Document:

EX-4.5

 Exhibit 4.5 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD,
PLEDGED, OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR PURSUANT TO RULE 144 OR AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE CORPORATION AND ITS COUNSEL, THAT SUCH REGISTRATION IS NOT REQUIRED. 

WARRANT TO PURCHASE STOCK 

Issuer: BIONANO GENOMICS, INC., a Delaware corporation (the “Company”) 

Number of Shares: 510,417, as the same may be from time to time adjusted pursuant to Article 2 hereof. 

Class of Stock: Series D Convertible Participating Preferred Stock, as the same may be from time to time adjusted pursuant to Article 2
hereof (the “Shares”) 
 Exercise Price: $0.48 per share, as the same may be from time to time adjusted pursuant to Article 2
hereof (the “Exercise Price”). 
 Issue Date: March 8, 2016 

Expiration Date: March 8, 2026 
 THIS
WARRANT CERTIFIES THAT, for the agreed upon value of $1.00 and for other good and valuable consideration, WESTERN ALLIANCE BANK, an Arizona corporation (“Holder”) is entitled to purchase the number of fully paid and nonassessable Shares of
the Company at the Exercise Price per Share set forth, subject to the provisions and upon the terms and conditions set forth in this Warrant. 
 ARTICLE 1
EXERCISE. 
 1.1 Method of Exercise. This Warrant is exercisable, in whole or in part, at any time and from time to
time on or before the Expiration Date set forth above. Holder may exercise this Warrant by delivering this Warrant and a duly executed Notice of Exercise, in substantially the form attached as Appendix 1, to the principal office of Company. Unless
Holder is exercising the conversion right set forth in Section 1.2, Holder shall also deliver to Company a check for the aggregate Exercise Price for Shares being purchased. 

1.2 Conversion Right. In lieu of exercising this Warrant as specified in Section 1.1, Holder may from time to time
convert this Warrant, in whole or in part, into a number of Shares determined by dividing (a) the aggregate fair market value of Shares or other securities otherwise issuable upon exercise of this Warrant minus the aggregate Exercise Price of
such Shares by (b) the fair market value of one Share. The fair market value of Shares shall be determined pursuant to Section 1.3. 

1.3 Fair Market Value. If the Shares are traded in a public market, the fair market value of the Shares shall be the
closing price of the Shares (or the closing price of the Company’s stock into which the Shares are convertible) reported for the business day immediately before Holder delivers its Notice of Exercise to the Company. If the Shares are not traded
in a public market, the Board of Directors of Company shall determine fair market value in its reasonable good faith judgment. The foregoing notwithstanding, if Holder advises the Board of Directors in writing that Holder disagrees with such
determination, then Company and Holder shall promptly agree upon a reputable valuation firm to undertake such valuation. If the valuation determined by such valuation firm is greater than that determined by the Board of Directors, then all fees and
expenses of such valuation firm shall be paid by Company. In all other circumstances, such fees and expenses shall be paid by Holder. 

1.4 Delivery of Certificate and New Warrant. Promptly after Holder exercises or converts this Warrant, Company shall
deliver to a Holder certificate for Shares acquired and, if this Warrant has not been fully exercised or converted and has not expired, a new Warrant representing Shares not so acquired. 

1.5 Replacement of Warrants. On receipt of evidence reasonably satisfactory to 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 amount to Company or, in the case of mutilation, on surrender and cancellation of this Warrant,
Company at its expense shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor. 

  
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 1.6 Repurchase on Sale, Merger, or Consolidation of Company. For the
purpose of this Warrant, “Acquisition” means any sale, license, or other disposition of all or substantially all of the assets of Company, or any reorganization, consolidation, sale of securities or merger of Company where the holders of
Company’s securities before the transaction beneficially own less than 50% of the outstanding voting securities of the surviving entity after the transaction. Upon the closing of any Acquisition, the successor entity shall assume the
obligations of this Warrant, and this Warrant shall be exercisable for the same securities, cash, and property as would be payable for Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on the
record date for the Acquisition and subsequent closing, and the Exercise Price shall be adjusted accordingly; provided that if pursuant to such Acquisition the entire outstanding class of Shares issuable upon exercise of the unexercised
portion of this Warrant are converted into the right to receive consideration and the total consideration payable to the holders of such class of Shares consists entirely of cash, publicly traded securities or any combination thereof, then, upon
payment to the Holder of an amount equal to the amount such holder would receive if such holder held Shares issuable upon exercise of the unexercised portion of this Warrant and such Shares were outstanding on the record date for the Acquisition
less the aggregate Exercise Price of such Shares, this Warrant shall be cancelled. 
 ARTICLE 2 ADJUSTMENTS. 

2.1 Stock Dividends, Splits, Etc. If Company declares or pays a dividend on its common stock (or Shares if Shares are
securities other than common stock) payable in common stock or other securities or other property, subdivides the outstanding common stock into a greater amount of common stock, or, if Shares are securities other than common stock, subdivides Shares
in a transaction that increases the amount of common stock into which Shares are convertible, then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total number and kind of securities to which
Holder would have been entitled had Holder owned Shares on the record date on which the dividend or subdivision occurred. 

