As filed with theSecurities and Exchange Commission on November 18, 2024.

Registration Statement No. 333-       

UNITED STATES

SECURITIES AND EXCHANGECOMMISSION

Washington, D.C.20549

FORM S-1

REGISTRATION STATEMENT

UNDER

THE SECURITIESACT OF 1933

Applied DNA Sciences, Inc.

(Exact name of Registrantas specified in its charter)

50 Health SciencesDrive

Stony Brook, NewYork 11790

631-240-8800

(Address, includingzip code, and telephone number, including area code, of Registrant’s principal executive offices)

James A. Hayward,Ph.D., Sc.D.
Chairman, Chief Executive Officer and President
Applied DNA Sciences, Inc.
50 Health Sciences Drive
Stony Brook, New York 11790
631-240-8801

(Name, address,including zip code, and telephone number, including area code, of agent for service)

Copies to:

Merrill M. Kraines

Todd Kornfeld

McDermott Will &Emery LLP

One Vanderbilt Avenue

New York, New York10017-3852

(212)

547-5616

Approximate date of commencement ofproposed sale to the public:

From time to time after this RegistrationStatement becomes effective.

Ifany of the securities being registered on this form are to be offered on a delayed or continuous basis pursuant to Rule 415 underthe Securities Act of 1933, check the following box.    x

Ifthis form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, pleasecheck the following box and list the Securities Act registration statement number of the earlier effective registration statementfor the same offering.    ¨

Ifthis form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box andlist the Securities Act registration statement number of the earlier effective registration statement for the same offering.    ¨

Ifthis form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box andlist the Securities Act registration statement number of the earlier effective registration statement for the same offering.    ¨

Indicate by checkmark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, oran emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smallerreporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Ifan emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complyingwith any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act.    ¨

The Registranthereby amends this Registration Statement on such date or dates as may be necessary to delay its effective date until the Registrantshall file a further amendment which specifically states that this Registration Statement shall thereafter become effective in accordancewith Section 8(a) of the Securities Act of 1933, as amended, or until the Registration Statement shall become effective onsuch date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

Theinformation contained in this prospectus is not complete and may be changed. The selling stockholders named in this prospectus may notsell these securities until the registration statement filed with the Securities and Exchange Commission is effective. This prospectusis not an offer to sell these securities and we are not soliciting offers to buy these securities in any jurisdiction where such offeror sale is not permitted.

Up to 20,312,500shares of Common Stock underlying the Series C Warrants

Up to 20,312,500shares of Common Stock underlying the Series D Warrants

Up to 1,015,625shares of Common Stock underlying the Placement Agent Warrants

AppliedDNA Sciences, Inc.

This prospectus relatesto the resale from time to time, by the selling stockholders (the “Selling Stockholders”) identified in this prospectus underthe caption “Selling Stockholders,” of up to an aggregate of 41,640,625 shares of common stock, par value $0.001 per share(the “Common Stock”), which the selling stockholders (the “Selling Stockholders”) may acquire upon the exerciseof outstanding warrants, consisting of (i) 20,312,500 Series C Warrants (the “Series C Warrants”), (ii) 20,312,500Series D Warrants (“Series D Warrants”, and, together with the Series C Warrants, the “Series Warrants”)and (iii) 1,015,625 Placement Agent Warrants (“Placement Agent Warrants”, and together with the Series Warrants,the “Private Placement Warrants”).

We issued the Series Warrantsto the Selling Stockholders in a private placement concurrent with a registered direct offering (the “Offering”) of 19,247,498shares of Common Stock and pre-funded warrants (the “Pre-Funded Warrants”) to purchase 1,065,002 shares of Common Stock.We issued the Placement Agent Warrants to the Selling Stockholders pursuant to that certain engagement letter dated August 23, 2024,by and between the Company and Craig-Hallum Capital Group LLC (“Craig Hallum”).

The exercisabilityof the Private Placement Warrants will be available only upon receipt of such stockholder approval (the “Warrant Stockholder Approval”)as may be required by the applicable rules and regulations of The Nasdaq Stock Market LLC. Each Series C Warrant has an exerciseprice of $0.32 per share of Common Stock, will become exercisable upon the first trading day (the “Stockholder Approval Date”)following the Company’s notice to warrantholders of Warrant Stockholder Approval, and will expire on the five-year anniversaryof the Stockholder Approval Date. Each Series D Warrant has an exercise price of $0.32 per share of Common Stock, will become exercisableupon the Stockholder Approval Date, and will expire on the 18-month anniversary of the Stockholder Approval Date. Each Placement Agentwarrant has an exerice price of $0.32, will become exercisable upon the Stockholder Approval date and will expire on October 30,2029.

The closing of theissuance and sale of the Private Placement Warrants, Common Stock and Pre-Funded Warrants was consummated on October 31, 2024.

The Selling Stockholdersof the securities and any of their pledgees, assignees and successors-in-interest may, from time to time, sell any or all of their securitiescovered hereby on the principal trading market or any other stock exchange, market or trading facility on which the securities are tradedor in private transactions. These sales may be at fixed or negotiated prices. See “Plan of Distribution” in this prospectusfor more information. We will not receive any proceeds from the resale or other disposition of the Common Stock by the Selling Stockholders.However, we will receive the proceeds of any cash exercise of the Private Placement Warrants. See “Use of Proceeds” beginningon page 13 and “Plan of Distribution” beginning on page 17 of this prospectus for more information.

Our Common Stock is listed on Nasdaq under the symbol “APDN.”On November 15, 2024, the last reported sale price of our Common Stock was $0.16 per share.

We are a “smallerreporting company,” as defined under the federal securities laws and, as such, have elected to comply with certain reduced reportingrequirements for this prospectus and may elect to do so in future filings. See the section titled “Implications of Being a SmallerReporting Company.”

Investingin our securities involves a high degree of risk. See “Risk Factors”beginning on page 8 of this prospectus and under similar headings in the other documents that are incorporated by reference intothis prospectus for a discussion of information that should be considered in connection with an investment in our securities.

Neither the Securitiesand Exchange Commission (“SEC”) nor any state securities commission has approved or disapproved of these securities or passedupon the adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense. The securities are not beingoffered in any jurisdiction where the offer is not permitted.

The date of this prospectusis                 , 2024.

TABLE OF CONTENTS

Prospectus

ABOUTTHIS PROSPECTUS

Theinformation contained in this prospectus is not complete and may be changed. You should rely only on the information provided in or incorporatedby reference in this prospectus, or in a related free writing prospectus, or documents to which we otherwise refer you. We have not authorizedanyone else to provide you with different information.

