Document:

Exhibit 10.25

 

WARRANT AGREEMENT

 

Applied DNA Sciences, Inc.

 

and

 

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

 

WARRANT AGREEMENT

 

THIS WARRANT AGREEMENT (this “Agreement”),
dated as of November ___, 2014, 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 is engaged in a public
offering (the “Offering”) of shares of common stock of the Company, par value $0.001 per share (“Common
Stock”), and warrants to purchase shares of Common Stock (“Warrants”) and, in connection
therewith, has determined to issue and deliver up to ___________Warrants (including up to ____________Warrants subject to an over-allotment
option granted to the underwriters by the Company) to public investors in the Offering, each such Warrant evidencing the right
of the holder thereof to purchase ______share of Common Stock for $______ per share, subject to adjustment as described herein;
and

 

WHEREAS, the Company has filed with the
Securities and Exchange Commission (the “Commission”) a registration statement, as amended, on Form S-1,
No. 333-199121 (the “Registration Statement”) and prospectus (the “Prospectus”),
for the registration, under the Securities Act of 1933, as amended (the “Securities Act”), of the Common
Stock and Warrants to be sold to investors in the Offering and the shares of Common Stock underlying the Warrants; 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; and

 

WHEREAS, the Company desires to provide
for the form and provisions of the Warrants, 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 of the Warrants (each, a “Holder”);
and

 

WHEREAS, all acts and things have been done
and performed which are necessary to make the Warrants, 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.	Appointment of Warrant Agent. The Company hereby appoints the Warrant Agent to act as agent for the Company for the
Warrants, and the Warrant Agent hereby accepts such appointment and agrees to perform the same in accordance with the terms and
conditions set forth in this Agreement.

 

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		2.	Warrants.

 

		2.1	Form of Warrant. Each Warrant shall be issued in registered form only and shall be in substantially the form of Exhibit A
hereto, the provisions of which are incorporated herein. Each Warrant shall be signed by, or bear the facsimile signature of, the
Chairman of the Board, President, Chief Executive Officer, Secretary or other principal officer of the Company. In the event the
person whose facsimile signature has been placed upon any Warrant shall have ceased to serve in the capacity in which such person
signed the Warrant before such Warrant is issued, it may be issued with the same effect as if he or she had not ceased to be such
at the date of issuance.

 

		2.2	Effect of Countersignature. Unless and until countersigned by the Warrant Agent pursuant to this Agreement, a Warrant
shall be invalid and of no effect and may not be exercised by the holder thereof.

 

		2.3	Registration.

 

		2.3.1	Warrant Register. The Warrant Agent shall maintain books (the “Warrant Register”), for the
registration of original issuance and the registration of transfer of the Warrants. Upon the initial issuance of the Warrants,
the Warrant Agent shall issue and register the Warrants in the names of the respective holders thereof in such denominations and
otherwise in accordance with instructions delivered to the Warrant Agent by the Company.

 

		2.3.2	Registered Holder. Prior to due presentment for registration of transfer of any Warrant, the Company and the Warrant
Agent may deem and treat the person in whose name such Warrant is registered in the Warrant Register (the “Registered
Holder”) as the absolute owner of such Warrant and of each Warrant represented thereby (notwithstanding any notation
of ownership or other writing on the Warrant Certificate (as defined below) made by anyone other than the Company or the Warrant
Agent), for the purpose of any exercise thereof, and for all other purposes, and neither the Company nor the Warrant Agent shall
be affected by any notice to the contrary.

 

		3.	Terms and Exercise of Warrants.

 

		3.1	Exercise Price. Each Warrant shall, when countersigned by the Warrant Agent, entitle the Registered Holder thereof,
subject to the provisions of such Warrant and of this Warrant Agreement, to purchase from the Company the number of shares of Common
Stock stated therein, at the price of $___ per share, subject to the adjustments provided herein. The term “Exercise
Price” as used in this Warrant Agreement shall mean the price per share at which shares of Common Stock may be purchased
at the time a Warrant is exercised.

 

		3.2	Duration of Warrants. A Warrant may be exercised only during the period (the “Exercise Period”)
commencing on the date of issuance thereof and ending on the earlier of: (a) November ___, 2019; or (b) upon the dissolution and
winding up of the Company (the “Expiration Date”); provided, however, that the exercise of any
Warrant shall be subject to the satisfaction of any applicable conditions, as set forth in subsection 3.3.2 below with respect
to an effective registration statement. Each Warrant not exercised on or before the Expiration Date shall become void, and all
rights thereunder and all rights in respect

 

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thereof under this Agreement shall
cease at 5:00 p.m. New York City time on the Expiration Date.

 

		3.3	Exercise of Warrants.

 

3.3.1      Payment.
Subject to the provisions of the Warrant and this Warrant Agreement, a Warrant, when countersigned by the Warrant Agent, may be
exercised by the Registered Holder thereof by submitting a duly executed election to purchase attached to the applicable Warrant,
at the office of the Warrant Agent in the Borough of Manhattan, City and State of New York or at the office of its successor as
Warrant Agent, in the Borough of Manhattan, City and State of New York, which may be done by fax or email delivery, and by paying,
within two days of the date of exercise, in full the Exercise Price for each full share of Common Stock as to which the Warrant
is exercised, in lawful money of the United States, by wire transfer or in good certified check or good bank draft payable to the
order of the Company or by Cashless Exercise in accordance with Section 3.2.2 hereof. Upon delivery of an exercise notice, the
Holder shall be deemed for all corporate purposes to have become the holder of record of the Warrant Shares with respect to which
a Warrant has been exercised, irrespective of the date such Warrant Shares are credited to the Holder’s DTC account or the
date of delivery of the certificates evidencing such Warrant Shares (as the case may be).

 

3.3.2      Cashless
Exercise. Notwithstanding anything contained herein to the contrary, if and only if an effective registration statement covering
the issuance of the shares of Common Stock that are subject to the exercise notice is not available for the issuance of such shares
of Common Stock, the Registered Holder may exercise this Warrant in whole or in part and, in lieu of making the cash payment otherwise
contemplated to be made to the Company upon such exercise in payment of the aggregate Exercise Price, elect instead to receive
upon such exercise the “Net Number” of shares of Common Stock determined according to the following formula (a “Cashless
Exercise”):

 

	Net Number =	(A x B) - (A x C)
	 	B

 

For purposes of the foregoing formula:

 

	 	A	=	the total number of shares with respect to which this Warrant is then being exercised.
	 	 	 	 
	 	B	=	the arithmetic average of the Closing Sale Prices (as defined below)  of the Common Stock for the five (5) consecutive Trading Days ending on the date immediately preceding the date of the Exercise Notice.
	 	 	 	 
	 	C	=	the Exercise Price then in effect for the applicable shares of Common Stock at the time of such exercise.