2.2 Reclassification, Recapitalization, Exchange or Substitution. Except in the case of an Acquisition to which
Section 1.6 is applicable, upon any reclassification, recapitalization, exchange, substitution, or other event that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this Warrant, Holder
shall be entitled to receive, upon exercise or conversion of this Warrant, the number and kind of securities and property that Holder would have received for Shares if this Warrant had been exercised immediately before such reclassification,
recapitalization, exchange, substitution, or other event. Company or its successor shall promptly issue to Holder a new Warrant for such new securities or other property. The new Warrant shall provide for adjustments which shall be as nearly
equivalent as may be practicable to the adjustments provided for in this Article 2 including, without limitation, adjustments to the Exercise Price and to the number of securities or property issuable upon exercise of the new Warrant. The provisions
of this Section 2.2 shall similarly apply to successive reclassifications, recapitalizations, exchanges, substitutions, or other events. 

2.3 Adjustments for Combinations, Etc. If the outstanding Shares are combined or consolidated, by reclassification or
otherwise, into a lesser number of shares, the Exercise Price shall be proportionately increased and the number of Shares as to which this Warrant is exercisable shall be proportionately decreased. 

2.4 Adjustments for Diluting Issuances. In the event of the issuance (a “Diluting Issuance”) by Company,
after the Issue Date of this Warrant, of securities at a price per share less than the then Exercise Price, then the number of shares of common stock issuable upon conversion of the Shares, and the conversion price, shall be adjusted in accordance
with those provisions (the “Provisions”) of Company’s Seventh Amended and Restated Certificate of Incorporation (as the same may be amended from time to time, the “Certificate of Incorporation”) which apply to Diluting
Issuances with the same effect as though the shares were outstanding at the time of the diluting issuance. Under no circumstances shall the aggregate Exercise Price payable by Holder upon exercise of this Warrant increase as a result of any
adjustment arising from a Diluting Issuance. 
 2.5 Adjustment for Pay-to-Play Transactions. In the event that the Certificate of Incorporation provides, or is amended to so provide, for the amendment or modification of the rights, preferences or privileges of the Shares, or
the reclassification, conversion or exchange of the outstanding shares of the Class of Stock, in the event that a holder of shares thereof fails to participate in an equity financing transaction (a 

  
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“Pay-to-Play Provision”), and in the event that such Pay-to-Play Provision becomes operative in a transaction occurring after the date hereof, this Warrant shall automatically and without any action required become exercisable for that number and type of shares
of equity securities as would have been issued or exchanged, or would have remained outstanding, in respect of the Shares issuable hereunder had this Warrant been exercised in full prior to such event, and had the Holder participated in the equity
financing to the maximum extent permitted. 
 2.6 No Impairment. Company shall not, by amendment of its Certificate
of Incorporation or through a reorganization, 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 under this Warrant by Company, but shall at all times in good faith assist in carrying out of all the provisions of this Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s rights under
this Article against impairment. If Company takes any dilutive action affecting Shares or its common stock other than as described above that adversely affects Holder’s rights under this Warrant, the Exercise Price shall be adjusted downward
and the number of Shares issuable upon exercise of this Warrant shall be adjusted upward in such a manner that such dilutive action is offset and the aggregate Exercise Price of this Warrant is unchanged. 

2.7 Fractional Shares. No fractional Shares shall be issuable upon exercise or conversion of this Warrant and the
number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise or conversion of this Warrant, Company shall eliminate such fractional share interest by paying Holder an amount
computed by multiplying the fractional interest by the fair market value of a full Share (as determined pursuant to Section 1.6 herein). 

2.8 Certificate as to Adjustments. Upon each adjustment of the Exercise Price, Company at its expense shall promptly
compute such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth such adjustment and the facts upon which such adjustment is based. Company shall, upon written request, furnish Holder a certificate setting
forth the Exercise Price in effect upon the date thereof and the series of adjustments leading to such Exercise Price. 
 ARTICLE 3 COVENANTS OF COMPANY.