We have not authorizedany dealer, agent or other person to give any information or to make any representation other than those contained or incorporated byreference in this prospectus or any related free writing prospectus. You must not rely upon any information or representation not containedor incorporated by reference in this prospectus or any related free writing prospectus. This prospectus and any related free writingprospectus, if any, do not constitute an offer to sell or the solicitation of an offer to buy any securities other than the registeredsecurities to which they relate, nor do this prospectus and any related free writing prospectus, if any, constitute an offer to sellor the solicitation of an offer to buy securities in any jurisdiction to any person to whom it is unlawful to make such offer or solicitationin such jurisdiction. You should not assume that the information contained in this prospectus and any related free writing prospectus,if any, is accurate on any date subsequent to the date set forth on the front of such document or that any information we have incorporatedby reference is correct on any date subsequent to the date of the document incorporated by reference, even though this prospectus andany related free writing prospectus is delivered or securities are sold on a later date.

We have not done anythingthat would permit this offering or possession or distribution of this prospectus or any free writing prospectus in any jurisdiction whereaction for that purpose is required, other than in the United States. You are required to inform yourself about and to observe any restrictionsrelating as to this offering and the distribution of this prospectus and any such free writing prospectus outside the United States.

We further note thatthe representations, warranties and covenants made by us in any agreement that is filed as an exhibit to any document that is incorporatedby reference in this prospectus were made solely for the benefit of the parties to such agreement, including, in some cases, for thepurpose of allocating risk among the parties to such agreements, and should not be deemed to be a representation, warranty or covenantto you. Moreover, such representations, warranties or covenants were accurate only as of the date when made. Accordingly, such representations,warranties and covenants should not be relied on as accurately representing the current state of our affairs.

The SEC allows usto “incorporate by reference” into this prospectus the information in documents we file with it, which means that we candisclose important information to you by referring you to those documents. The information incorporated by reference is considered tobe a part of this prospectus, and information that we file later with the SEC will automatically update and supersede this information.Any statement contained in any document incorporated or deemed to be incorporated by reference herein shall be deemed to be modifiedor superseded for purposes of this prospectus to the extent that a statement contained in or omitted from this prospectus or any accompanyingprospectus supplement, or in any other subsequently filed document which also is or is deemed to be incorporated by reference herein,modifies or supersedes such statement. Any such statement so modified or superseded shall not be deemed, except as so modified or superseded,to constitute a part of this prospectus.

PROSPECTUSSUMMARY

This summary highlightscertain information about us, this offering and information appearing elsewhere in this prospectus and in the documents we incorporateby reference in this prospectus. This summary is not complete and does not contain all of the information that you should consider beforeinvesting in our securities. After you carefully read this summary, to fully understand our Company and this offering and its consequencesto you, you should read this entire prospectus and any related free writing prospectus authorized by us, including the information referredto under the heading “Risk Factors” in this prospectus beginning on page 8, and any related free writing prospectus,as well as the other documents that we incorporate by reference into this prospectus, including our financial statements and the notesto those financial statements, which are incorporated herein by reference from our AnnualReport on Form 10-K for the year ended September 30, 2023, filed December 7, 2023, as amendedon January 26, 2024, and our QuarterlyReports on Form 10-Q for the three month periods ended December 31, 2023, filed on February 8, 2024, March 31,2024, filed on May 10,2024 and June 30, 2024, filed on August 8,2024, respectively. Please read “Where You Can Find More Information” on page 23 of this prospectus.

In this prospectus,unless context requires otherwise, references to “we,” “us,” “our,” or “the Company”refer to Applied DNA Sciences, Inc., a Delaware corporation and its consolidated subsidiaries. Our trademarks currently used inthe United States include Applied DNA Sciences®, SigNature® molecular tags, SigNature® T molecular tags, fiberTyping®,SigNify®, Beacon®, CertainT®, LineaDNA®, Linea RNAP^TM, Linea™ COVID-19 Diagnostic Assay Kit, safeCircle®COVID-19 testing and TR8^TM pharmacogenetic testing.  We do not intend our use or display of other companies’trade names or trademarks to imply a relationship with, or endorsement or sponsorship of us by, any other companies. All trademarks,service marks and trade names included in this prospectus are the property of the respective owners.

Applied DNA Sciences, Inc.

Introduction

We are a biotechnologycompany developing and commercializing technologies to produce and detect deoxyribonucleic acid (“DNA”) and ribonucleic acid(“RNA”). Using polymerase chain reaction (“PCR”) to enable the production and detection of DNA and RNA, we currentlyoperate in three primary business markets: (i) the enzymatic manufacture of synthetic DNA for use in the production of nucleic acid-basedtherapeutics (including biologics and drugs), as well as the development and sale of a proprietary RNA polymerase (“RNAP”)for use in the production of messenger RNA (“mRNA”) therapeutics (“Therapeutic DNA Production Services”); (ii) thedetection of DNA and RNA in molecular diagnostics and genetic testing services (“MDx Testing Services”); and (iii) themanufacture and detection of DNA for industrial supply chains and security services (“DNA Tagging and Security Products and Services”).

Our current growthstrategy is to primarily focus our resources on the further development, commercialization, and customer adoption of our TherapeuticDNA Production Services, including the expansion of our contract development and manufacturing operation (“CDMO”) for themanufacture of synthetic DNA for use in the production of nucleic acid-based therapies.

We will continue toupdate our business strategy and monitor the use of our resources regarding our various business segments. The Company’s managementis currently engaged in a strategic review of the Company’s business segments that may result in the closure or divestiture ofthe Company’s MDx Testing Services and/or DNA Tagging and Security Products and Services, as well as workforce reductions and potentialmanagement changes. The terms and structure of any possible closure or divestiture have not been determined or agreed to by the Company’sBoard of Directors. Although the purpose of any closure or divestiture would be to reduce the Company’s expenses and effectuatecost savings, it is possible that there may be restructuring costs. We expect that based on available opportunities and our beliefs regardingfuture opportunities, we will continue to modify and refine our business strategy.

Therapeutic DNAProduction Services

Through our LineaRX, Inc.subsidiary we are developing and commercializing our Linea DNA and Linea IVT platforms for the manufacture of synthetic DNA and proprietaryenzymes for use in the production of nucleic acid-based therapeutics.

Linea DNA Platform

Our Linea DNA platformis our core enabling technology, and enables the rapid, efficient, and large-scale cell-free manufacture of high-fidelity DNA sequencesfor use in the manufacturing of a broad range of nucleic acid-based therapeutics. The Linea DNA platform enzymatically produces a linearform of DNA we call “LineaDNA” that is an alternative to plasmid-based DNA manufacturing technologies that have suppliedthe DNA used in biotherapeutics for the past 40 years.

