsibilities to other employees of the
Company. Both parties acknowledge that such transition shall not require the Executive to do more than make introductions, facilitate meetings and attend telephonic meetings with employees of the Company. All such activities during the transition
period shall be via telephone and at both parties mutual convenience and shall not require Executive to travel. 
  
 2.    Severance Compensation. 
  
 (a)    Cash Payments. The Company will continue to pay Executive a salary of $17,500 per month through the Severance Date. Such
payments shall be made according to the customary and regular payroll policies then in effect for the Company. On September 5, 2003, the Company shall pay Executive all accrued vacation pay due through the Severance Date and the Company shall make a
lump sum payment equal to two (2) months salary to Executive plus Executive’s regular salary through the Severance Date via automatic deposit, all such payments shall be less standard tax withholdings and any other required deductions.

  

 -1- 

 CONFIDENTIAL 
  
 (b)    Extend Exercise Date for Certain Stock Options. On the Severance Date, Executive’s
vested incentive stock options and nonqualified stock options for 39,583 shares of the Company’s Common Stock with an exercise price of $5.35 per share and for 658 shares of the Company’s Commons Stock with an exercise price of $1.901 per
share shall remain exercisable for a period of two (2) years from the Severance Date, subject to the restrictions described below in Section 5. Any incentive stock options held by Executive with an exercise price below the closing price of the
Company’s Common Stock on the Severance Date shall become nonqualified stock options on the Severance Date and any incentive stock options with an exercise price above the closing price of the Company’s Common Stock on the Severance Date
shall remain incentive stock options for up to three (3) months after the Severance Date and thereafter shall become nonqualified stock options. Executive acknowledges and agrees that he must consult with his own tax advisor or attorney regarding
the appropriate tax treatment for all of his incentive stock options, nonqualified stock options and restricted stock options and that he is not depending on any employee of the Company to provide such advice. The Company agrees that in the event of
a reorganization, merger, acquisition or similar transaction, that the Executive’s stock options shall remain as options in the new entity (subject to dilution) and Executive shall not be required to exercise such options in order to
participate in such reorganization (it being the intent of the parties that such options shall remain as options in the new entity); provided, however that this sentence shall not apply to any such transaction that is ordered by a Federal or state
Court or any such transaction which would be prohibited by law or regulation if such options were offered in the new entity. 
  
 3.    Other Benefits. Other than as provided for in Section 2 and this Section 3, following the Severance Date, Executive shall
not be eligible to participate in any of the Company’s employee benefit plans (including, without limitation, the 401(k) plan), fringe benefit programs, and group insurance arrangements, except under COBRA, the stock option agreements and stock
vesting programs described in Section 2 (b) for the periods described therein. 
  
 4.    Tax Liability. Executive shall be responsible for all tax liability associated with any payments made pursuant to Section 2 or Section 3, except as described herein. 
  
 5.    Non-Competition. As consideration for the
severance compensation described in Section 2 and in order to protect the Company’s trade secret and other “confidential information” of the Company as described below in Section 7, during a period of two (2) months from the Severance
Date, Executive shall not, other than with the prior written consent of the Board of Directors of the Company, engage, directly or indirectly, in any other business activity (whether or not pursued for pecuniary advantage) with a company currently
commercializing microarray technology for use in clinical molecular diagnostics, provided that Executive may own less than two percent of the outstanding securities of any such publicly traded competing corporation. Any violation by Executive of
this Section 5 shall result in the immediate cancellation of the extended exercise period for all options described in Section 2 and the Company may thereafter take whatever other legal steps it deems necessary to enforce 

  

 -2- 

 CONFIDENTIAL 
 this provision and protect the Company’s confidential information. 
  
 6.    Nonsolicitation. During a period of one (1) year after the Severance Date, Executive will not directly or indirectly engage, encourage or participate in the solicitations of any
employee or consultant of the Company to leave the Company for any reason or to devote less than all of any such employee’s efforts to the affairs of the Company. 
  
 7.    Nondisclosure. During the term of this Agreement and thereafter, Executive shall not,
without the prior written consent of management, disclose or use for any purpose (except in the course of his service under this Agreement and in furtherance of the business of the Company) confidential information or proprietary data of the
Company, except as required by applicable law or legal process; provided, however, that “confidential information” shall not include any information known generally to the public or ascertainable from public or published information (other
than as a result of unauthorized disclosure by Executive) or any information of a type not otherwise considered confidential by persons engaged in the same business or a business similar to that conducted by the Company. Executive agrees to deliver
to the Company at the termination of his service, or at any other time that the Company may request, all memoranda, notes, plans, records, reports and other documents (and copies thereof) relating to the business of the Company which he may then
possess or have under his control. Executive’s obligations to the Company under the Proprietary Information, Inventions and Dispute Resolution Agreement, dated December 17, 2001 by and between the Company and Executive (the “Proprietary
Inventions Agreement”) shall remain in full force and effect, notwithstanding the release contained herein. 
  