 3.1 Valid Issuance. Company shall take all steps necessary to insure that all Shares which may be issued upon the
exercise of this Warrant, and all securities, if any, issuable upon conversion of Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except for restrictions on
transfer provided for herein or under applicable federal and state securities laws. 
 3.2 Notice of Certain Events.
If Company proposes at any time (a) to declare any dividend or distribution upon its common stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; (b) to offer for subscription pro rata to
the holders of any class or series of its stock any additional shares of stock of any class or series or other rights; (c) to effect any reclassification or recapitalization of common stock; (d) to effect an Acquisition; or (e) offer
holders of registration rights the opportunity to participate in an underwritten public offering of the company’s securities for cash, then, in connection with each such event, Company shall give Holder (1) in the case of the matters
referred to in (a) and (b) above at least 20 days prior written notice of the date on which a record will be taken for such dividend, distribution, or subscription rights (and specifying the date on which the holders of common stock will be
entitled thereto) or for determining rights to vote, if any, in respect of the matters referred to in (c) and (d) above; (2) in the case of the matters referred to in (c) and (d) above at least 20 days prior written notice of the date
when the same will take place (and specifying the date on which the holders of common stock will be entitled to exchange their common stock for securities or other property deliverable upon the occurrence of such event); and (3) in the case of
the matter referred to in (e) above, the same notice as is given to the holders of such registration rights. 
 3.3
Information. So long as the Holder holds this Warrant and/or any of the Shares, Company shall deliver to Holder (a) promptly, copies of all notices or other written communications to which Holder would be entitled if it held Shares as to
which this Warrant was then exercisable and (b) such other financial statements required under and in accordance with any loan documents between Holder and Company, or if there are no such requirements or if the subject loan(s) are no longer
are outstanding, then within 90 days after the end of 

  
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each of the first three quarters of each fiscal year, Company’s quarterly, unaudited financial statements and within 180 days after the end of each fiscal year, Company’s annual,
audited financial statements. 
 3.4 Notice of Expiration. Company shall give Holder written notice of Holder’s
right to exercise this Warrant in the form attached as Appendix 2 not more than 90 days and not less than 15 days before the Expiration Date and, in the case of an Acquisition to which the proviso of Section 1.6 shall be applicable, 15 days
before such Acquisition. If the notice is not so given, the Expiration Date shall automatically be extended until 15 days after the date Company delivers the notice to Holder. 

3.5 Registration Rights. The common stock issuable upon conversion of Shares, shall have the same “piggyback”
registration rights as are set forth in the Fourth Amended and Restated Investors’ Rights Agreement, dated as of March 4, 2016 between Company and its investors, as from time to time in effect (the “Investors’ Rights Agreement”
— a true copy of which as in effect on the date hereof has been furnished by Company to Holder) and by accepting this Warrant, Holder agrees to be subject to corresponding obligations of the holders of “piggyback” registration rights.
Company agrees that no amendments will be made to the Investors’ Rights Agreement which would have an adverse impact on Holder’s registration rights thereunder. 

ARTICLE 4 MISCELLANEOUS. 
 4.1
Legends. This Warrant and the Shares (and the securities issuable, directly or indirectly, upon conversion of Shares, if any) shall be imprinted with a legend in substantially the following form: 

THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED
WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR PURSUANT TO RULE 144 OR AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO COMPANY AND ITS COUNSEL THAT SUCH REGISTRATION IS NOT REQUIRED. 

4.2 Compliance with Securities Laws on Transfer. This Warrant and the Shares issuable upon exercise of this Warrant
(and the securities issuable, directly or indirectly, upon conversion of Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and state securities laws by the transferor and the transferee
(including, without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to Company, as reasonably requested by Company). Company shall not require Holder to provide an opinion of counsel if the
transfer is to Holder’s parent company, Western Alliance Bancorporation, or any other affiliate or successor of Holder, or if there is no material question as to the availability of current information as referenced in Rule 144(c), Holder
represents that it has complied with Rule 144(d) and (e) in reasonable detail, the selling broker represents that it has complied with Rule 144(f), and the Company is provided with a copy of Holder’s notice of proposed sale. 

4.3 Transfer Procedure. After receipt by Holder of the executed Warrant, Holder will transfer all of this Warrant to
Holder’s parent company, Western Alliance Bancorporation, by execution of an Assignment substantially in the form of Appendix 3. Subject to the provisions of Section 4.2 above and upon providing Company with written notice, Western
Alliance Bancorporation and any subsequent Holder may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or the Shares issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee,
provided, however, in connection with any such transfer, Western Alliance Bancorporation or any subsequent Holder will give the Company notice of the portion of this Warrant being transferred with the name, address and taxpayer identification number
of the transferee and Holder will surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable). Unless Company is filing financial information with the SEC pursuant to the Securities Exchange Act of 1934,
Company shall have the right to refuse to transfer any portion of this Warrant to any person who directly or indirectly competes with Company. 

4.4 Notices. All notices and other communications from Company to Holder, or vice versa, shall be in writing and shall
be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, or by overnight courier, at such address as may have been furnished to Company or Holder, as the case may be, in writing
by Company or such Holder from time to time. 
 4.5 Attorneys Fees. In the event of any dispute between the parties
concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees. 

  
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 4.6 Governing Law. This Warrant shall be governed by and construed in
accordance with the laws of the State of California, without giving effect to its principles regarding conflicts of law. 