As of the third quarterof calendar year 2024, there were 4,099 gene, cell and RNA therapies in development from preclinical through pre-registration stages,almost all of which use DNA in their manufacturing process. (Source: ASGCT Gene, Cell & RNA Therapy Landscape: Q3 2024 QuarterlyReport ). Due to what we believe are the Linea DNA platform’s numerous advantages over legacy nucleic acid-based therapeuticmanufacturing platforms, we believe this large number of therapies under development represents a substantial market opportunity forthe Linea DNA platform to supplant legacy manufacturing methods in the manufacture of nucleic acid-based therapies although no assurancecan be given that we will be successful in exploiting this market opportunity.

We believe our LineaDNA platform holds several important advantages over existing cell-based plasmid DNA manufacturing platforms. Plasmid-based DNA manufacturingis based on the complex, costly and time-consuming biological process of amplifying DNA in living bacterial cells. Once amplified, theDNA must be separated from the living cells and other process contaminants via multiple rounds of purification, adding further complexityand costs. Unlike plasmid-based DNA manufacturing, the Linea DNA platform does not require living cells and instead amplifies DNA viathe enzymatic process of PCR. The Linea DNA platform is simple and can rapidly produce very large quantities of DNA without the needfor complex purification steps.

We believe the keyadvantages of the Linea DNA platform include:

Preclinical studies  conducted by the Company have shown that Linea DNA is substitutable for plasmid DNA in numerous nucleic acid-based therapies, including:

Further, we believethat Linea DNA is also substitutable for plasmid DNA in the following nucleic acid-based therapies:

Linea IVT Platform

The number of mRNAtherapies under development is growing at a rapid rate, thanks in part to the success of the mRNA COVID-19 vaccines. mRNA therapeuticsare produced via a process called in vitro transcription (“IVT”) that requires DNA as a starting material. As ofthe third quarter of calendar 2024, there were over 450 mRNA therapies under development, with the majority of these therapies (67%)in the preclinical stage (Source: ASGCT Gene, Cell & RNA Therapy Landscape: Q2 2024 Quarterly Report). The Company believesthat the mRNA market is in a nascent stage that represents a large growth opportunity for the Company via the production and supply ofDNA critical starting materials and RNAP to produce mRNA therapies.

In August 2022,the Company launched DNA IVT templates manufactured via its Linea DNA platform that have resulted in evaluations of the Company’sIVT templates by numerous therapeutic developers and CDMOs in the United States and the Asia-Pacific. In addition, the Company’sIVT templates are under late-stage evaluations by two therapeutic developers and one CDMO for use as templates for the production ofmRNA intended for clinical use. However there can be no assurance that related contracts will be entered into. In response to this demand,the continued growth of the mRNA therapeutic market, and the unique abilities of the Linea DNA platform, the Company acquired Spindlein July 2023 to potentially increase its mRNA-related total addressable market (“TAM”).

Through our acquisitionof Spindle, we launched our Linea IVT platform in July 2023, which combines Spindle’s proprietary high-performance RNAP, nowmarketed by the Company as Linea RNAP, with our enzymatically produced Linea DNA IVT templates. We believe the Linea IVT platform enablesour customers to make better mRNA, faster. Based on data generated by the Company, we believe the integrated Linea IVT platform offersthe following advantages over conventional mRNA production to therapy developers and manufacturers:

According to the Company’sinternal modeling, the ability to sell both Linea DNA IVT templates and Linea RNAP under the Linea IVT platform potentially increasesthe Company’s mRNA-related TAM by approximately 3-5x as compared to selling Linea DNA IVT templates alone, while also providinga more competitive offering to the mRNA manufacturing market. Currently, Linea RNAP is produced for the Company under an ISO 13485 qualitysystem by Alphazyme, LLC a third-party CDMO located in the United States. The Company recently completed manufacturing process developmentwork on its Linea RNAP to increase the production scale of the enzyme and reduce unit costs.

Manufacturing Scale-up

The Company plansto offer several quality grades of Linea DNA, each of which will have different permitted uses.

We are currently manufacturingLinea DNA pursuant to Good Laboratory Practices (“GLP”) and, are in the final stages of creating a fit for purpose manufacturingfacility within our current Stony Brook, NY laboratory space capable of producing Linea DNA IVT templates under Good Manufacturing Practices(“GMP”) suitable for use as a critical starting material for clinical and commercial mRNA therapeutics, with an anticipatedcompletion date in the fourth quarter of calendar year 2024 (“GMP Site 1”). We also plan to offer additional capacity forLinea DNA IVT templates as well as capacity for Linea DNA materials manufactured under GMP suitable for use as, or incorporation into,a biologic, drug substance and/or drug product, with availability expected during the second half of calendar year 2025, dependent uponthe availability of future funding (“GMP Site 2”). GMP is a quality standard used globally and by the U.S. Food and DrugAdministration (“FDA”) to ensure pharmaceutical quality. Drug substances are the pharmaceutically active components of drugproducts.

Segment BusinessStrategy

Our business strategyfor our Therapeutic DNA Production Services is to capitalize upon the rapid growth of mRNA therapies in the near term via our plannednear term future availability of Linea DNA IVT templates manufactured under GMP at our GMP Site 1, while at the same time laying thebasis for additional clinical and commercial applications of Linea DNA with our future planned availability of Linea DNA manufacturedunder GMP suitable for use as, or incorporation into, a biologic, drug substance and/or drug product at planned GMP Site 2. Planned GMPSite 2 may also be used for additional Linea DNA IVT template manufacturing if customer demand exceeds capacity of GMP Site 1. Our currentplan is: (i) through our Linea IVT platform and planned near term future GMP manufacturing capabilities for IVT templates at GMPSite 1 to secure commercial-scale supply contracts with clinical and commercial mRNA and/or self-amplifying mRNA (“sa-RNA”)manufacturers for Linea DNA IVT templates and/or Linea RNAP as critical starting materials; (ii) to utilize our current GLP productioncapacity for non-IVT template applications to secure supply and/or development contracts with pre-clinical therapy developers that useDNA in their therapy manufacturing, and (iii) upon our development of our planned future Linea DNA production under GMP suitablefor use as, or incorporation into, a biologic, drug substance and/or drug product at planned GMP Site 2, to convert existing and newLinea DNA customers into large-scale supply contracts to supply Linea DNA for clinical and commercial use as, or incorporation into,a biologic, drug substance and/or drug product in a wide range of nucleic acid therapies. Until we complete our GMP Site 1 to produceDNA critical starting materials (DNA IVT templates) for mRNA manufacturing, we will not be able to realize significant revenues fromthis business. We estimate the remaining capital expenditure (“CAPEX”) costs to creating GMP Site 1 will be less than $0.30million. If we were to expand our facilities to enable GMP production of Linea DNA for use as, or incorporation, into a biologic, drugsubstance and/or drug product as planned for GMP Site 2, the additional CAPEX may be up to approximately $10 million which would requireadditional funding. We are currently building GMP Site 1 within our existing laboratory space. We anticipate that a GMP Site 2 wouldrequire us to acquire additional space.