 8.    Release. Executive acknowledges that the severance package described herein is given in exchange for his signing this
Agreement, and he is not otherwise entitled to receive such benefits from the Company. Executive agrees that the severance package is in full satisfaction of any claims, liabilities, demands or causes of action, known or unknown and he hereby
releases and forever discharges the Company and each of its past and present directors, managers, officers, shareholders, agents, consultants, advisers, employees, attorneys, servants, parents, subsidiaries, employee benefit plans, predecessors,
successors and assigns, and each of them separately and collectively (the “Releasees”) from any and all claims, liens, demands, causes of action, obligations, damages and liabilities of any nature whatsoever, known or unknown, that he ever
had, now has or may hereafter claim to have against the Releasees. The release includes, but is not limited to: 
  
 (a)    any and all claims relating to mental, physical or emotional injuries sustained from invasion of privacy, to defamation, to
interference with prospective economic advantage, to intentional or negligent infliction of emotional distress, to Executive’s employment or nonemployment by the Company, to the termination of his employment, to any status, term or condition in
such employment, or to any physical or mental harm or distress from such employment or from termination of such employment;: 
  
 (b)    any and all claims under California statutory or decisional law pertaining to 

  

 -3- 

 CONFIDENTIAL 
  
 wrongful discharge, discrimination, retaliation or breach of contract or breach of public policy; 
  
 (c)     any and all claims under the Fair Employment and
Housing Act, Title VII of the Civil Rights Act of 1964 or the Americans with Disabilities Act; 
  
 (d)    any and all claims for costs, expenses or attorneys’ fees; 
  
 (e)    any claims to rehire rights; provided, however, that claims for vested benefits and claims for workers’ compensation and
unemployment insurance benefits are not waived; and 
  
 (f)    any and all claims relating to the tax obligation for which Executive may become liable as a result of this release or the payment of consideration referred to above. 
  
 Execution of this Agreement does not bar any claims for breach of this
Agreement. The Company releases Executive from any claims it may have against Executive prior to the date of this Agreement, including (but not limited to) such claims as are specified in this Section 8. This Agreement recognizes the rights and
responsibilities of the Equal Employment Opportunity Commission (“EEOC”) to enforce the statutes which come under its jurisdiction and is not intended to prevent Executive from participating in any investigation or proceeding conducted by
the EEOC; provided, however, that nothing in this section limits or affects the finality or the scope of the release provided in this Section 8, the waiver provided in Section 9 or the agreement to submit claims to final and binding arbitration.

  
 (g)    Opportunity to Revoke.
Executive acknowledges that he is aware that he has twenty-one (21) calendar days to decide whether to enter into this agreement and release of claims, and return this executed agreement to the Company. Executive agrees that he was offered
twenty-one (21) calendar days to consider this agreement and release. This period is designed to allow Executive to consult with a financial advisor, accountant, attorney or anyone else whose advice Executive needs. Executive should consult
appropriate advisors, including an attorney, during this period. 
  
 Executive further acknowledges that he is aware that he may revoke this agreement and release of claims within seven (7) business days after it is signed and received by the Company. He further agrees that he is aware that in the event he
timely exercises his right of rescission he will have no rights to the severance payment or other rights under this Agreement offered by the Company. . 
  
 9.    Waiver. The parties expressly waive all rights under Section 1542 of the Civil Code of California which provides:

  
 “A general release does not extend to claims which the
creditor does not know or suspect to exist in his favor at the time of executing the release, which if known by him must have materially affected his settlement with 
  

 -4- 

 CONFIDENTIAL 
  
 the debtor.” 
  
 The parties agree that the possibility that such unknown claims exist was taken into account in determining the amount of consideration to be paid for the
giving of this Agreement. 
  
 10.    Covenant Not To Sue. Executive covenants and agrees that he will never, individually or with any person or in any way, commence or aid in any way, except as required by due legal process, prosecute or cause
or permit to be commenced or prosecuted, any action or other proceeding based upon any claim which is the subject of this Agreement. This Agreement shall be deemed breached and a cause of action shall be deemed to have accrued immediately upon the
commencement or prosecution of any action or proceeding contrary to this Agreement. Executive agrees that if he brings an action to challenge the enforceability of this Agreement, he will tender to a neutral escrow, as designated by the Company, all
consideration that he received pursuant to this Agreement. 
  