4.7 Market Stand-Off Agreement. Holder hereby agrees that it shall not sell,
dispose of, transfer, make any short sale of, grant any option for the purchase of, or enter into any hedging or similar transaction with the same economic effect as a sale, any shares of the Company’s Common Stock or other securities held by
such Holder (other than those included in the registration) during (i) the 180-day period following the effective date of the Company’s first underwritten public offering of its Common Stock
registered under the Securities Act of 1933, as amended (the “Securities Act”) (or such longer period as the underwriters or the Company shall request in order to facilitate compliance with NASD Rule 2711 or NYSE Member Rule 472 or any
successor or similar rule or regulation), and (ii) the 90-day period following the effective date of a registration statement of the Company filed under the Securities Act (or such longer period as the
underwriters or the Company shall request in order to facilitate compliance with NASD Rule 2711 or NYSE Member Rule 472 or any successor or similar rule or regulation); provided, that, with respect to (i) and (ii) above, all officers and
directors of the Company are bound by and have entered into similar agreements. The underwriters of the Company’s stock are intended third party beneficiaries of this Section 4.7 and shall have the right, power and authority to enforce the
provisions hereof as though they were a party hereto. 
 [Balance of Page Intentionally Left Blank] 

  
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 IN WITNESS WHEREOF, Company has caused this Warrant to be duly executed by its
authorized officers, all as of the day and year first above written. 
  

			
	COMPANY
	
	BIONANO GENOMICS, INC.

 
			
		
	 By:
	 	 

 
			
	 Name:
	 	 
	 Title:
	 	 

 APPENDIX 1 

Notice of Exercise 
 [Strike
paragraph that does not apply.] 
 1. The undersigned hereby elects to purchase
            shares of the Common/Series             Preferred [strike one] Stock of BIONANO GENOMICS, INC. pursuant
to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full. 
 1. The undersigned
hereby elects to convert the attached Warrant into Shares/cash [strike one] in the manner specified in the Warrant. This conversion is exercised with respect to
                            of the Shares covered by the Warrant. 

2. Please issue a certificate or certificates representing said shares in the name of the undersigned or in such other name as is specified
below: 
  

			
	 Name:
	 	 
	 Address:
	 	 
	 

 3. The undersigned represents it is acquiring the shares solely for its own account and not as a nominee for
any other party and not with a view toward the resale or distribution thereof except in compliance with applicable securities laws. 
  

	
	
	   

	 (Signature)

	
	 
	 (Date)

 APPENDIX 2 

Notice that Warrant Is About to Expire 

[Insert Date of Notice] 
  

	To:	 BRIDGE BANK, A DIVISION OF WESTERN ALLIANCE BANK 

Attn:                    
             
 55 Almaden Boulevard 

San Jose, California 95113 

The Warrant issued to you described below will expire
on                         ,        . 

 

			
	 Issuer:
	  	 BIONANO GENOMICS, INC.

		
	 Issue Date:
	  	 March 8, 2016

		
	 Class of Security Issuable:
	  	
                       
 

		
	 Exercise Price per Share:
	  	 $        per share

		
	 Number of Shares Issuable:
	  	             

 Procedure for Exercise: 

Please
contact                    at
(    )            -            with any questions you may have concerning exercise of
the Warrant. This is your only notice of pending expiration. 
  

			
	 BIONANO GENOMICS, INC.

			
		
	 By
	 	 
	 Its:
	 	 

 APPENDIX 3 

Assignment 
 For value received,
WESTERN ALLIANCE BANK, an Arizona corporation hereby sells, assigns and transfers unto: 
  

			
	 Name:
	  	 WESTERN ALLIANCE BANCORPORATION

	 Address:
	  	 55 Almaden Boulevard

		  	 San Jose, California 95113

		
	 Tax ID:
	  	
                       
 

 that certain Warrant to Purchase Stock issued by BIONANO GENOMICS, INC. (the “Company”), on
March 8, 2016 (the “Warrant”) together with all rights, title and interest therein. 
  

			
	WESTERN ALLIANCE BANK, AN ARIZONA CORPORATION

 
			
		
	 By:
	 	 
	 Name:
	 	 
	 Title:
	 	 

  

			
	 Date:
	 	 

 By its execution below, and for the benefit of the Company, Western Alliance Bancorporation agrees to all
provisions of the Warrant as of the date hereof. 
  

			
	WESTERN ALLIANCE BANCORPORATION

 
			
		
	 By:
	 	 
	 Name:
	 	 
	 Title:EX-4.6

 Exhibit 4.6 

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT BE
SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO SUCH SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED. 

BIONANO GENOMICS, INC. 

WARRANT TO PURCHASE SERIES D PREFERRED STOCK 
  

			
	PD — [___]	 	[•], 2016

 VOID AFTER MARCH [•], 2026 

THIS CERTIFIES THAT, for value received,
[                            ] (the “Holder”), is entitled to subscribe
for and purchase from BIONANO GENOMICS, INC., a Delaware corporation, with its principal office at 9640 Towne Centre Drive, Suite 100, San Diego, CA 92121 (the
“Company”), an aggregate of [                        ] Exercise Shares at the Exercise Price (each
subject to adjustment as provided herein). This Warrant is part of a series of substantially similar warrants issued to certain persons and entities pursuant to the terms of that certain Series D Convertible Participating Preferred Stock and Warrant
Purchase Agreement dated as of March [•], 2016, by and among the Company and the purchasers listed therein (as may be amended from time to time, the “Purchase Agreement”). 