MDx TestingServices

Through Applied DNAClinical Labs, LLC (“ADCL”), we leverage our expertise in DNA and RNA detection via PCR to provide and develop clinical moleculardiagnostics and genetic (collectively “MDx”) Testing Services. ADCL is a New York State Department of Health (“NYSDOH”)clinical laboratory improvement amendments (CLIA)-certified laboratory which is currently permitted for virology and genetics (molecular).In providing MDx Testing Services, ADCL employs its own or third-party molecular diagnostic tests.

We have successfullyinternally validated our pharmacogenomics testing services (the “PGx Testing Services”). Our PGx Testing Services utilizesa 120-target PGx panel test to evaluate the unique genotype of a specific patient to help guide the patient’s healthcare providerin making individual drug therapy decisions. Our PGx Testing Services are designed to interrogate DNA targets on over 33 genes and providegenotyping information relevant to certain cardiac, mental health, oncology, and pain management drug therapies.

On June 12, 2024we received full approval from NYSDOH for our PGx Testing Services. Recently published studies show that population-scale PGx enabledmedication management can significantly reduce overall population healthcare costs, reduce adverse drug events, and increase overallpopulation wellbeing. These benefits can result in significant cost savings to large entities and self-insured employers, the latteraccounting for approximately 65% of all U.S. employers in 2022.We plan to leverage our PGx Testing Services to provide PGx testing servicesto large entities, self-insured employers and healthcare providers, as well as concierge healthcare providers.

On September 11,2024, we announced that ADCL has launched an expansion of its clinical testing services for the detection of Mpox (formerly monkeypox)to include testing for both Mpox Clade I and Clade II. The launch of the expanded Mpox testing service comes after ADCL’s interactionwith relevant regulatory bodies, including the New York State Department of Health (NYSDOH) and the U.S. Food and Drug Administration(FDA).The Company believes that ADCL will be able to support New York and other states’ response to the threat of Mpox. ADCL’sLinea Mpox Virus 1.0 Assay was previously approved as a laboratory-developed test for the detection of Mpox Clade II by NYSDOH in September 2022.In August 2024, ADCL conducted additional validation testing showing the Assay can also detect the genetic sequence of Mpox CladeI, which is the subject of the World Health Organization’s (WHO) August 14, 2024 declaration of a public health emergencyof international concern. ADCL will provide the testing service from its CLEP/CLIA molecular diagnostics laboratory in Stony Brook, N.Y.There can be no assurance that we will be able to generate revenue and and profits from Mpox testing.

Historically, themajority of our revenue attributable to our MDx Testing Services has been derived from our safeCircle® COVID-19 testing solutions,for which testing demand has significantly declined commencing in our fiscal third quarter of 2023, resulting in substantially reducedrevenues. We expect future demand for COVID-19 testing to continue to be reduced and we may terminate COVID-19 testing services in thefuture.

DNA Tagging andSecurity Products and Services

By leveraging ourexpertise in both the manufacture and detection of DNA via PCR, our DNA Tagging and Security Products and Services allow our customersto use non-biologic DNA tags manufactured on our Linea DNA platform to mark objects in a unique manner and then identify these objectsby detecting the absence or presence of the DNA tag. The Company’s core DNA Tagging and Security Products and Services, which aremarketed collectively as a platform under the trademark CertainT®, include:

To date, our largestcommercial application for our DNA Tagging and Security Products and Services is in the tracking and provenance authentication of cotton.

The Uyghur ForcedLabor Prevention Act (“UFLPA”) signed into law on December 23, 2021 establishes that any goods mined, produced, or manufacturedwholly or in part in the Xinjiang Uyghur Autonomous Region (“XUAR”) of the People’s Republic of China are not entitledto entry to the United States. On June 17, 2022, the UFLPA additionally listed DNA tagging and isotopic analysis as evidence thatimporters may use to potentially prove that a good did not originate in XUAR. Recently, in July of 2024, the Company announced amulti-year commercialization agreement for its CertainT platform with Indus Group, a multinational apparel/textile manufacturing andsourcing company.

Our business planis to leverage consumer and governmental awareness for product traceability to expand our existing partnerships and seek new partnershipsfor our DNA Tagging and Security Products and Services with a focus on cotton.

Recent Developments

Nasdaq Minimum Bid Price RequirementDeficiency Notification

On November 12,2024, the Company received written notice (the “Notification Letter”) from the Listing Qualifications Department of The NasdaqStock Market LLC (“Nasdaq”) notifying the Company that it is not in compliance with the minimum bid price requirements setforth in Nasdaq Listing Rule 5550(a)(2) for continued listing on The Nasdaq Capital Market. Nasdaq Listing Rule 5550(a)(2) requireslisted securities to maintain a minimum bid price of $1.00 per share, and Nasdaq Listing Rule 5810(c)(3)(A) provides that afailure to meet the minimum bid price requirement exists if the deficiency continues for a period of thirty (30) consecutive businessdays (collectively, the “Bid Price Rule”). Based on the closing bid price of the Company’s Common Stock for the thirty-one(31) consecutive business days from September 27, 2024 to November 11, 2024, the Company no longer meets the requirements ofthe Bid Price Rule.

The Notification Letterdoes not impact the Company’s listing on The Nasdaq Capital Market at this time. The Notification Letter states that the Companyhas 180 calendar days, or until May 12, 2025, to regain compliance with the Bid Price Rule. To regain compliance, the bid priceof the Company’s Common Stock must have a closing bid price of at least $1.00 per share for a minimum of ten (10) consecutivebusiness days, with a longer period potentially required by the staff of Nasdaq (the “Staff”). If the Company does not regaincompliance with the Bid Price Rule by May 12, 2025, the Company may be eligible for an additional 180 calendar day complianceperiod. To qualify, the Company would be required to meet the continued listing requirement for market value of publicly held sharesand all other initial listing standards for The Nasdaq Capital Market, with the exception of the Bid Price Rule, and would need to providewritten notice of its intention to cure the deficiency during the second compliance period, by effecting a reverse stock split, if necessary,no later than ten (10) business days prior to May 12, 2025.