 

The term “Closing Sale Price”
means, for any security as of any date, the last closing bid price and last closing trade price, respectively, for such security
on the Nasdaq Capital Market, as reported by Bloomberg, or, if the Nasdaq Capital Market begins to operate on an extended hours
basis and does not designate the closing bid price or the closing trade price, as the case may be, then the last bid price or the
last trade price, respectively, of such security prior to 4:00:00 p.m., New York time, as reported by Bloomberg, or, if the Nasdaq
Capital Market is not the principal

 

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securities exchange or trading market for
such security, the last closing bid price or last trade price, respectively, of such security on the principal securities exchange
or trading market where such security is listed or traded as reported by Bloomberg, or if the foregoing do not apply, the last
closing bid price or last trade price, respectively, of such security in the over-the-counter market on the electronic bulletin
board for such security as reported by Bloomberg, or, if no closing bid price or last trade price, respectively, is reported for
such security by Bloomberg, the average of the bid prices, or the ask prices, respectively, of any market makers for such security
as reported in the OTC Link or “pink sheets” by OTC Markets Group Inc. (formerly Pink OTC Markets Inc.). If the Closing
Sale Price cannot be calculated for a security on a particular date on any of the foregoing bases, the Closing Sale Price of such
security on such date shall be the fair market value as mutually determined by the Company and the Registered Holder. If the Company
and the Registered Holder are unable to agree upon the fair market value of such security, then such dispute shall be resolved
pursuant to Section 8.3 hereof. All such determinations to be appropriately adjusted for any stock dividend, stock split, stock
combination or other similar transaction during the applicable calculation period

 

For purposes of Rule 144(d) promulgated
under the Securities Act, as in effect on the date hereof, assuming the Registered Holder is not an affiliate of the Company, the
shares of Common Stock issued in a Cashless Exercise shall be deemed to have been acquired by the Registered Holder, and the holding
period for the shares of Common Stock shall be deemed to have commenced, on the date this Warrant was originally issued.

 

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 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, 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.

 

		3.3.4	Valid Issuance. All Common Stock issued or issuable upon the proper exercise of a Warrant in conformity with this Agreement
shall be validly issued, fully paid and nonassessable.

 

		3.3.5	Date of Issuance. Each person in whose name any certificate for the Common Stock is issued shall for all purposes be
deemed to have become the holder of record of such Common Stock on the date on which the Warrant was surrendered and, other than
in the case of a Cashless Exercise, payment of the Exercise Price was made, irrespective of the date of delivery of such certificate,
except that, if the date of such surrender and payment is a date when the share 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
share transfer books are open.

 

3.3.6     Share
Delivery Failure. If the Company shall fail, for any reason or for no reason, to issue to the Holder within three (3) trading
days after receipt of the applicable exercise notice (the

 

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“Share Delivery Deadline”),
a certificate for the number of shares of Common Stock to which the Holder is entitled upon Holder’s exercise of a Warrant
or credit the Holder’s balance account with DTC for such number of shares of Common Stock to which the Holder is entitled
upon the Holder’s exercise of this Warrant (as the case may be, but in each case without a restrictive legend) (a “Delivery
Failure”), and if on such or after such Share Delivery Deadline the Holder purchases (in an open market transaction
or otherwise) shares of Common Stock to deliver in satisfaction of a sale by the Holder of all or any portion of the number of
shares of Common Stock issuable upon such exercise that the Holder so anticipated receiving from the Company, then, in addition
to all other remedies available to it, the Company shall, within three (3) Business Days after the Holder’s request and in
the Holder’s discretion, either (i) pay cash to the Holder in an amount equal to 100% of the Holder’s total purchase
price (including brokerage commissions and other out-of-pocket expenses, if any) for the shares of Common Stock so purchased (including,
without limitation, by any other person in respect, or on behalf, of the Holder) (the “Buy-In Price”),
at which point the Company’s obligation to so issue and deliver such certificate or credit the Holder’s balance account
with DTC for the number of shares of Common Stock to which the Holder is entitled upon the Holder’s exercise hereunder (as
the case may be) (and to issue such shares of Common Stock) shall terminate, or (ii) promptly honor its obligation to so issue
and deliver to the Holder a certificate or certificates representing such shares of Common Stock or credit the Holder’s balance
account with DTC for the number of shares of Common Stock to which the Holder is entitled upon the Holder’s exercise hereunder
(as the case may be) and pay cash to the Holder in an amount equal to the excess (if any) of the Buy-In Price over the product
of (A) such number of shares of Common Stock multiplied by (B) the lowest Closing Sale Price of the shares of Common Stock on any
trading day during the period commencing on the date of the applicable exercise notice and ending on the date immediately preceding
the date of such issuance and payment under this clause (ii)

 

		3.4	Beneficial Ownership Limitation on Exercises. The Company shall not affect the exercise of any portion of a Warrant,
and the Registered Holder of such Warrant shall not have the right to exercise any portion of such Warrant, to the extent that
after giving effect to such exercise, the Registered Holder (together with the Registered Holder’s affiliates, and any persons
acting as a group together with the Holder or any Registered Holder’s affiliates) would beneficially own in excess of 4.99%
(the “Maximum Percentage”) of the Common Stock outstanding immediately after giving effect to such exercise,
provided, however, that the foregoing limitation on exercise shall not apply to any Registered Holder who, together with such Registered
Holder’s affiliates, and any persons acting as a group together with such Registered Holder and such Registered Holder’s
affiliates, owns in excess of the Maximum Percentage immediately prior to the closing of the Offering. For purposes of the foregoing
sentence, the aggregate number of shares of Common Stock beneficially owned by such Registered Holder and its affiliates shall
include the number of shares of Common Stock issuable upon exercise of the Warrant with respect to which the determination of such
sentence is being made, but shall exclude shares of Common Stock which would be issuable upon (i) exercise of the remaining, unexercised
portion of the Warrant beneficially owned by the Registered Holder and its affiliates and (ii) exercise or conversion of the unexercised
or unconverted portion of any other securities of the Company beneficially owned by the Registered Holder and its affiliates (including,
without limitation, any convertible notes or convertible preferred stock or warrants) subject to a limitation on conversion or
exercise analogous to the limitation contained herein beneficially owned by the Registered Holder or any of its affiliates. Except
as set forth in the preceding sentence, for purposes of this paragraph, beneficial ownership shall be calculated in accordance
with Section 13(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). To the extent
that the limitation contained in this Section 3.4 applies, the Registered Holder’s

 

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submission of an Election to Purchase
shall be deemed to be the Registered Holder’s determination of whether a Warrant is exercisable (in relation to any other
securities owned by the Registered Holder together with any affiliates) and of which portion of a Warrant is exercisable, in each
case subject to the Maximum Percentage, and the Company shall have no obligation to verify or confirm the accuracy of such determination.
In addition, a determination as to any group status as contemplated above shall be determined in accordance with Section 13(d)
of the Exchange Act and the rules and regulations promulgated thereunder. For purposes of the Warrants, in determining the number
of outstanding shares of Common Stock, the Registered Holder may rely on the number of outstanding shares of Common Stock as reflected
in the most recent of (1) the Company’s most recent Form 10-K, Form 10-Q, Current Report on Form 8-K or other public filing
with the Commission, as the case may be, (2) a more recent public announcement by the Company or (3) any other notice by the Company
or its transfer agent setting forth the number of shares of Common Stock outstanding. For any reason at any time, upon the written
or oral request of the Registered Holder, the Company shall within three (3) trading days confirm to the Registered Holder the
number of shares of Common Stock then outstanding. In any case, the number of outstanding shares of Common Stock shall be determined
after giving effect to the conversion or exercise of securities of the Company, including any Warrant, by the Registered Holder
and its affiliates since the date as of which such number of outstanding shares of Common Stock was reported. By written notice
to the Company, the Registered Holder may from time to time increase or decrease the Maximum Percentage to any other percentage
of the number of shares of the Common Stock outstanding immediately after giving effect to the issuance of shares of Common Stock
upon exercise of a Warrant and the provisions of this Section 3.4 shall continue to apply; provided that (i) any such increase
will not be effective until the sixty-first (61st) day after such notice is delivered to the Company, and (ii) any such increase
or decrease will apply only to that Registered Holder. For purposes of clarity, the Common Stock underlying any Warrant in excess
of the Maximum Percentage for a Registered Holder shall not be deemed to be beneficially owned by that Registered Holder for any
purpose including for purposes of Section 13(d) or Rule 16a-1(a)(1) of the Exchange Act. The provisions of this paragraph shall
be construed and implemented in a manner otherwise than in strict conformity with the terms of this Section 3.4 to the extent necessary
to correct this paragraph (or any portion hereof) which may be defective or inconsistent with the intended beneficial ownership
limitation herein contained or to make changes or supplements necessary or desirable to properly give effect to such limitation.