1. DEFINITIONS. As used herein, the following terms shall have the following respective meanings:

 (a) “Acquisition” shall mean (A) any consolidation or merger of the Company with or
into any other corporation or other entity or person, or any other corporate reorganization, other than any such consolidation, merger or reorganization in which the stockholders of the Company immediately prior to such consolidation, merger or
reorganization, continue to hold at least a majority of the voting power of the surviving entity in substantially the same proportions (or, if the surviving entity is a wholly owned subsidiary, its parent) immediately after such consolidation,
merger or reorganization; or (B) any transaction or series of related transactions in which in excess of 50% of the Company’s voting power is transferred; provided that an Acquisition shall not include any transaction or series of related
transactions solely for bona fide equity financing purposes in which cash is received by the Company or any successor or indebtedness of the Company is cancelled or converted or a combination thereof. 

(b) “Asset Transfer” shall mean the sale, lease, transfer, exclusive license or other
disposition, in a single transaction or series of related transactions, by the Company or any subsidiary of the Company of all or substantially all the assets of the Company and its subsidiaries taken as a whole, or the sale or disposition (whether
by merger or otherwise) of one or more subsidiaries of the Company if substantially all of the assets of the Company and its subsidiaries taken as a whole are held by such subsidiary or subsidiaries, except where such sale, lease, transfer,
exclusive license or other disposition is to a wholly owned subsidiary of the Company. 

  
 1. 

 (c) “Exercise Period” shall mean the period
commencing with the date of the Purchase Agreement and ending on March [•], 2026, unless sooner terminated as provided below. 

(d) “Exercise Price” shall initially mean $0.41 per Exercise Share subject to adjustment
pursuant to Section 5 below. 
 (e) “Exercise Shares” shall mean shares of the
Company’s Series D Preferred Stock issuable upon exercise of this Warrant. 
 (f) “Termination
Date” shall mean the earlier of: (i) the date of the expiration of the Exercise Period or (ii) the date of the termination of this Warrant pursuant to Section 7 below. 

2. EXERCISE OF WARRANT.  

2.1 The rights represented by this Warrant may be exercised in whole or in part at any time during the Exercise Period,
by delivery of the following to the Company at its address set forth above (or at such other address as it may designate by notice in writing to the Holder): 

(a) An executed Notice of Exercise in the form attached hereto; 

(b) Payment of the Exercise Price either (i) in cash or by check, or (ii) by cancellation of indebtedness;
and 
 (c) This Warrant. 

Upon the exercise of the rights represented by this Warrant, a certificate or certificates for the Exercise Shares so
purchased, registered in the name of the Holder or persons affiliated with the Holder, if the Holder so designates, shall be issued and delivered to the Holder within a reasonable time after the rights represented by this Warrant shall have been so
exercised. In the event that this Warrant is being exercised for less than all of the then-current number of Exercise Shares purchasable hereunder, the Company shall, concurrently with the issuance by the Company of the number of Exercise Shares for
which this Warrant is then being exercised, issue a new Warrant exercisable for the remaining number of Exercise Shares purchasable hereunder. 

The person in whose name any certificate or certificates for Exercise Shares are to be issued upon exercise of this Warrant
shall be deemed to have become the holder of record of such shares on the date on which this Warrant was surrendered and payment of the Exercise Price was made, irrespective of the date of delivery of such certificate or certificates, except that,
if the date of such surrender and payment is a date when the stock transfer books of the Company are closed, such person shall be deemed to have become the holder of such shares at the close of business on the next succeeding date on which the stock
transfer books are open. 
 2.2 Net Exercise. Notwithstanding any provisions herein to the contrary, if the
fair market value of one Exercise Share is greater than the Exercise Price (at the date of calculation as set forth below), in lieu of exercising this Warrant pursuant to Section 2.1, the 

  
 2. 

 
Holder may elect to receive Exercise Shares equal to the value (as determined below) of this Warrant (or the portion thereof being cancelled pursuant to this Section 2.2) by surrender of
this Warrant at the principal office of the Company together with the properly endorsed Notice of Exercise in which event the Company shall issue to the Holder a number of Exercise Shares computed using the following formula: 

 

					
		 		  	 X = Y (A-B)

A

			
		 	Where X =	  	the number of Exercise Shares to be issued to the Holder
			
		 	Y =	  	 the number of Exercise Shares purchasable under the Warrant or, if only a portion of the Warrant is being exercised,
that portion of the Warrant being cancelled pursuant to this Section 2.2 (at the date of such calculation)

			
		 	A =	  	the fair market value of one Exercise Share (at the date of such calculation)
			
