EX-4.1





 Exhibit 4.1 

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 COMMON STOCK 
  

					
	CSW-[    ]	 		 	[●], 20    
		 	VOID AFTER [●], 20    	 	

 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 being issued to the
Holder in full satisfaction of the Company’s obligation to pay the Holder and/or its affiliates an aggregate of $[        ] for
[                    ]. 

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. 

(c)    “Common Stock” shall mean the Company’s Common Stock. 

  
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 (d)    “Exercise Period” shall mean the
period commencing with the date of the Purchase Agreement and ending on November [●], 20    , unless sooner terminated as provided below. 

(e)    “Exercise Price” shall initially mean
$[        ] per Exercise Share subject to adjustment pursuant to Section 5 below. 

(f)    “Exercise Shares” shall mean the shares of Common Stock issuable upon exercise
of this Warrant. 
 (g)    “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. 

(h)    “Trading Market” means whichever of the New York Stock Exchange, NYSE American, the
Nasdaq Capital Market, the Nasdaq Global Market, the Nasdaq Global Select Market or OTC Bulletin Board on which the Common Stock is listed or quoted for trading on the date in question. 

(i)     “Trading Day” shall mean (i) a day on which the Common Stock is traded or
quoted on a Trading Market, or (ii) if the Common Stock is not traded or quoted on any Trading Market, a day on which the Common Stock is quoted in the
over-the-counter market as reported by the Pink Sheets LLC (or any similar organization or agency succeeding to its functions of reporting prices); provided, that in the
event that the Common Stock is not traded or quoted as set forth in (i) or (ii) hereof, then Trading Day shall mean a Business Day. 

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. 

  
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 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 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 arithmetic average of the closing sales prices of the Common Stock for the five consecutive Trading Days
ending on the date immediately preceding the date of the Notice of Exercise 


  

	 	B=	 Exercise Price (as adjusted to the date of such calculation) 



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, a
sufficient number of shares of Common Stock to provide for the exercise of the rights represented by this Warrant. 

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. 

  
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 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 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: 

  
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 (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. 

(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.    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. 

  
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 5.2    Whenever there is any adjustment pursuant to this
Section 5, the Company shall prepare a certificate signed by an officer of the Company 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 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 of this Warrant unless exercised immediately prior to the date such public offering is closed or the closing of such Acquisition or
Asset Transfer. 
 8.    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. 

9.    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. 
 10.    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. 

11.    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. 

  
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12.    AMENDMENT. Any term of this Warrant may be amended or
waived only with the written consent of the Company and the Holder. 
 13.    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, electronic mail 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 Agreement or at such other address as the Company or Holder may designate by 10 days advance written notice to the other parties hereto. 

14.    ACCEPTANCE. Receipt of this Warrant by the Holder shall constitute acceptance of and
agreement to all of the terms and conditions contained herein. 
 15.    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] 

  
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 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 Common 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 Common 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.