 

		4.	Adjustments.

 

		4.1	Stock Dividends.

 

		4.1.1	Split-Ups. If after the date hereof, and subject to the provisions of Section 4.5 below, the number of outstanding
shares of Common Stock is increased by a stock dividend payable in Common Stock, or by a split-up of Common Stock or other similar
event, then, on the effective date of such stock dividend, split-up or similar event, the number of shares of Common Stock issuable
on exercise of each Warrant shall be increased in proportion to such increase in the outstanding shares of Common Stock and the
Exercise Price shall be proportionally decreased such that the aggregate Exercise Price, after such adjustments, remains the same
for each Warrant.

 

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		4.1.2	Dividends and Other Distributions. If the Company shall declare or make any dividend or other distribution of its assets
(or rights to acquire its assets) to holders of Common Stock, by way of return of capital or otherwise (including, without limitation,
any distribution of cash, stock or other securities, property or options by way of a dividend, spin off, reclassification, corporate
rearrangement, scheme of arrangement or other similar transaction), except to the extent an adjustment was already made pursuant
to Section 4.1.1 or 4.2 (a “Distribution”), at any time after the issuance of this Warrant, then, in
each such case, the Company shall reserve and put aside the maximum Distribution amount the Holder would have been entitled to
receive if the Holder had held the number of shares of Common Stock acquirable upon complete exercise of this Warrant (without
regard to any limitations on exercise hereof, including without limitation, the Maximum Percentage) immediately before the date
on which a record is taken for such Distribution, or, if no such record is taken, the date as of which the record holders of Common
Stock are to be determined for the participation in such Distribution. Upon exercise of this Warrant, in whole or in part, the
Company shall, contemporaneously with the delivery of the Warrant Shares, distribute to the Holder a pro rata portion of such Distribution
based on the portion of the Warrant that has been exercised (provided, however, to the extent that the Holder’s right to
participate in any such Distributions would result in the Holder exceeding the Maximum Percentage, then the Holder shall not be
entitled to participate in such Distribution at such time and to such extent (or the beneficial ownership of any such Common Stock
as a result of such Distribution to such extent) and such Distribution to such extent shall be held in abeyance for the benefit
of the Holder until such time, if ever, as its right thereto would not result in the Holder exceeding the Maximum Percentage, at
which time or times the Holder shall be granted such Distribution (and any Distributions declared or made on such initial Distribution
or on any subsequent Distribution to be held similarly in abeyance) to the same extent as if there had been no such limitation).

 

		4.2	Aggregation of Shares. If after the date hereof, and subject to the provisions of Section 4.5 hereof, the number
of outstanding shares of Common Stock is decreased by a consolidation, combination, reverse stock split or reclassification of
Common Stock or other similar event, then, on the effective date of such consolidation, combination, reverse stock split, reclassification
or similar event, the number of shares of Common Stock issuable on exercise of each Warrant shall be decreased in proportion to
such decrease in outstanding shares of Common Stock and the Exercise Price shall be proportionally increased such that the aggregate
Exercise Price, after such adjustments, remains the same for each Warrant.

 

		4.3	Purchase Rights. If at any time the Company grants, issues or sells any options, convertible securities or rights to
purchase stock, warrants, securities or other property pro rata to the record holders of any class of Common Stock (the “Purchase
Rights”), then the Holder will be entitled to acquire, upon the terms applicable to such Purchase Rights, the aggregate
Purchase Rights which the Holder could have acquired if the Holder had held the number of shares of Common Stock acquirable upon
complete exercise of this Warrant (without regard to any limitations on exercise hereof, including without limitation, the Maximum
Percentage) immediately before the date on which a record is taken for the grant, issuance or sale of such Purchase Rights, or,
if no such record is taken, the date as of which the record holders of Common Stock are to be determined for the grant, issue or
sale of such Purchase Rights (provided, however, to the

 

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extent that the Holder’s right
to participate in any such Purchase Right would result in the Holder exceeding the Maximum Percentage, then the Holder shall not
be entitled to participate in such Purchase Right to such extent (or beneficial ownership of such Common Stock as a result of such
Purchase Right to such extent) and such Purchase Right to such extent shall be held in abeyance for the Holder until such time,
if ever, as its right thereto would not result in the Holder exceeding the Maximum Percentage, at which time or times the Holder
shall be granted such right (and any Purchase Right granted, issued or sold on such initial Purchase Right or on any subsequent
Purchase Right to be held similarly in abeyance) to the same extent as if there had been no such limitation).

 

		4.4	Fundamental Transactions. If, at any time while the Warrants are outstanding, (i) the Company, directly or indirectly,
in one or more related transactions effects any merger or consolidation of the Company with or into another person, (ii) the Company,
directly or indirectly, effects any sale, lease, license, assignment, transfer, conveyance or other disposition of all or substantially
all of its assets in one or a series of related transactions, (iii) any, direct or indirect, purchase offer, tender offer or exchange
offer (whether by the Company or another person) is completed pursuant to which holders of Common Stock are permitted to sell,
tender or exchange their shares for other securities, cash or property and has been accepted by the holders of 50% or more of the
outstanding Common Stock, (iv) the Company, directly or indirectly, in one or more related transactions effects any reclassification,
reorganization or recapitalization of the Common Stock or any compulsory share exchange pursuant to which the Common Stock is effectively
converted into or exchanged for other securities, cash or property, (v) the Company, directly or indirectly, in one or more related
transactions consummates a stock or share purchase agreement or other business combination (including, without limitation, a reorganization,
recapitalization, spin-off or scheme of arrangement) with another person or group of persons whereby such other person or group
acquires more than 50% of the outstanding shares of Common Stock (not including any shares of Common Stock held by the other person
or other persons making or party to, or associated or affiliated with the other persons making or party to, such stock or share
purchase agreement or other business combination) (each a “Fundamental Transaction”), then, upon any
subsequent exercise of a Warrant, the Registered Holder of each Warrant shall have the right to receive, for each share of Common
Stock that would have been issuable upon such exercise immediately prior to the occurrence of such Fundamental Transaction, at
the option of the Registered Holder (without regard to any limitation in Section 3.4 on the exercise of the Warrants), the number
of shares of Common Stock of the successor or acquiring corporation or of the Company, if it is the surviving corporation, and
any additional consideration (the “Alternate Consideration”) receivable as a result of such Fundamental
Transaction by a holder of the number of shares of Common Stock for which a Warrant is exercisable immediately prior to such Fundamental
Transaction (without regard to any limitation in Section 3.4 on the exercise of the Warrants). For purposes of any such exercise,
the determination of the Exercise Price shall be appropriately adjusted to apply to such Alternate Consideration based on the amount
of Alternate Consideration issuable in respect of one share of Common Stock in such Fundamental Transaction, and the Company shall
apportion the Exercise Price among the Alternate Consideration in a reasonable manner reflecting the relative value of any different
components of the Alternate Consideration. If holders of Common Stock are given any choice as to the securities, cash or property
to be received in a Fundamental Transaction, then each Registered Holder shall be given the same choice as to the Alternate Consideration
such Registered Holder receives upon any exercise of a Warrant