		 	B =	  	Exercise Price (as adjusted to the date of such calculation)

 For purposes of the above calculation, the fair market value of one Exercise Share shall be
determined by the Company’s Board of Directors in good faith; provided, however, that in the event that this Warrant is exercised pursuant to this Section 2.2 in connection with the Company’s initial public offering of its Common
Stock, the fair market value per share shall be the product of (i) the per share offering price to the public of the Company’s initial public offering, and (ii) the number of shares of Common Stock into which each Exercise Share is
convertible at the time of such exercise. 
 2.3 Net Exercise on Termination Date. If this Warrant has not
been exercised prior to the Termination Date, this Warrant shall be deemed to have been automatically exercised on the Termination Date pursuant to the “Net Exercise” provisions set forth in Section 2.2 hereof. 

3. COVENANTS AS TO EXERCISE
SHARES. The Company covenants and agrees that all Exercise Shares that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly issued and outstanding,
fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issuance thereof. The Company further covenants and agrees that the Company will at all times during the Exercise Period, have authorized and reserved, free
from preemptive rights, a sufficient number of shares of the series of equity securities comprising the Exercise Shares to provide for the exercise of the rights represented by this Warrant. If at any time during the Exercise Period the number of
authorized but unissued shares of such series of the Company’s equity securities shall not be sufficient to permit exercise of this Warrant, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to
increase its authorized but unissued shares of such series of the Company’s equity securities to such number of shares as shall be sufficient for such purposes and a sufficient number of shares of Common Stock to provide for the conversion of
Exercise Shares issued upon the exercise of the rights represented by this Warrant, including, 

  
 3. 

 
without limitation, engaging in reasonable best efforts to obtain the requisite stockholder approval of any necessary amendment to the Company’s Certificate of Incorporation. 

4. REPRESENTATIONS OF HOLDER. 

4.1 Acquisition of Warrant for Personal Account. The Holder represents and warrants that it is acquiring the
Warrant and the Exercise Shares solely for its account for investment and not with a view to or for sale or distribution of said Warrant or Exercise Shares or any part thereof. The Holder also represents that the entire legal and beneficial
interests of the Warrant and Exercise Shares the Holder is acquiring is being acquired for, and will be held for, its account only. 

4.2 Information and Sophistication. Holder hereby: (i) acknowledges that it has received all the
information it has requested from the Company and it considers necessary or appropriate for deciding whether to acquire this Warrant and the Exercise Shares, (ii) represents that it has had an opportunity to ask questions and receive answers
from the Company regarding the financial condition of the Company and the risks associated with the acquisition of this Warrant and the Exercise Shares and (iii) further represents that it has such knowledge and experience in financial and
business matters that it is capable of evaluating the merits and risk of this investment. 
 4.3 Ability to Bear
Economic Risk. Holder acknowledges that investment in the securities of the Company involves a high degree of risk, and represents that it is able, without materially impairing its financial condition, to hold the Exercise Shares for an
indefinite period of time and to suffer a complete loss of its investment. 
 4.4 Securities Are Not Registered. 

(a) The Holder understands that the Warrant and the Exercise Shares have not been registered under the Securities Act
of 1933, as amended (the “Act”), on the basis that no distribution or public offering of the stock of the Company is to be effected. The Holder realizes that the basis for the exemption may not be present if, notwithstanding
its representations, the Holder has a present intention of acquiring the securities for a fixed or determinable period in the future, selling (in connection with a distribution or otherwise), granting any participation in, or otherwise distributing
the securities. The Holder has no such present intention. 
 (b) The Holder recognizes that the Warrant and the
Exercise Shares must be held indefinitely unless they are subsequently registered under the Act or an exemption from such registration is available. The Holder recognizes that the Company has no obligation to register the Warrant or the Exercise
Shares of the Company, or to comply with any exemption from such registration. 
 (c) The Holder is aware that
neither the Warrant nor the Exercise Shares may be sold pursuant to Rule 144 adopted under the Act unless certain conditions are met, including, among other things, the existence of a public market for the shares, the availability of certain current
public information about the Company, the resale following the required holding period under Rule 144 and the number of shares being sold during any three 

  
 4. 

 
month period not exceeding specified limitations. Holder is aware that the conditions for resale set forth in Rule 144 have not been satisfied and that the Company presently has no plans to
satisfy these conditions in the foreseeable future. 
 4.5 Disposition of Warrant and Exercise Shares. 

(a) The Holder further agrees not to make any disposition of all or any part of the Warrant or Exercise Shares in any
event unless and until: 
 (i) The Company shall have received a letter secured by the Holder from the Securities and
Exchange Commission (the “Commission”) stating that no action will be recommended to the Commission with respect to the proposed disposition; 

(ii) There is then in effect a registration statement under the Act covering such proposed disposition and such
disposition is made in accordance with said registration statement; or 
 (iii) The Holder shall have notified the
Company of the proposed disposition and shall have furnished the Company with a statement of the circumstances surrounding the proposed disposition, and if reasonably requested by the Company, the Holder shall have furnished the Company with an
opinion of counsel, reasonably satisfactory to the Company, for the Holder to the effect that such disposition will not require registration of such Warrant or Exercise Shares under the Act or any applicable state securities laws. The Company agrees
that it will not require an opinion of counsel with respect to transactions under Rule 144 of the Act, except in unusual circumstances. 