However, if it appearsto the Staff that the Company will not be able to cure the deficiency, or if the Company is otherwise not eligible, Nasdaq would notifythe Company that its securities would be subject to delisting. In the event of such a notification, the Company may appeal the Staff’sdetermination to delist its securities, but there can be no assurance the Staff would grant the Company’s request for continuedlisting.

Pursuant to the securitiespurchase agreement entered into in connection with the Offering (the “Purchase Agreement”), the Company is required to effecta reverse stock split of its outstanding shares of Common Stock if, at any time after the Stockholder Approval Date, it is not in compliancewith Nasdaq’s Bid Price Rule and has received a deficiency letter from the Listing Qualifications Department of The NasdaqStock Market LLC (the “Reverse Stock Split”). The Company must effect the Reverse Stock Split within 30 days of the StockholderApproval Date; provided that if within such 30 day period the Company regains compliance with the Bid Price Rule, the Company shall haveno obligation to effect the Reverse Stock Split. The Company intends to implement a reverse stock split of its outstanding securitiesto regain compliance with the Bid Price Rule and to comply with the provisions of the Purchase Agreement.

Amendment to Series A Warrant

As previously disclosedon our current report on Form 8-K filed on May 29, 2024 we closed on such date a public offering (the “May 2024Offering”) of common stock and warrants, including 9,230,769 series A common stock purchase warrants (“May 2024 Series AWarrants”) and 9,230,769 series B common stock purchase warrants (“May 2024 Series B Warrants”, and, withthe May 2024 Series A Warrants, the “May 2024 Series Warrants”), with Craig-Hallum and Laidlaw &Company (UK) Ltd. (“Laidlaw”) as placement agents. As part of the May 2024 Offering, the Company entered into aPlacement Agency Agreement, dated May 28, 2024, with Craig-Hallum and Laidlaw (the “May 2024 Placement Agency Agreement”).

Subject to certainexceptions, the Series A Warrants provide for an adjustment to the exercise price and number of shares underlying the Series AWarrants upon the Company’s issuance of Common Stock or Common Stock equivalents at a price per share that is less than the exerciseprice of the Series A Warrants (the “Price Reset Mechanism”).

On October 30,2024, the Company and certain holders of the May 2024 Series A Warrants entered into an amendment to such holders’ May 2024Series A Warrants (the “Warrant Amendment”), pursuant to which the Price Reset Mechanism became subject to a floor equalto $0.20.

In connection withthe Offering, the Price Reset Mechanism in the May 2024 Series A Warrants was triggered, which resulted in the number of sharesof Common Stock issuable upon exercise of the May 2024 Series A Warrants increasing from 9,230,769 to 91,890,698. The exerciseprice of the May 2024 Series A Warrants was adjusted from $1.99 per share to $0.20 per share with respect to the May 2024Series A Warrants amended by the Warrant Amendment, and to $0.19 with respect to the May 2024 Series A Warrants not amendedby the Warrant Amendment.

Company Information

We are a Delawarecorporation, which was initially formed in 1983 under the laws of the State of Florida as Datalink Systems, Inc. In 1998, we reincorporatedin the State of Nevada, and in 2002, we changed our name to our current name, Applied DNA Sciences, Inc. On December 17, 2008,we reincorporated from the State of Nevada to the State of Delaware.

Our corporate headquartersare located at the Long Island High Technology Incubator at Stony Brook University in Stony Brook, New York, where we have establishedlaboratories for the manufacture and detection of nucleic acids (DNA and mRNA) to support our various business units. In addition, thislocation also houses our NYSDOH CLEP-permitted, Clinical Laboratory Improvement Amendments (“CLIA”)-certified clinical laboratorywhere we perform MDx Testing Services. The mailing address of our corporate headquarters is 50 Health Sciences Drive, Stony Brook, NewYork 11790, and our telephone number is (631) 240-8800.

Implications of Being a Smaller ReportingCompany

We are a “smallerreporting company” as defined in the Securities Exchange Act of 1934, as amended, or the Exchange Act, and have elected to takeadvantage of certain of the scaled disclosures available to smaller reporting companies. We will continue to be a “smaller reportingcompany” until we have $250 million or more in public float (based on our Common Stock) measured as of the last business dayof our most recently completed second fiscal quarter or, in the event we have no public float (based on our Common Stock) or a publicfloat (based on our Common Stock) that is less than $700 million, annual revenues of $100 million or more during the most recentlycompleted fiscal year.

We may choose to takeadvantage of some, but not all, of these exemptions. We have taken advantage of reduced reporting requirements in this prospectus. Accordingly,the information contained herein may be different from the information you receive from other public companies in which you hold stock.

THEOFFERING

Thenumber of shares of our Common Stock to be outstanding after this offering is based on the 50,896,710shares of our Common Stock outstanding as of November 15, 2024, and excludes the following:

Unless otherwise indicated,this prospectus reflects and assumes no exercise of outstanding options and warrants.

RISKFACTORS

Investing in oursecurities involves a high degree of risk. In addition to the other information included or incorporated by reference in this prospectus,you should carefully consider the risks described below and in the section titled “Risk Factors” in our Annual Report onForm 10-K for our most recent fiscal year filed with the SEC, subsequent Quarterly Reports on Form 10-Q, any amendment or updatesthereto reflected in subsequent filings with the SEC, and in other reports we file with the SEC that are incorporated by reference herein,before making an investment decision. The following risks are presented as of the date of this prospectus and we expect that these willbe updated from time to time in our periodic and current reports filed with the SEC, which will be incorporated herein by reference.Please refer to these subsequent reports for additional information relating to the risks associated with investing in our securities.

The risks and uncertaintiesdescribed therein and below could materially adversely affect our business, operating results and financial condition, as well as causethe value of our securities to decline. You may lose all or part of your investment as a result. You should also refer to the other informationcontained in this prospectus, or incorporated by reference, including our financial statements and the notes to those statements, andthe information set forth under the caption “Special Note Regarding Forward-Looking Statements.” Our actual results coulddiffer materially from those anticipated in these forward-looking statements as a result of certain factors, including the risks mentionedbelow. Forward-looking statements included in this prospectus are based on information available to us on the date hereof, and all forward-lookingstatements in documents incorporated by reference are based on information available to us as of the date of such documents. We disclaimany intent to update any forward-looking statements. The risks described below and contained in our Annual Report on Form 10-K,Quarterly Reports on Form 10-Q and in our other periodic reports are not the only ones that we face. Additional risks not presentlyknown to us or that we currently deem immaterial may also adversely affect our business operations.

Risks Related to our Business:

We may not successfully implementour business strategies, including achieving our growth objectives.