 In
the event of any breach of this Section 10, the Company shall be entitled to recover not only the amount of judgment which may be awarded against such releasee, but also all such other damages, costs and expenses as may be incurred by such releasee,
including court costs, attorneys’ fees and all costs and expenses, taxable or otherwise, in preparing the defense of or defending against, or seeking or obtaining an abatement of or injunction against, any action or proceeding brought in
violation of this Section 10 and in prosecuting any claim, counterclaim or cross-claim based hereon. 
  
 11.    No Assignment; Authority. The parties represent and warrant that no other person had or has or claims any interest in
the claims referred to in Section 8 above; that they have the sole right and exclusive authority to execute this Agreement; that they have the sole right to receive the consideration paid therefor; and that they have not sold, assigned, transferred,
conveyed or otherwise disposed of any claim or demand relating to any matter covered by this Agreement. 
  
 12.    No Admission. The parties acknowledge that the payment of consideration, referred to herein, is made solely for the
purpose of purchasing peace and eliminating possible involvement in protracted litigation based upon disputed claims that the other could make and does not constitute an admission or concession of any liability on account of any of said claims,
liability for which is expressly denied by all releasees. 
  
 13.    Confidentiality. The parties covenant and agree to maintain the confidentiality of the existence and terms of this Agreement, including (without limitation) the nature and payment of consideration referred
to in this Agreement and to make no voluntary statement, except as may be necessary for the purposes of audit, taxation returns or other disclosures required by law. 
  
 14.    Miscellaneous Provisions. 
  

 -5- 

 CONFIDENTIAL 
  
 (a)    Notice. Notices and all other communications contemplated by this Agreement shall be in
writing and shall be deemed to have been duly given when personally delivered or when mailed by U.S. certified mail, return receipt requested and postage prepaid. In the case of Executive, mailed notices shall be addressed to him at the home address
which he most recently communicated to the Company in writing. In the case of the Company, mailed notices shall be addressed to its corporate headquarters, and all notices shall be directed to the attention of its Assistant Secretary. 
  
 (b)    Waiver. No provision of this Agreement
shall be modified, waived or discharged unless the modification, waiver or discharge is agreed to in writing and signed by Executive and by an authorized officer of the Company. No waiver by either party of any breach of, or of compliance with, any
condition or provision of this Agreement by the other party shall be considered a waiver of any other condition or provision or of the same condition or provision at another time. 
  
 (c)    Whole Agreement. No agreements (including any employment agreement), representations or
understandings (whether oral or written and whether express or implied) which are not expressly set forth in this Agreement have been made or entered into by either party with respect to the subject matter hereof, except that the Proprietary
Inventions Agreement shall remain in full force and effect. 
  
 (d)    Choice of Law. The validity, interpretation, construction and performance of this Agreement shall be governed by the laws of the State of California (other than choice-of-law provisions). 
  
 (e)    Arbitration. Any dispute arising out of or
relating to this Agreement, or the breach termination or validity thereof (including the determination of the interpretation or scope of this agreement to arbitrate), shall be resolved first by mediation pursuant to the Employment Mediation Rules of
the American Arbitration Association. If mediation is not successful, then the dispute shall be resolved by a single neutral arbitrator in binding arbitration administered by the American Arbitration Association under its Rules for the Resolution of
Employment Disputes. The arbitration shall take place in San Diego, California, and judgment upon the award rendered by the arbitrator may be entered by any court having jurisdiction thereof. The Company shall bear the costs of arbitration if
Executive prevails. If the Company prevails, Executive shall pay half the cost of the arbitration or $500.00, whichever is less. Each party shall pay its own attorneys’ fees, unless the arbitrator orders otherwise, pursuant to applicable law,
except as provided in Section 10. 
  
 (f)    Consultation with Counsel. Executive acknowledges that he has been advised and had the opportunity to consult legal counsel prior to signing this Agreement and that he is entering into this Agreement
knowingly and voluntarily. 
  
 (g)    Severability. The invalidity or unenforceability of any provision of this Agreement shall not affect the validity or enforceability of any other provision hereof, which 

  

 -6- 

 CONFIDENTIAL 
  
 shall remain in full force and effect. 
  
 (h)    Assignment and Successors. Neither party shall assign any right or delegate any obligation hereunder without the other
party’s written consent, and any purported assignment or delegation by a party hereto without the other party’s written consent shall be void. This Agreement shall be binding upon and inure to the benefit of the Company and its successors
and Executive, his heirs, executors, administrators and legal representatives. 
  
 IN WITNESS WHEREOF, each of the parties has executed this Agreement, in the case of the Company by its duly authorized officer. 
  

			
	 
		
	By:	 	 /s/    Ira Marks        

	 	 	

	 	 	 Ira Marks

  

			
	NANOGEN, INC.
		
	By:	 	 /s/    Bruce A. Huebner        

	 	 	

	 	 	 Bruce A. Huebner
 Chief Operating Officer

  

 -7-

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00064-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00064-of-00352.parquet"}]]