(iv) Notwithstanding the foregoing or anything to the contrary herein, the provisions of this Section 4.5 shall
not apply to the proposed disposition of all or any part of this Warrant or Exercise Shares by the Holder to (x) any of its current or former stockholders, members, partners or other equity holders or (y) any person who is
managed by, or has the same management company or investment advisor or similar company of the Holder or (z) any of the Holder’s affiliates. 

(b) The Holder understands and agrees that all certificates evidencing the shares to be issued to the Holder may bear
the following legend: 
 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
“ACT”). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THE SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH
REGISTRATION IS NOT REQUIRED. 
 4.6 Accredited Investor Status. The Holder is an “accredited
investor” as defined in Regulation D promulgated under the Act. 

  
 5. 

 5. ADJUSTMENT OF EXERCISE
PRICE AND NUMBER OF EXERCISE SHARES. 

5.1 In the event of changes in the series of equity securities of the Company comprising the Exercise Shares by reason
of stock dividends, splits, recapitalizations, reclassifications, combinations or exchanges of shares, separations, reorganizations, liquidations or the like, the number and class of Exercise Shares available under the Warrant in the aggregate and
the Exercise Price shall be correspondingly adjusted to give the Holder of the Warrant, on exercise for the same Aggregate Exercise Price, the total number, class, and kind of shares as the Holder would have owned had the Warrant been exercised
prior to the event and had the Holder continued to hold such shares until after the event requiring adjustment; provided, however, that such adjustment shall not be made with respect to, and this Warrant shall terminate if not exercised prior
to, the events set forth in Section 7 below. For purposes of this Section 5, the “Aggregate Exercise Price” shall mean the aggregate Exercise Price payable in connection with the exercise in full of this Warrant.
The form of this Warrant need not be changed because of any adjustment in the number of Exercise Shares subject to this Warrant. 

5.2 Whenever there is any adjustment pursuant to this Section 5, the Company shall prepare a certificate signed by
the Company’s chief executive officer 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 Exercise Price and number of Exercise
Shares issuable upon exercise of the Warrant after giving effect to such adjustment, and shall cause copies of such certificate to be mailed (by certified or registered mail, return receipt required, postage prepaid) within thirty (30) days of
such adjustment to the Holder of this Warrant. 
 6. FRACTIONAL SHARES. No
fractional shares shall be issued upon the exercise of this Warrant as a consequence of any adjustment pursuant hereto. All Exercise Shares (including fractions) to be issued upon exercise of this Warrant shall be aggregated for purposes of
determining whether the exercise would result in the issuance of any fractional share. If, after aggregation, the exercise would result in the issuance of a fractional share, the Company shall, in lieu of issuance of any fractional share, pay the
Holder otherwise entitled to such fraction a sum in cash equal to the product resulting from multiplying the then current fair market value of one Exercise Share by such fraction. 

7. EARLY TERMINATION. In the event of, at any time during the Exercise
Period, an initial public offering of securities of the Company registered under the Act, or an Acquisition or Asset Transfer, the Company shall provide to the Holder 10 days advance written notice of such public offering, Acquisition or Asset
Transfer, and this Warrant shall be automatically exercised in accordance with Section 2.3 unless exercised immediately prior to the date such public offering is closed or the closing of such Acquisition or Asset Transfer. 

8. MARKET STAND-OFF
AGREEMENT. Holder shall not sell, dispose of, transfer, make any short sale of, grant any option for the purchase of, or enter into any hedging or similar transaction with the same economic effect as a sale, any Common Stock (or
other securities) of the Company held by Holder, for a period of time specified by the representative of the underwriters of Common Stock (or other securities) of the Company not to exceed 180 days following the effective date of a registration
statement of the Company filed under the Act (or such longer period as necessary to permit compliance with NASD Rule 2711 or NYSE Member 

  
 6. 

 
Rule 472 and similar or successor regulatory rules and regulations). Holder agrees to execute and deliver such other agreements as may be reasonably requested by the Company and/or the managing
underwriter(s) which are consistent with the foregoing or which are necessary to give further effect thereto. In order to enforce the foregoing covenant, the Company may impose stop-transfer instructions with respect to such Common Stock (or other
securities) until the end of such period. The underwriters of the Company’s stock are intended third party beneficiaries of this Section 8 and shall have the right, power and authority to enforce the provisions hereof as though they were a
party hereto. 
 9. NO STOCKHOLDER RIGHTS. This Warrant in and of
itself shall not entitle the Holder to any voting rights or other rights as a stockholder of the Company. 
 10.
TRANSFER OF WARRANT. Subject to applicable laws and the restriction on transfer set forth on the first page and Section 4.5 of this Warrant, this Warrant and all rights hereunder are
transferable, by the Holder in person or by duly authorized attorney, upon delivery of this Warrant and the form of assignment attached hereto to any transferee designated by Holder. 