We may not be ableto fully implement our business strategies or realize, in whole or in part within the expected time frames, the anticipated benefitsof our various growth or other initiatives. Our various business strategies and initiatives, including our growth, operational and managementinitiatives and the development in particular of our Therapeutic DNA Production Services, are subject to business, economic and competitiveuncertainties and contingencies, many of which are beyond our control. The execution of our business strategy and our financial performancewill continue to depend in significant part our ability to obtain sufficient financing and on our executive management team and otherkey management personnel, our ability to identify and complete suitable acquisitions, our executive management team’s ability toexecute new operational initiatives, and certain matters outside of our control. In addition, we may incur certain costs as we pursueour growth, operational and management initiatives, and we may not meet anticipated implementation timetables or stay within budgetedcosts. As these initiatives are undertaken, we may not fully achieve our expected efficiency improvements or growth rates, or these initiativescould adversely impact our customer retention, supplier relationships or operations. Also, our business strategies may change from timeto time in light of our ability to implement our business initiatives, competitive pressures, economic uncertainties or developments,or other factors.

We may modify and refine our businessstrategy, including possible divestures or closings.

Our management iscurrently engaged in a strategic review of the Company’s business segments that may result in the divestiture or closure of theCompany’s MDx Testing Services and/or DNA Tagging and Security Products and Services, as well as workforce reductions and potentialmanagement changes. The terms and structure of any possible divestiture or closure, including financial terms, have not been determinedor approved by our Board of Directors. Although the purpose of any divestiture or closure would be to reduce our expenses and effectuatecost savings, it is possible that there may be related restructuring costs and the benefits of any divesture or closing may be less thananticipated.  The initial cash received from any divestiture, if any, may be limited, although the terms of a divesture may includefuture royalties, earn-outs or similar terms, any of which could fail to be earned or received.

Stockholders may suffer substantialdilution if certain provisions in the May 2024 Series Warrants are utilized.

On May 29, 2024,we closed on such date the May 2024 Offering, which included the May 2024 Series A Warrants and May 2024 Series BWarrants, pursuant to the May 2024 Placement Agency Agreement.

If the May 2024Series B Warrants are exercised by way of an alternative cashless exercise, such exercising holder will receive three times thenumber of shares of Common Stock they would receive in a cash exercise for each May 2024 Series B Warrant they exercise, withoutany cash payment to us.   In addition, the Series A Warrants and Series B Warrants each include a provision thatresets their exercise price in the event of a reverse split of our Common Stock, to a price equal to the lesser of (i) the thenexercise price and (ii) lowest volume weighted average price (VWAP) during the period commencing five trading days immediately precedingand the five trading days commencing on the date we effect a reverse stock split in the future with a proportionate adjustment to thenumber of shares underlying the applicable warrant,

In addition, and subjectto certain exemptions, if we sell, enter into an agreement to sell, or grant any option to purchase, or sell, enter into an agreementto sell, or grant any right to reprice (excluding Exempt Issuances, as defined in the May 2024 Placement Agency Agreement), or otherwisedispose of or issue (or announce any offer, sale, grant or any option to purchase or other disposition) any shares of common stock, atan effective price per share less than the exercise price of the May 2024 Series A Warrants then in effect, the exercise priceof the May 2024 Series A Warrants will be reduced to the lower of such price or (i) $0.20 with respect to the May 2024Series A Warrants as amended by the Warrant Amendment or (ii) the lowest volume weighted average price (VWAP) during the fiveconsecutive trading days immediately following such dilutive issuance or announcement thereof with respect to the the remaining May 2024Series A Warrants not amended by the Warrant Amendment. The number of shares issuable upon exercise after the aforementioned mechanismhas been triggered will be proportionately adjusted such that the aggregate exercise price will remain unchanged.

In connection withthe Offering, the Price Reset Mechanism in the May 2024 Series A Warrants was triggered, which resulted in the number of sharesof Common Stock issuable upon exercise of the May 2024 Series A Warrants increasing from 9,230,769 to 91,890,698. The exerciseprice of the May 2024 Series A Warrants was adjusted from $1.99 per share to $0.20 per share with respect to the May 2024Series A Warrants amended by the Warrant Amendment, and to $0.19 with respect to the May 2024 Series A Warrants not amendedby the Warrant Amendment.

If any of the above provisions in the May 2024Series Warrants are further utilized, our stockholders may suffer substantial dilution.

Stockholders may suffer substantialdilution if certain provisions in the Series D Warrants are utilized.

If the Series DWarrants are exercised by way of an alternative cashless exercise, assuming receipt of Warrant Stockholder Approval, such exercisingholder will receive one share of Common Stock for each share of Common Stock they would receive in a cash exercise for each May 2024Series D Warrant they exercise, without any cash payment to us.

In addition, the Series DWarrants include a provision that resets their exercise price in the event of a reverse split of our Common Stock, to a price equal tothe lesser of (i) the then exercise price and (ii) lowest volume weighted average price (VWAP) during the period commencingfive trading days immediately preceding and the five trading days commencing on the date we effect a reverse stock split in the futurewith a proportionate adjustment to the number of shares underlying the Series D Warrants, subject to a floor of $0.0634.

If any of the above provisions in the Series Warrantsare utilized, our stockholders may suffer substantial dilution.

The exercisabilityof the Private Placement Warrants is contingent upon us obtaining Warrant Stockholder Approval. If we do not obtain such Warrant StockholderApproval, the Series Warrants may never become exercisable.

The Private PlacementWarrants are not immediately exercisable, as their exercisability is contingent upon us obtaining Warrant Stockholder Approval. The Series Warrantswill become exercisable upon the Stockholder Approval Date and will expire on the five-year anniversary of such date with respect tothe Series C Warrants, and on the eighteen-month anniversary of such date with respect to the Series D Warrants. The PlacementAgent Warrants will become exercisable upon the Stockholder Approval Date and will expire on October 30, 2029. While we intend topromptly seek Warrant Stockholder Approval for these mechanisms, there is no guarantee that it will ever be obtained. In the event thatwe cannot obtain Warrant Stockholder Approval, the Series Warrants may never become exercisable. If we are unable to obtainthe Warrant Stockholder Approval, the Series Warrants will have no value.

We have agreed tohold a special meeting of shareholders (which may also be at the annual meeting of shareholders) at the earliest practicable date afterthe date hereof, but in no event later than ninety days after the closing of the offering, in order to obtain Warrant Stockholder Approval.There is no guarantee we will be able to hold a special meeting within this timeframe, or at all. If we do not obtain Warrant StockholderApproval at the first meeting, we are obligated to call a meeting every ninety days thereafter to seek Warrant Stockholder Approval untilthe earlier of the date on which Stockholder Approval is obtained or the Series Warrants are no longer outstanding.