 

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following such Fundamental Transaction.
Notwithstanding anything to the contrary, in the event of a Fundamental Transaction, the Company shall, at a Registered Holder’s
option, exercisable at any time prior to the consummation of the Fundamental Transaction, purchase such Registered Holder’s
Warrant immediately prior to the consummation of such Fundamental Transaction from the Registered Holder by paying cash by wire
transfer of immediately available funds in an amount equal to the Black Scholes Value of the remaining unexercised portion of such
Registered Holder’s Warrant immediately prior to the consummation of such Fundamental Transaction. “Black Scholes
Value” means the value of a Warrant based on the Black and Scholes Option Pricing Model obtained from the “OV”
function on Bloomberg, L.P. (“Bloomberg”) determined immediately prior to the consummation of the applicable
Fundamental Transaction for pricing purposes and reflecting (A) a risk-free interest rate corresponding to the U.S. Treasury rate
for a period equal to the time between the date of the public announcement of the applicable Fundamental Transaction and the Expiration
Date, (B) an expected volatility equal to the greater of 100% and the 100 day volatility obtained from the HVT function on Bloomberg
as of the trading day immediately following the public announcement of the applicable Fundamental Transaction, (C) the underlying
price per share used in such calculation shall be the sum of the price per share of Common Stock being offered in cash, if any,
plus the value of any non-cash consideration, if any, being offered in such Fundamental Transaction (the “FMV”)
and (D) a remaining option time equal to the time between the date of the public announcement of the applicable Fundamental Transaction
and the Expiration Date. The Company shall cause any successor entity in a Fundamental Transaction in which the Company is not
the survivor (the “Successor Entity”) to assume in writing all obligations of the Company under each
Warrant in accordance with the provisions of this Section 4.3 pursuant to agreements in form and substance reasonably satisfactory
to the Registered Holders and approved by the Registered Holder (without unreasonable delay) prior to such Fundamental Transaction
and shall, at the option of each Registered Holder, deliver to such Registered Holder in exchange for such Registered Holder’s
Warrant a security of the Successor Entity evidenced by a written instrument substantially similar in form and substance to such
Registered Holder’s Warrant which is exercisable for a corresponding number of shares of capital stock of such Successor
Entity (or its parent entity) equivalent to the shares of Common Stock acquirable and receivable upon exercise of such Warrant
(without regard to the limitations on exercise set forth in Section 3.4) prior to such Fundamental Transaction, and with an exercise
price which applies the Exercise Price hereunder to such shares of capital stock (but taking into account the relative value of
the shares of Common Stock pursuant to such Fundamental Transaction and the value of such shares of capital stock, such number
of shares of capital stock and such exercise price being for the purpose of protecting the economic value of such Warrant immediately
prior to the consummation of such Fundamental Transaction), and which is reasonably satisfactory in form and substance to the Registered
Holder. Upon the occurrence of any such Fundamental Transaction, the Successor Entity shall succeed to, and be substituted for
(so that from and after the date of such Fundamental Transaction, the provisions of this Agreement and each Warrant referring to
the “Company” shall refer instead to the Successor Entity), and may exercise every right and power of the Company and
shall assume all of the obligations of the Company under this Agreement and each Warrant with the same effect as if such Successor
Entity had been named as the Company herein.

 

		4.5	Calculations. All calculations under this Section 4 shall be made to the nearest cent or the nearest whole share, as
the case may be. For purposes of this Section 4, any

 

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calculation of the number of shares
of Common Stock deemed to be issued and outstanding as of a given date shall not include treasury shares, if any. Notwithstanding
anything to the contrary in this Section 4, no adjustment in the Exercise Price shall be required unless such adjustment would
require an increase or decrease of at least 1% in such price; provided however, that any adjustments which by reason of the immediately
preceding sentence are not required to be made shall be carried forward and taken into account in any subsequent adjustment. In
any case in which this Section 4 shall require that an adjustment in the Exercise Price be made effective as of a record date for
a specified event, if the Registered Holder exercises a Warrant after such record date, the Company may elect to defer, until the
occurrence of such event, the issuance of the shares of Common Stock and other capital stock of the Company in excess of the shares
of Common Stock and other capital stock of the Company, if any, issuable upon such exercise on the basis of the Exercise Price
in effect prior to such adjustment; provided, however, that in such case the Company or the Warrant Agent shall deliver to the
Registered Holder a due bill or other appropriate instrument evidencing the Registered Holder’s right to receive such additional
shares and/or other capital securities upon the occurrence of the event requiring such adjustment.

 

		4.6	Notices of Changes in Warrant. Upon every adjustment of the Exercise Price or the number of shares issuable upon exercise
of a Warrant, the Company shall give written notice thereof to the Warrant Agent, which notice shall state the Exercise Price resulting
from such adjustment and the increase or decrease, if any, in the number of shares purchasable at such price upon the exercise
of a Warrant, setting forth in reasonable detail the method of calculation and the facts upon which such calculation is based.
Upon occurrence of any event specified in  Sections 4.1, 4.2 or 4.3, the Company shall give written notice of the
occurrence of such event to each Warrant holder, at the last address set forth for such holder in the Warrant Register, of the
record date or the effective date of the event. Failure to give such notice, or any defect therein, shall not affect the legality
or validity of such event.

 

		4.7	No Fractional Shares. Notwithstanding any provision contained in this Warrant Agreement to the contrary, the Company
shall not issue fractional shares upon exercise of Warrants. If, by reason of any adjustment made pursuant to this Section 4, the
holder of any Warrant would be entitled, upon the exercise of such Warrant, to receive a fractional interest in a share, the Company
shall, upon such exercise, round to the nearest whole number, the number of the shares of Common Stock to be issued to such holder.

 

		4.8	Form of Warrant. The form of Warrant need not be changed because of any adjustment pursuant to this Section 4,
and Warrants issued after such adjustment may state the same Exercise Price and the same number of shares as is stated in the Warrants
initially issued pursuant to this Agreement.

 

		4.9	Other Events. In case any event shall occur affecting the Company as to which none of the provisions of preceding subsections
of this Section 4 are strictly applicable, but which would require an adjustment to the terms of the Warrants in order
to (i) avoid an adverse impact on the Warrants and (ii) effectuate the intent and purpose of this Section 4, then,
in each such case, the Company shall appoint a firm of independent public accountants, investment banking or other appraisal firm
of recognized national standing, which shall give its opinion as to whether or not any adjustment to the rights represented by
the Warrants is necessary to effectuate the intent and purpose of this  Section 4 and, if they determine that an
adjustment is necessary, the terms of such adjustment. The Company

 

    	10

    	 

    

  

shall adjust the terms of the Warrants
in a manner that is consistent with any adjustment recommended in such opinion.