11. LOST, STOLEN, MUTILATED OR DESTROYED
WARRANT. If this Warrant is lost, stolen, mutilated or destroyed, the Company may, on such terms as to indemnity or otherwise as it may reasonably impose (which shall, in the case of a mutilated Warrant, include the surrender
thereof), issue a new Warrant of like denomination and tenor as the Warrant so lost, stolen, mutilated or destroyed. Any such new Warrant shall constitute an original contractual obligation of the Company, whether or not the allegedly lost, stolen,
mutilated or destroyed Warrant shall be at any time enforceable by anyone. 
 12. CHARGES,
TAXES, AND EXPENSES. Issuance of certificates for Exercise Shares upon the exercise of this Warrant shall be made without charge to the Holder for any United States or state of the United States
documentary stamp tax or other incidental expense within respect to the issuance of such certificate, all of which taxes and expenses shall be paid by the Company (other than income or similar taxes), and such certificates shall be issued in the
name of the Holder. 
 13. AMENDMENT. Any term of this Warrant may
be amended or waived only with the written consent of the Company and the Requisite Holders (as defined in the Purchase Agreement). Any amendment, modification or waiver affected in accordance with this Section 13 shall be binding upon the
Holder, whether or not the Holder has consented to such amendment, modification or waiver. 
 14.
NOTICES, ETC. All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed
telex or facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one
day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be sent to the Company at the address listed on the signature page and to Holder at the
address set forth on the Schedule of Purchasers attached to the Purchase 

  
 7. 

 
Agreement or at such other address as the Company or Holder may designate by 10 days advance written notice to the other parties hereto. 

15. ACCEPTANCE. Receipt of this Warrant by the Holder shall constitute acceptance of and
agreement to all of the terms and conditions contained herein. 
 16. GOVERNING LAW.
This Warrant and all rights, obligations and liabilities hereunder shall be governed by and construed under the laws of the State of Delaware, without giving effect to conflicts of laws principles. 

[Signature Page Follows] 

  
 8. 

 IN WITNESS
WHEREOF, the Company has caused this Warrant to be executed by its duly authorized officer as of the date first written above. 

 

			
	BIONANO GENOMICS, INC.

 
			
		
	 By:
	 	 

 
			
		
	 Name:
	 	 Erik Holmlin

		
	 Title:
	 	 Chief Executive Officer

		
	 Address:
	 	
	
	9640 Towne Centre Drive, Suite 100
	San Diego, CA 92121

  

			
	 Acknowledged and Accepted by:
  

	[                                   
     ]

			
		
	By:	 	 

			
		
	Name:	 	 

			
		
	Title:	 	 

 NOTICE OF EXERCISE 

TO: BIONANO GENOMICS, INC. 

(1) ☐ The undersigned hereby elects to purchase
                     shares of Series D Preferred Stock (the “Exercise Shares”) of BioNano Genomics, Inc. (the
“Company”) pursuant to the terms of the attached Warrant, and tenders herewith payment of the exercise price in full, together with all applicable transfer taxes, if any. 

☐ The undersigned hereby elects to purchase
                     shares of Series D Preferred Stock (the “Exercise Shares”) of BioNano Genomics, Inc. (the
“Company”) pursuant to the terms of the net exercise provisions set forth in Section 2.2 of the attached Warrant, and shall tender payment of all applicable transfer taxes, if any. 

(2) Please issue a certificate or certificates representing said Exercise Shares in the name of the undersigned or in
such other name as is specified below: 
  

					
		  	(Name)	  	
		  		  	
		  	 	  	
		  	(Address)	  	

  

							
			
	 	 		 	 
	 (Date)
	 		 	 (Signature)

			
		 		 	 
		 		 	 (Print name)

 ASSIGNMENT FORM 

(To assign the foregoing Warrant, execute this form 

and supply required information. Do not use this 

form to purchase shares.) 

FOR VALUE RECEIVED, the foregoing Warrant and all rights
evidenced thereby are hereby assigned to 
  

			
	 Name: 
	  	 

			
	(Please Print)
		
	 Address: 
	  	 

			
	(Please Print)
		
	 Dated:
	  	                 ,
20     

					
			
	Holder’s	  		  	
	Signature: 	  	 	  	
			
	Holder’s	  		  	
	Address: 	  	 	  	

 NOTE: The signature to this Assignment Form must correspond with the name as it appears on the face of
the Warrant, without alteration or enlargement or any change whatever. Officers of corporations and those acting in a fiduciary or other representative capacity should file proper evidence of authority to assign the foregoing Warrant.

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