There are alarge number of shares of Common Stock underlying our outstanding options and warrants and the sale of these shares may depress the marketprice of our Common Stock and cause immediate and substantial dilution to our existing stockholders.

Asof November 15, 2024, we had 50,896,710 shares of Common Stock issued and outstanding, outstandingoptions to purchase 108,176 shares of Common Stock, outstanding warrants to purchase 96,083,181 shares of Common Stock, and 269,069 sharesavailable for grant under our equity incentive plan. The issuance of shares upon exercise of our outstanding options and warrants willcause immediate and substantial dilution to our stockholders and any sale thereof may depress the market price of our Common Stock.

There is substantial doubt relatingto our ability to continue as a going concern.

We have recurringnet losses, which have resulted in an accumulated deficit of $306,376,012 as of June 30, 2024. We have incurred a net loss of $3,774,563for the nine months ended June 30, 2024. At June 30, 2024, we had cash and cash equivalents of $10,442,131. We have concludedthat these factors raise substantial doubt about our ability to continue as a going concern for one year from the issuance of the June 30,2024 financial statements. We will continue to seek to raise additional working capital through public equity, private equity or debtfinancings. If we fail to raise additional working capital, or do so on commercially unfavorable terms, it would materially and adverselyaffect our business, prospects, financial condition and results of operations, and we may be unable to continue as a going concern. Ifwe seek additional financing to fund our business activities in the future and there remains substantial doubt about our ability to continueas a going concern, investors or other financing sources may be unwilling to provide additional funding to us on commercially reasonableterms, if at all.

There can be no assurance that thata commercial demand for our Linea™ Mpox Virus Assay and/or mpox testing services will develop.

On September 11,2024 the Company announced that after interactions with relevant regulatory bodies, including NYSDOH and U.S. FDA, it was launching clinicaltesting services for both mpox clade I and clade II utilizing the Linea mpox Virus Assay (the “Assay”) in New York Stateand in states that recognize New York’s CLEP/CLIA certification. To date, the Company has not performed clinical testing for mpoxclade I or clade II. Future commercial demand for the Assay and/or associated mpox testing services is based upon the unknown and unpredictablefuture path of the mpox public health emergency. Currently, mpox disease prevalence (both clade I and clade II) is extremely low theUnited States, resulting in minimal demand for clinical mpox testing. It is unknown whether a future commercial demand for the Assaywill develop.

We have receivedwritten notice from Nasdaq that we are not in compliance with Nasdaq’s minimum bid price requirements and if we are unable to regaincompliance with Nasdaq continued listing standards, which may require effecting a reverse stock split of our Common Stock, we could bedelisted from Nasdaq, which would negatively impact our business, our ability to raise capital, and the market price and liquidity ofour Common Stock.

On November 12,2024, the Company received the Notification Letter from the Listing Qualifications Department of Nasdaq notifying the Company that, becausethe closing bid price for its Common Stock has been below $1.00 per share for 30 consecutive business days, it no longer complies withthe Bid Price Rule for continued listing on The Nasdaq Stock Market LLC. There is no assurance that we will be able to regain compliancewith the Bid Price Rule. The Notification Letter had no immediate effect on the listing of the Company’s Common Stock on The NasdaqStock Market LLC. The Company has been provided an initial compliance period of 180 calendar days, or until May 12, 2025, toregain compliance with the Bid Price Rule. During the compliance period, the Company’s shares of Common Stock will continue tobe listed and traded on The Nasdaq Stock Market LLC. To regain compliance, the closing bid price of the Company’s Common Stockmust meet or exceed $1.00 per share for a minimum of ten consecutive business days during the 180-day compliance period, with a longerperiod potentially required by the Staff.

If our Common Stockis delisted by Nasdaq, our Common Stock may be eligible for quotation on an over-the-counter quotation system or on the pink sheets butwill lack the market efficiencies associated with Nasdaq. Upon any such delisting, our Common Stock would become subject to the regulationsof the SEC relating to the market for penny stocks. A penny stock is any equity security not traded on a national securities exchangethat has a market price of less than $5.00 per share. The regulations applicable to penny stocks may severely affect the market liquidityfor our Common Stock and could limit the ability of stockholders to sell securities in the secondary market. In such a case, an investormay find it more difficult to dispose of or obtain accurate quotations as to the market value of our Common Stock, and there can be noassurance that our Common Stock will be eligible for trading or quotation on any alternative exchanges or markets.

Delisting from Nasdaqcould adversely affect our ability to raise additional financing through public or private sales of equity securities, would significantlyaffect the ability of investors to trade our securities and would negatively affect the value and liquidity of our Common Stock. Delistingcould also have other negative results, including the potential loss of confidence by employees and customers, the loss of institutionalinvestor interest and fewer business development opportunities.

Pursuant to the PurchaseAgreement, the Company is required to effect a reverse stock split of its outstanding shares of Common Stock if, at any time after theStockholder Approval Date, it is not incompliance with Nasdaq’s Bid Price Rule and has received a deficiency letter from theListing Qualifications Department of The Nasdaq Stock Market LLC (the “Reverse Stock Split”). The Company must effect theReverse Stock Split within 30 days of the Stockholder Approval Date; provided that if within such 30 day period the Company regains compliancewith the Bid Price Rule, the Company shall have no obligation to effect the Reverse Stock Split. The Company intends to implement a reversestock split of its outstanding securities to regain compliance with the Bid Price Rule and to comply with the provisions of thePurchase Agreement.