 

		5.	Transfer and Exchange of Warrants.

 

		5.1	Registration of Transfer. The Warrant Agent shall register the transfer, from time to time, of any outstanding Warrant
upon the Warrant Register, upon surrender of such Warrant for transfer, properly endorsed with signatures properly guaranteed and
accompanied by appropriate instructions for transfer. Upon any such transfer, a new Warrant representing an equal aggregate number
of Warrants shall be issued and the old Warrant shall be cancelled by the Warrant Agent. The Warrants so cancelled shall be delivered
by the Warrant Agent to the Company from time to time upon request.

 

		5.2	Procedure for Surrender of Warrants. Warrants may be surrendered to the Warrant Agent, together with a written request
for exchange or transfer, and thereupon the Warrant Agent shall issue in exchange therefor one or more new Warrants as requested
by the Registered Holder of the Warrants so surrendered, representing an equal aggregate number of Warrants.

 

		5.3	Fractional Warrants. The Warrant Agent shall not be required to effect any registration of transfer or exchange which
shall result in the issuance of a warrant certificate for a fraction of a warrant.

 

		5.4	Warrant Execution and Countersignature. The Warrant Agent is hereby authorized to countersign and to deliver, in accordance
with the terms of this Agreement, the Warrants required to be issued pursuant to the provisions of this Section 5.

 

		6.	Other Provisions Relating to Rights of Holders of Warrants.

 

		6.1	No Rights as Stockholder. A Warrant does not entitle the Registered Holder thereof to any of the rights of a stockholder
of the Company, including, without limitation, except as otherwise set forth herein or in any Warrant, the right to receive dividends,
or other distributions, exercise any preemptive rights to vote or to consent or to receive notice as stockholders in respect of
the meetings of stockholders or the election of directors of the Company or any other matter.

 

		6.2	Lost, Stolen, Mutilated, or Destroyed Warrants. If any Warrant is lost, stolen, mutilated, or destroyed, the Company
and the Warrant Agent may on such terms as to indemnity bond or otherwise as they may in their discretion impose (which shall,
in the case of a mutilated Warrant, include the surrender thereof), issue a new Warrant of like denomination, tenor, and date as
the Warrant so lost, stolen, mutilated, or destroyed. Any such new Warrant shall constitute a substitute contractual obligation
of the Company, whether or not the allegedly lost, stolen, mutilated, or destroyed Warrant shall be at any time enforceable by
anyone.

 

		6.3	Reservation of Common Stock. The Company shall at all times reserve and keep available a number of its authorized but
unissued shares of Common Stock that shall be sufficient to permit the exercise in full of all outstanding Warrants issued pursuant
to this Agreement.

 

    	11

    	 

    

  

		6.4	Registration of Common Stock.   The Company registered the Warrants and shares of Common Stock underlying
the Warrants in the Registration Statement. The Company will use its reasonable best efforts to maintain the effectiveness of such
Registration Statement and the current status of the Prospectus or to file and maintain the effectiveness of another registration
statement and another current prospectus covering the shares of Common Stock issuable upon exercise of the Warrants at any time
that the Warrants are exercisable. In addition, the Company agrees to use its reasonable best efforts to register such shares of
Common Stock under the blue sky laws of the states of residence of the exercising Warrant holders to the extent an exemption from
such registration is not available. If at any time, the Company does not have an effective registration statement covering the
shares of Common Stock underlying the Warrants, and Rule 144 is not available to cover such shares of Common Stock due to the failure
of the Company to be currently reporting under the Securities Exchange Act of 1934 (“Public Information Failure”),
then the Company shall pay in cash by wire transfer of immediately available funds an amount per month equal to 1% of the aggregate
VWAP of the shares into which a Warrant is converted which are not able to be delivered without legend because of such Public Information
Failure to the Holder thereof until such shares are able to be delivered without legend (to be pro-rated for any periods which
are less than one month).

 

		7.	Concerning the Warrant Agent and Other Matters.

 

		7.1	Payment of Taxes. The Company shall from time to time promptly pay all taxes and charges that may be imposed upon the
Company or the Warrant Agent in respect of the issuance or delivery of shares of Common Stock upon the exercise of the Warrants,
but the Company shall not be obligated to pay any transfer taxes in respect of the Warrants or such shares.

 

		7.2	Resignation, Consolidation, or Merger of Warrant Agent.

 

		7.2.1	Appointment of Successor Warrant Agent. The Warrant Agent, or any successor hereafter appointed, may resign its duties
and be discharged from all further duties and liabilities hereunder after giving sixty (60) days’ notice in writing
to the Company. If the office of the Warrant Agent becomes vacant by resignation or incapacity to act or otherwise, the Company
shall appoint in writing a successor Warrant Agent in place of the Warrant Agent. If the Company shall fail to make such appointment
within a period of thirty (30) days after it has been notified in writing of such resignation or incapacity by the Warrant
Agent or by the holder of a Warrant (who shall, with such notice, submit his Warrant for inspection by the Company), then the holder
of any Warrant may apply to the Supreme Court of the State of New York for the County of New York for the appointment of a successor
Warrant Agent at the Company’s cost. Any successor Warrant Agent, whether appointed by the Company or by such court, shall
be a corporation in good standing in the State of New York and having its principal office in the Borough of Manhattan, City and
State of New York, and authorized under such laws to exercise corporate trust powers and subject to supervision or examination
by federal or state authority. After appointment, any successor Warrant Agent shall be vested with all the authority, powers, rights,
immunities, duties, and obligations of its predecessor Warrant Agent with like effect as if originally named as Warrant Agent hereunder,
without any further act or deed; but if for any reason it becomes necessary or appropriate, the predecessor Warrant Agent shall
execute and deliver, at the expense of the Company, an

 

    	12

    	 

    

  

instrument transferring to such
successor Warrant Agent all the authority, powers, and rights of such predecessor Warrant Agent hereunder; and upon request of
any successor Warrant Agent the Company shall make, execute, acknowledge, and deliver any and all instruments in writing for more
fully and effectually vesting in and confirming to such successor Warrant Agent all such authority, powers, rights, immunities,
duties, and obligations.

 

		7.2.2	Notice of Successor Warrant Agent. In the event a successor Warrant Agent shall be appointed, the Company shall give
notice thereof to the predecessor Warrant Agent and the transfer agent for the Common Stock not later than the effective date of
any such appointment.

 

		7.2.3	Merger or Consolidation of Warrant Agent. Any company into which the Warrant Agent may be merged or with which it may
be consolidated or any corporation resulting from any merger or consolidation to which the Warrant Agent shall be a party shall
be the successor Warrant Agent under this Agreement without any further act.

 

		7.3	Fees and Expenses of Warrant Agent.

 

		7.3.1	Remuneration. The Company agrees to pay the Warrant Agent reasonable remuneration for its services as such Warrant Agent
hereunder and any transfer agent fees which are in addition thereto and shall, pursuant to its obligations under this Agreement,
reimburse the Warrant Agent upon demand for all expenditures that the Warrant Agent may reasonably incur in the execution of its
duties hereunder.

 

		7.3.2	Further Assurances. The Company agrees to perform, execute, acknowledge, and deliver or cause to be performed, executed,
acknowledged, and delivered all such further and other acts, instruments, and assurances as may reasonably be required by the Warrant
Agent for the carrying out or performing of the provisions of this Agreement.

