Exhibit 10.4


 


Execution Copy


 


SECOND AMENDMENT TO WARRANT AGREEMENT


 


THIS SECOND AMENDMENT TO WARRANT AGREEMENT (this
“Second Amendment”), dated as of November 2, 2016, is by and between Applied DNA Sciences, Inc.,
a Delaware corporation (the “Company”), and American Stock Transfer & Trust Company, LLC, a New York
limited liability trust company, as Warrant Agent (the “Warrant Agent”).


 


WHEREAS, the Company and the Warrant Agent have
previously entered into that certain Warrant Agreement, dated as of November 20, 2014 (the “Original Warrant Agreement”),
which was amended as of April 1, 2015 (the “First Amendment”; the Original Warrant Agreement as amended
by the First Amendment is herein referred to as the “Warrant Agreement”) and the Company and the Warrant
Agent now desire to further amend the Warrant Agreement on the terms and subject to the conditions set forth herein (with capitalized
terms used and not defined in this Second Amendment having the respective meanings given them in the Warrant Agreement);


 


WHEREAS, pursuant to a Placement Agency Agreement,
dated November 2, 2016, by and among the Company, Maxim Group, LLC and Imperial Capital, LLC, the Company is engaged in a private
offering (the “Private Offering”) of shares of its Common Stock, $.001 par value (“Common
Stock”), and Warrants to purchase shares of its Common Stock (“Warrants”) and, in connection
therewith, has determined to issue and deliver up to 2,000,000 Warrants to one or more investors in the Private Offering, each
such Warrant evidencing the right of the holder thereof to purchase one share of Common Stock at an exercise price of $3.50 per
share, subject to adjustment as described in the Warrant Agreement; and


 


WHEREAS, the Company intends that at a future
date a registration statement (“Registration Statement”) will be filed with the Securities and Exchange
Commission and upon effectiveness will be available for the public resale of the Warrants, and the related underlying Common Stock,
sold in the Private Offering; and


 


WHEREAS, the Company desires the Warrant Agent
to act on behalf of the Company, and the Warrant Agent is willing to so act, in connection with the issuance, registration, transfer,
exchange and exercise of the Warrants to be issued to investors in the Private Offering and then to subsequent holders of the Warrants
(“Holders”) as a result of the resale thereof pursuant to the Registration Statement; and


 


WHEREAS, the Company desires to provide for
the form and provisions of the Warrants to be issued to investors in the Private Offering, the terms upon which they shall be issued
and exercised, and the respective rights, limitation of rights, and immunities of the Company, the Warrant Agent, and the Holders;
and


 


WHEREAS, all acts and things have been done
and performed which are necessary to make the Warrants to be issued to investors in the Private Offering, when executed on behalf
of the Company and countersigned by or on behalf of the Warrant Agent, as provided herein, the valid, binding and legal obligations
of the Company, and to authorize the execution and delivery of this Agreement.


 


NOW, THEREFORE, in consideration of the mutual
agreements herein contained, the parties hereto agree as follows:


 


		1.	Recitals. The foregoing Recitals are hereby incorporated into and made part of this Amendment.



 




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		2.	Appointment of Warrant Agent. The Company hereby appoints the Warrant Agent to act as agent for the Company for the
Warrants to be issued to one or more investors in the Private Offering, and the Warrant Agent hereby accepts such appointment and
agrees to perform the same in accordance with the terms and conditions set forth in the Warrant Agreement, as amended hereby.



 


		3.	Amendments to the Warrant Agreement. The Warrant Agreement is hereby amended as follows:



 


		3.1	Section 3.3.3 of the Warrant Agreement is hereby amended and restated to read in its entirety as follows:



 


“3.3.3   Issuance
of Common Stock on Exercise. Assuming funds for exercise are paid on or before the second trading day following the date of
receipt by the Company of an exercise notice, then on or before the third trading day following the date upon which the Company
has received an exercise notice for a Warrant, the Company shall cause its transfer agent to (i) provided that the transfer agent
is participating in The Depository Trust Company (“DTC”) Fast Automated Securities Transfer Program and there is an
effective registration statement applicable to the Common Stock underlying such Warrant, credit such aggregate number of shares
of Common Stock to which the Holder is entitled pursuant to such exercise to the Holder’s or its designee’s balance
account with DTC through its Deposit/Withdrawal at Custodian System, or (ii) if the transfer agent is not participating in the
DTC Fast Automated Securities Transfer Program or if there is no effective registration statement applicable to the Common Stock
underlying such Warrant, issue and deliver to the Holder, or at the Holder’s instruction pursuant to the delivered exercise
notice, the Holder’s agent or designee, in each case pursuant to this clause (ii), sent by reputable overnight courier to
the address specified in the applicable exercise notice, a certificate, registered in the Company’s share register in the
name of the Holder or its designee (as indicated in the applicable exercise notice), for the number of shares of Common Stock to
which the Holder is entitled pursuant to such exercise.”


 


		3.2	Section 3.4 of the Warrant Agreement is hereby amended by inserting immediately following the words “or Follow-on Offering“
the words “or Private Offering, as applicable”.



 


		3.3	Section 6.4 of the Warrant Agreement is hereby amended by inserting immediately following (x) the word “Statement”
in the first sentence of such Section the words “except for the Warrants and related underlying shares of Common Stock sold
in the Private Offering” and (y) the first sentence of such Section the words “At a future date an effective registration
statement will be available for the public resale of the Warrants, and the related underlying Common Stock, sold in the Private
Offering and such registration statement will be a Registration Statement for purposes of this Agreement.”



 




    	 	 	 



     


    

  


		4.	Entire Agreement. The terms and conditions of this Second Amendment shall be incorporated by reference in the Warrant
Agreement as though set forth in full in the Warrant Agreement. In the event of any inconsistency between the provisions of this
Second Amendment and any other provision of the Warrant Agreement, the terms and provisions of this Second Amendment shall govern
and control. Except to the extent specifically amended or superseded by the terms of this Second Amendment, all of the provisions
of the Warrant Agreement shall remain in full force and effect to the extent in effect on the date of this Second Amendment. The
Warrant Agreement, as modified by this Second Amendment, constitutes the complete agreement among the parties and supersedes any
prior written or oral agreements, writings, communications or understandings of the parties with respect to the subject matter
the Warrant Agreement.



 


		5.	Miscellaneous Provisions. The provisions of Section 8 of the Warrant Agreement are hereby incorporated into this Amendment
as if set forth fully herein and shall apply mutatis mutandis.



 


[Signature Page Follows]


 




    	 	 	 



     


    

 


IN WITNESS WHEREOF, the parties hereto have
caused this Agreement to be duly executed as of the date first above written.


 


	 	APPLIED DNA SCIENCES, INC.
	 	 	 	 
	 	By:	/s/ James Hayward	 
	 	 	Name: James Hayward
	 	 	Title: Chief Executive Officer
	 	 	 	 
	 	AMERICAN STOCK TRANSFER & TRUST COMPANY, LLC, as Warrant Agent
	 	 	 	 
	 	By:	/S/ Michael A. Nespoli	 
	 	 	Name: Michael A. Nespoli	 
	 	 	Title: Executive Director	 


 


Signature Page to Second Amendment to Warrant
Agreement by and between Applied DNA Sciences, Inc.


and American Stock Transfer & Trust Company,
LLC, as Warrant Agent