 

		7.4	Liability of Warrant Agent.

 

		7.4.1	Reliance on Company Statement. Whenever in the performance of its duties under this Agreement, the Warrant Agent shall
deem it necessary or desirable that any fact or matter be proved or established by the Company prior to taking or suffering any
action hereunder, such fact or matter (unless other evidence in respect thereof be herein specifically prescribed) may be deemed
to be conclusively proved and established by a statement signed by the President or Chairman of the Board of the Company and delivered
to the Warrant Agent. The Warrant Agent may rely upon such statement for any action taken or suffered in good faith by it pursuant
to the provisions of this Agreement.

 

		7.4.2	Indemnity. The Warrant Agent shall be liable hereunder only for its own gross negligence, willful misconduct or bad
faith. The Company agrees to indemnify the Warrant Agent and save it harmless against any and all liabilities, including judgments,
costs and reasonable counsel fees, for anything done or omitted by the Warrant Agent in the execution of this Agreement, except
as a result of the Warrant Agent’s gross negligence, willful misconduct or bad faith.

 

    	13

    	 

    

  

		7.4.3	Exclusions. The Warrant Agent shall have no responsibility with respect to the validity of this Agreement or with respect
to the validity or execution of any Warrant (except its countersignature thereof). The Warrant Agent shall not be responsible for
any breach by the Company of any covenant or condition contained in this Agreement or in any Warrant. The Warrant Agent shall not
be responsible to make any adjustments required under the provisions of  Section 4 hereof or responsible for
the manner, method, or amount of any such adjustment or the ascertaining of the existence of facts that would require any such
adjustment; nor shall it by any act hereunder be deemed to make any representation or warranty as to the authorization or reservation
of any shares of Common Stock to be issued pursuant to this Agreement or any Warrant or as to whether any shares of Common Stock
shall, when issued, be valid and fully paid and nonassessable.

 

		7.5	Acceptance of Agency. The Warrant Agent hereby accepts the agency established by this Agreement and agrees to perform
the same upon the terms and conditions herein set forth and among other things, shall account promptly to the Company with respect
to Warrants exercised and concurrently account for, and pay to the Company, all monies received by the Warrant Agent for the purchase
of shares of Common Stock through the exercise of the Warrants.

 

		8.	Miscellaneous Provisions.

 

		8.1	Successors. All the covenants and provisions of this Agreement by or for the benefit of the Company or the Warrant Agent
shall bind and inure to the benefit of their respective successors and assigns.

 

		8.2	Notices. Any notice, statement or demand authorized by this Warrant Agreement to be given or made by the Warrant Agent
or by the holder of any Warrant to or on the Company shall be sufficiently given (i) when so delivered if by hand or overnight
delivery, (ii) when sent, if delivered by facsimile (provided confirmation of transmission is mechanically or electronically generated
and kept on file by the sending party) or by electronic mail, or (iii) if sent by certified mail or private courier service within
five (5) days after deposit of such notice, postage prepaid, addressed (until another address is filed in writing by the Company
with the Warrant Agent), as follows:

 

	 	Applied DNA Sciences, Inc.
	 	50 Health Sciences Drive
	 	Stony Brook, New York 11790
	 	Attention: James A. Hayward, Chief Executive Officer

  

Any notice, statement or demand authorized by this Agreement
to be given or made by the holder of any Warrant or by the Company to or on the Warrant Agent shall be sufficiently given (i) upon
receipt if by hand or overnight delivery, (ii) when sent, if delivered by facsimile (provided confirmation of transmission is mechanically
or electronically generated and kept on file by the sending party) or by electronic mail or (iii) if sent by certified mail or
private courier service within five (5) days after deposit of such notice, postage prepaid, addressed (until another address is
filed in writing by the Warrant Agent with the Company), as follows:

 

    	14

    	 

    

  

	 	
        American Stock Transfer & Trust Company, LLC

        6201 15th Avenue

        Brooklyn, NY 11219

        Attention: Corporate Trust Department

  

		8.3	Applicable Law. The validity, interpretation, and performance of this Agreement and of the Warrants shall be governed
in all respects by the laws of the State of New York, without giving effect to conflicts of law principles that would result in
the application of the substantive laws of another jurisdiction. The Company hereby agrees that any action, proceeding or claim
against it arising out of or relating in any way to this Agreement shall be brought and enforced in the courts of the State of
New York or the United States District Court for the Southern District of New York, and irrevocably submits to such jurisdiction,
which jurisdiction shall be exclusive. The Company hereby waives any objection to such exclusive jurisdiction and that such courts
represent an inconvenient forum.

 

		8.4	Persons Having Rights under this Agreement. Nothing in this Agreement shall be construed to confer upon, or give to,
any person or corporation other than the parties hereto and the Registered Holders of the Warrants any right, remedy, or claim
under or by reason of this Warrant Agreement or of any covenant, condition, stipulation, promise, or agreement hereof. All covenants,
conditions, stipulations, promises, and agreements contained in this Warrant Agreement shall be for the sole and exclusive benefit
of the parties hereto and their successors and assigns and of the Registered Holders of the Warrants.

 

		8.5	Examination of the Warrant Agreement. A copy of this Agreement shall be available at all reasonable times at the office
of the Warrant Agent in the Borough of Manhattan, City of New York and State of New York, for inspection by the Registered Holder
of any Warrant. The Warrant Agent may require any such holder to submit his Warrant for inspection by it.

 

		8.6	Counterparts. This Agreement may be executed in any number of original or facsimile counterparts and each of such counterparts
shall for all purposes be deemed to be an original, and all such counterparts shall together constitute but one and the same instrument.

 

		8.7	Effect of Headings. The section headings herein are for convenience only and are not part of this Warrant Agreement
and shall not affect the interpretation thereof.

 

		8.8	Amendments. This Agreement may be amended by the parties hereto without the consent of any Registered Holder for the
purpose of curing any ambiguity, or curing, correcting or supplementing any defective provision contained herein or adding or changing
any other provisions with respect to matters arising under this Agreement as the parties may deem necessary or desirable and that
the parties deem shall not adversely affect the interest of the Registered Holders. All other modifications or amendments shall
require the written consent of the Company and the Registered Holders holding Warrants to purchase at least 65% of the shares of
Common Stock underlying the then outstanding Warrants. No consideration shall be offered by the Company to any Registered Holder
in connection with a modification, amendment or waiver of this Warrant Agreement or any Warrant without also offering the same
consideration to all Registered Holders.

 

    	15

    	 

    

  

		8.9	Severability. This Warrant Agreement shall be deemed severable, and the invalidity or unenforceability of any term or
provision hereof shall not affect the validity or enforceability of this Warrant Agreement or of any other term or provision hereof.
Furthermore, in lieu of any such invalid or unenforceable term or provision, the parties hereto intend that there shall be added
as a part of this Warrant Agreement a provision as similar in terms to such invalid or unenforceable provision as may be possible
and be valid and enforceable.

 

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:	 	 
	 	 	Name: 
	 	 	Title: 
	 	 	 	 
	 	AMERICAN STOCK TRANSFER & TRUST COMPANY, LLC, as Warrant Agent
	 	 	 	 
	 	By:	 	 
	 	 	Name:	 
	 	 	Title:	 

 

    	16

    	 

    

 

EXHIBIT A

 

[FORM OF WARRANT CERTIFICATE]

 

Number

 

Warrants

 

THIS WARRANT
SHALL BE VOID IF NOT EXERCISED PRIOR TO

THE EXPIRATION OF THE EXERCISE PERIOD PROVIDED FOR

IN THE WARRANT AGREEMENT DESCRIBED BELOW

 

APPLIED DNA SCIENCES, INC.

 

Incorporated Under the Laws of the State
of Delaware

 

CUSIP 03815U 110

 

Warrant Certificate

 

This Warrant
Certificate certifies that, or registered assigns, is the registered holder of warrant(s) (the “Warrants”
and each, a “Warrant”) to purchase shares of Common Stock, no par value (“Common Stock”),
of Applied DNA Sciences, Inc., a Delaware corporation (the “Company”). Each Warrant entitles the holder,
upon exercise during the period set forth in the Warrant Agreement referred to below, to receive from the Company that number of
fully paid and nonassessable shares of Common Stock as set forth below, at the exercise price (the “Exercise Price”)
as determined pursuant to the Warrant Agreement, payable in lawful money (or through “cashless exercise”
as provided for in the Warrant Agreement) of the United States of America upon surrender of this Warrant Certificate and payment
of the Exercise Price at the office or agency of the Warrant Agent referred to below, subject to the conditions set forth herein
and in the Warrant Agreement. Defined terms used in this Warrant Certificate but not defined herein shall have the meanings given
to them in the Warrant Agreement (as defined on the reverse hereof).

 

Each Warrant is initially
exercisable for one fully paid and non-assessable share of Common Stock. The number of the shares of Common Stock issuable upon
exercise of the Warrants is subject to adjustment upon the occurrence of certain events set forth in the Warrant Agreement.

 

The initial Exercise
Price per share of Common Stock for any Warrant is equal to $_____ per share. The Exercise Price is subject to adjustment upon
the occurrence of certain events set forth in the Warrant Agreement.

 

Subject to the conditions
set forth in the Warrant Agreement, the Warrants may be exercised only during the Exercise Period and to the extent not exercised
by the end of such Exercise Period, such Warrants shall become void.

 

    	A-1

    	 

    

  

Reference is hereby
made to the further provisions of this Warrant Certificate set forth on the reverse hereof and such further provisions shall for
all purposes have the same effect as though fully set forth at this place.

 

This Warrant Certificate
shall not be valid unless countersigned by the Warrant Agent, as such term is used in the Warrant Agreement.

 

This Warrant Certificate
shall be governed by and construed in accordance with the internal laws of the State of New York, without regard to conflicts of
laws principles thereof.

 

	 	APPLIED DNA SCIENCES, INC.
	 	 	 	 
	 	By:	 	 
	 	 	Name: 
	 	 	Title: 
	 	 	 	 
	 	AMERICAN STOCK TRANSFER & TRUST COMPANY, LLC, as Warrant Agent
	 	 	 	 
	 	By:	 	 
	 	 	Name:	 
	 	 	Title:	 

 

[Signature Page to Warrant Certificate]

 

    	A-2

    	 

    

  

[Form of Warrant Certificate]

 

[Reverse]

 

The Warrants evidenced
by this Warrant Certificate are part of a duly authorized issue of Warrants entitling the holder on exercise to receive shares
of Common Stock and are issued or to be issued pursuant to a Warrant Agreement dated as of November ___, 2014 (the “Warrant
Agreement”), duly executed and delivered by the Company to American Stock Transfer & Trust Company, LLC, a New
York limited liability trust company, as warrant agent (the “Warrant Agent”), which Warrant Agreement
is hereby incorporated by reference in and made a part of this instrument and is hereby referred to for a description of the rights,
limitation of rights, obligations, duties and immunities thereunder of the Warrant Agent, the Company and the holders (the words
“holders” or “holder” meaning the Registered Holders or Registered Holder)
of the Warrants. A copy of the Warrant Agreement may be obtained by the holder hereof upon written request to the Company. Defined
terms used in this Warrant Certificate but not defined herein shall have the meanings given to them in the Warrant Agreement.

 

Warrants may be exercised
at any time during the Exercise Period set forth in Section 3.3 of the Warrant Agreement.

 

Notwithstanding anything
else in this Warrant Certificate or the Warrant Agreement, no Warrant may be exercised unless at the time of exercise (i) a registration
statement covering the shares of Common Stock to be issued upon exercise is effective under the Securities Act and (ii) a prospectus
thereunder relating to the shares of Common Stock is current, except through “cashless exercise” as provided
for in the Warrant Agreement.

 

The Warrant Agreement
provides that upon the occurrence of certain events the number of shares of Common Stock issuable upon exercise of the Warrants
set forth on the face hereof may, subject to certain conditions, be adjusted. If, upon exercise of a Warrant, the holder thereof
would be entitled to receive a fractional interest in a share of Common Stock, the Company shall, upon exercise, round up to the
nearest whole number of shares of Common Stock to be issued to the holder of the Warrant.

 

Warrant Certificates,
when surrendered at the principal corporate trust office of the Warrant Agent by the Registered Holder thereof in person or by
legal representative or attorney duly authorized in writing, may be exchanged, in the manner and subject to the limitations provided
in the Warrant Agreement, but without payment of any service charge, for another Warrant Certificate or Warrant Certificates of
like tenor evidencing in the aggregate a like number of Warrants.

 

Upon due presentation
for registration of transfer of this Warrant Certificate at the office of the Warrant Agent a new Warrant Certificate or Warrant
Certificates of like tenor and evidencing in the aggregate a like number of Warrants shall be issued to the transferee(s) in exchange
for this Warrant Certificate, subject to the limitations provided in the Warrant Agreement, without charge except for any tax or
other governmental charge imposed in connection therewith.

 

    	A-3

    	 

    

  

The Company and the
Warrant Agent may deem and treat the Registered Holder(s) hereof as the absolute owner(s) of this Warrant Certificate (notwithstanding
any notation of ownership or other writing hereon made by anyone), for the purpose of any exercise hereof, of any distribution
to the holder(s) hereof, and for all other purposes, and neither the Company nor the Warrant Agent shall be affected by any notice
to the contrary. Neither the Warrants nor this Warrant Certificate entitles any holder hereof to any rights of a stockholder of
the Company.

 

    	A-4

    	 

    

  

Election to Purchase

 

(To Be Executed Upon Exercise of Warrant)

 

The undersigned hereby
irrevocably elects to exercise the right, represented by this Warrant Certificate, to receive shares of Common Stock and herewith
tenders payment for such shares to the order of Applied DNA Sciences, Inc. (the “Company”) in the amount
of $______ in accordance with the terms hereof. The undersigned requests that a certificate for such shares be registered in the
name of _____________________, whose address is and that such shares be delivered to whose address is ______________________. If
said number of shares is less than all of the shares of Common Stock purchasable hereunder, the undersigned requests that a new
Warrant Certificate representing the remaining balance of such shares be registered in the name of ,___________________ whose address
is _______________, and that such Warrant Certificate be delivered to _________________, whose address is ______________________.

 

In the event that the
Warrant is to be exercised on a “cashless” basis pursuant to Section 3.3.2 of the Warrant Agreement, the number
of shares that this Warrant is exercisable for shall be determined in accordance with Section 3.3.2 of the Warrant Agreement.

 

	 	________________	a “Cash Exercise” with respect to ____________________________ Warrant Shares; and/or
	 	 	 
	 	________________	a “Cashless Exercise” with respect to Warrant Shares, resulting in a delivery obligation by the Company to the Holder of shares of Common Stock representing the applicable Net Number, subject to adjustment.

 

 

In the event that the
Warrant may be exercised, to the extent allowed by the Warrant Agreement, through cashless exercise (i) the number of shares that
this Warrant is exercisable for would be determined in accordance with the relevant section of the Warrant Agreement which allows
for such cashless exercise and (ii) the holder hereof shall complete the following: The undersigned hereby irrevocably elects to
exercise the right, represented by this Warrant Certificate, through the cashless exercise provisions of the Warrant Agreement,
to receive shares of Common Stock. If said number of shares is less than all of the shares of Common Stock purchasable hereunder
(after giving effect to the cashless exercise), the undersigned requests that a new Warrant Certificate representing the remaining
balance of such shares be registered in the name of , whose address is , and that such Warrant Certificate be delivered to , whose
address is                              .

 

	Date: ____________, 20	 	(Signature)
	 	 	 
	 	 	(Address)
	 	 	 
	 	 	 
	 	 	(Tax Identification Number)

 

    	A-5Exhibit 10.29

 

Applied DNA Sciences, Inc.

 

November 11, 2014

 

James A. Hayward

Chairman, President & CEO

Applied DNA Sciences

50 Health Sciences Drive

Stony Brook, NY 11790

 

		Re:	Exchange of Promissory Note

 

Dear Dr. Hayward:

 

Reference is made to
that certain 12.5% Promissory Note issued by Applied DNA Sciences, Inc. (the “Company”), to you (the “Holder”),
as of September 11, 2014, in the original principal amount of One Million Dollars ($1,000,000.00) (the “Note”).

 

As you know, the Company
has filed a Registration Statement on Form S-1 (File No. 333-199121) with the Securities Exchange Commission in connection with
the proposed sale of up to $12,000,000 of shares of the Company’s common stock, par value $0.001 per share (“Common
Stock”), and related warrants to purchase Common Stock (“Warrants”), plus up to $1,800,000 of shares
of Common Stock and Warrants subject to an over-allotment option granted by the Company to the underwriters (the “Public
Offering”).

 

This letter shall confirm
our understanding that in connection with the Public Offering, the Company and Holder shall exchange the Note for shares of Common
Stock and Warrants, as set forth herein, in reliance upon the exemption from registration provided by Section 3(a)(9) of the Securities
Act of 1933, as amended (the “Securities Act”), it being understood, for the avoidance of doubt, that such payment
is in full satisfaction of all amounts otherwise owed to Holder with respect to the Note, including for accrued interest on the
Note.

 

The Exchange.
At the Closing (as defined below), the Company will, in exchange and as full consideration for the Note, issue such number of shares
of Common Stock determined by the quotient obtained by dividing the outstanding principal and interest of the Note by the per share
price of the Common Stock sold in the Public Offering (the “Exchange Shares”) and related Warrants (collectively
with the Exchange Shares, the “Exchange Securities”).

 

Closing.
The closing of the transactions contemplated hereunder (the “Closing”) will take place immediately prior to
the closing of the Public Offering. The Company shall deliver to Holder the Exchange Securities upon receipt from Holder of the
original Note for cancellation.

 

Certain Representations
and Warranties. Holder hereby represents and warrants to the Company that the following statements are complete and accurate
as of the date of this letter and will be complete and accurate as of the Closing:

 

    	1

    	 

    

  

Ownership.
Holder is the sole beneficial owner of the aggregate principal amount and any and all accrued and unpaid interest thereon, as the
case may be, of the Note, such Note is owned free and clear of all liens and other claims, encumbrances or restrictions on sale
of any sort whatsoever, and upon the occurrence of the Closing hereunder, the Company shall acquire sole beneficial ownership of
the Note, free and clear of all liens and other claims, encumbrances or restrictions on sale of any sort whatsoever arising from
or through Holder. To the knowledge of Holder, no proceedings relating to Holder are pending or threatened before any court, arbitrator
or administrative or governmental body that would adversely affect Holder’s right to transfer the Note to the Company.

 

Authorization
and Binding Obligation. Holder has the requisite competence and authority to enter into this letter agreement, to carry out
his obligations hereunder and to consummate the transactions contemplated hereby. Holder has taken all actions necessary to authorize
the execution and delivery of this letter agreement, the performance by Holder of his obligations hereunder and the consummation
by Holder of the transactions contemplated hereby. This letter agreement has been duly executed and delivered by Holder and constitutes
the legal, valid and binding obligations of Holder enforceable against Holder in accordance with their respective terms.

 

Accredited
Investor; Investment. Holder is an “accredited investor” (as such term is defined in Rule 501(a) of Regulation
D under the Securities Act). Holder is knowledgeable, sophisticated and experienced in business and financial matters and has previously
invested in securities similar to the Exchange Securities. Holder is able to bear the economic risk of his investment in the Exchange
Securities and is presently able to afford the complete loss of such investment and has been afforded access to information about
the Company and its financial condition, results of operations, business, property and management sufficient to enable Holder to
evaluate his investment in the Exchange Securities. The Exchange Securities will be acquired by Holder for investment for Holder’s
own account, not as a nominee or agent, and not with a view to the public resale or distribution thereof within the meaning of
the Securities Act, except pursuant to resales registered or exempt under the Securities Act. Holder has a pre-existing personal
or business relationship with the Company and/or one or more of its officers or directors. Holder has made an independent decision
to exchange the Note based on the information available to Holder, which he has determined is adequate for that purpose. Holder
acknowledges that he has independently made his own analysis and decision to sell the Note without reliance upon the Company and
based on such information as he has deemed appropriate in his independent judgment. Holder has not relied on any information (in
any form, whether written or oral, including any representation or warranty of the Company) furnished by the Company or on the
Company’s behalf in making that decision (other than the representations of the Company expressly set forth herein). Holder
further acknowledges that it has not relied on the Company or the Company’s representatives for any tax advice related to
the transactions contemplated hereunder and that Holder has consulted with his own tax advisor with respect to the application
of the United States Federal income tax laws to his particular situation as well as any tax consequences of the exchange of the
Note for the Exchange Securities and the ownership and disposition of the Exchange Securities. Neither the Company nor its affiliates,
respective officers, employees, agents or

 

    	2

    	 

    

  

controlling
persons have provided any investment advice or rendered any opinion to Holder as to whether the exchange of the Note for the Exchange
Securities is prudent or suitable.

 

This letter agreement
and the Note constitute and contain the entire agreement among the Company and Holder regarding the subject matter hereof and supersedes
any and all prior agreements, negotiations, correspondence, understandings and communications among the parties, whether written
or oral, respecting the subject matter hereof.

 

The provisions of Section
7 of the Note regarding governing law, exclusive jurisdiction and waiver of jury trial are hereby incorporated into this letter
agreement as if set forth fully herein and shall apply mutatis mutandis.

 

Please acknowledge
your agreement to the foregoing in the space provided below and return your signed acknowledgment to me at your earliest convenience.

 

	 	Applied DNA Sciences, Inc.
	 	 
	 	 	 
	 	By:	   /s/ Karol Kain Gray
	 	Name:	   Karol Kain Gray
	 	Title:	   Chief Financial Officer

 

Acknowledged and Agreed:

 

 

	By:	   /s/ James A. Hayward	 
	 	   James A. Hayward	 

 

    	3

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