SPECIALNOTE REGARDING FORWARD-LOOKING STATEMENTS

This prospectus andthe documents that we incorporate herein by reference contain forward-looking statements concerning our business, operations andfinancial performance and condition, as well as our plans, objectives and expectations for our business operations and financial performanceand condition. Any statements contained herein that are not statements of historical facts may be deemed to be forward-looking statements.In some cases, you can identify forward-looking statements by terminology such as “can”, “may”, “could”, “should”, “assume”, “forecasts”, “believe”, “designed to”, “will”, “expect”, “plan”, “anticipate”, “estimate”, “potential”, “position”, “predicts”, “strategy”, “guidance”, “intend”, “budget”, “seek”, “project” or “continue”, or the negative thereof or other comparable terminology regarding beliefs, plans, expectationsor intentions regarding the future. You should read statements that contain these words carefully because they:

We believe it is importantto communicate our expectations. However, forward-looking statements are based on our current expectations, assumptions, estimates andprojections about our business and our industry and are subject to known and unknown risks, uncertainties and other factors. Accordingly,our actual results and the timing of certain events may differ materially from those expressed or implied in such forward-looking statementsdue to a variety of factors and risks, including, but not limited to, those set forth under “Risk Factors” in this prospectus,and the following factors and risks:

Any or all of ourforward-looking statements may turn out to be wrong. They may be affected by inaccurate assumptions that we might make or by known orunknown risks and uncertainties. Actual outcomes and results may differ materially from what is expressed or implied in our forward-lookingstatements. Among the factors that could affect future results are:

All forward-lookingstatements and risk factors included in this prospectus are made as of the date hereof, and all forward-looking statements and risk factorsincluded in documents incorporated herein by reference are made as of their original date, in each case based on information availableto us as of the date hereof, or in the case of documents incorporated by reference, the original date of any such document, and we assumeno obligations to update any forward-looking statement or risk factor, unless we are required to do so by law. If we do update one ormore forward-looking statements, no inference should be drawn that we will make updates with respect to other forward-looking statementsor that we will make any further updates to those forward-looking statements at any future time.

Forward-looking statementsmay include our plans and objectives for future operations, including plans and objectives relating to our products and our future economicperformance, projections, business strategy and timing and likelihood of success. Assumptions relating to the foregoing involve judgmentswith respect to, among other things, future economic, competitive and market conditions, future business decisions, demand for our productsand services, and the time and money required to successfully complete development and commercialization of our technologies, all ofwhich are difficult or impossible to predict accurately and many of which are beyond our control.

Any of the assumptionsunderlying the forward-looking statements contained in this prospectus could prove inaccurate and, therefore, we cannot assure you thatany of the results or events contemplated in any of such forward-looking statements will be realized. Based on the significant uncertaintiesinherent in these forward-looking statements, the inclusion of any such statement should not be regarded as a representation or as aguarantee by us that our objectives or plans will be achieved, and we caution you against relying on any of the forward looking-statementscontained herein.

MARKET, INDUSTRYAND OTHER DATA

Marketdata and certain industry data and forecasts used throughout this prospectus were obtained from sources we believe to be reliable, includingmarket research databases, publicly available information, reports of governmental agencies and industry publications and surveys. Wehave relied on certain data from third-party sources, including internal surveys, industry forecasts and market research, which we believeto be reliable based on our management’s knowledge of the industry. Forecasts are particularly likely to be inaccurate, especiallyover long periods of time. In addition, we do not necessarily know what assumptions regarding general economic growth were used in preparingthe third-party forecasts we cite. Statements as to our market position are based on the most currently available data. While we arenot aware of any misstatements regarding the industry data presented in this prospectus and the documents incorporated by reference intothis prospectus, our estimates involve risks and uncertainties and are subject to change based on various factors, including those discussedunder the heading “Risk Factors” in this prospectus and the documents incorporated by reference into this prospectus.

USEOF PROCEEDS

We will not receiveany proceeds from the sale of the shares of Common Stock by the Selling Stockholders. However, we will receive proceeds from the exerciseof the Private Placement Warrants by the Selling Stockholders to the extent they are exercised for cash. We estimate that the maximumproceeds that we may receive from the exercise of the Private Placement Warrants, assuming all the Private Placement Warrants are exercisedat their exercise price of $0.32, will be $13,325,000. We do not know, however, whether any of the Private Placement Warrants will beexercised for cash or, if any of the Private Placement Warrants are exercised for cash, when they will be exercised. It is possible thatthe Private Placement Warrants will expire and never be exercised.

There are circumstancesunder which the Private Placement Warrants may be exercised on a cashless basis, including pursuant to the alternative cashless exercisemechanism of the Series D Warrants. In these circumstances, even if the Private Placement Warrants are exercised, we may not receiveany proceeds, or the proceeds that we do receive may be significantly less than what we might expect. We intend to use the aggregatenet proceeds from the exercise of the Private Placement Warrants for the further development of our Therapeutic DNA Production Services,as well as for general corporate purposes, including working capital. The actual allocation of proceeds realized from the exercise ofthese Private Placement Warrants will depend upon the amount and timing of such exercises, our operating revenues and cash position atsuch time and our working capital requirements. The Selling Stockholders will pay any expenses incurred by the Selling Stockholders forbrokerage, accounting, tax or legal services or any other expenses incurred by the Selling Stockholders in disposing of their sharesof Common Stock. We will bear all other costs, fees and expenses incurred in effecting the registration of the shares covered by thisprospectus, including, without limitation, all registration fees and fees and expenses of our counsel and our accountants.

MARKETPRICE OF OUR COMMON STOCK AND RELATED STOCKHOLDER MATTERS

Market Information

Our Common Stock islisted on The Nasdaq Capital Market under the symbol “APDN.” A description of our Common Stock is set forth under the heading “Description of Capital Stock” beginning on page 19 of this prospectus.

The last reported sale price for our Common Stock on November 15,2024 was $0.16 per share.

Holders

As of November 15, 2024, we had 375 record holders of our CommonStock and no preferred stock issued and outstanding. The number of record holders was determined from the records of our transferagent and does not include beneficial owners of Common Stock whose shares are held in the names of various security brokers, dealers,and registered clearing agencies. The transfer agent of our Common Stock is Equiniti Trust Company, LLC. The transfer agent and registrar’saddress is 90 Park Avenue, New York, NY 10016.

Dividend Policy

The Company has neverpreviously declared or paid any cash dividends on its Common Stock. We currently intend to retain earnings and profits, if any, to supportour business strategy and do not intend to pay any cash dividends within the foreseeable future. Any future determination to pay cashdividends will be at the sole discretion of our Board of Directors and will depend upon the financial condition of the Company, its operatingresults, capital requirements, general business conditions and any other factors that our board of directors deems relevant.

PRIVATEPLACEMENT OF WARRANTS

Concurrently with the sale of shares of Common Stock and Pre-Funded Warrants, we also issued and sold to the Selling Stockholders thePrivate Warrants to purchase an aggregate of up to 41,640,625 shares of our Common Stock, consisting of (i) 20,312,500 Series CWarrants, (ii) 20,312,500 Series D Warrants and (iii) 1,015,625 Placement Agent Warrants.

The exercisabilityof the Private Placement Warrants will be available only upon receipt of Warrant Stockholder Approval. Each Series C Warrant hasan exercise price of $0.32 per share of Common Stock, will become exercisable upon the Stockholder Approval Date, and will expire onthe five-year anniversary of the Stockholder Approval Date. Each Series D Warrant has an exercise price of $0.32 per share of CommonStock, will become exercisable upon the Stockholder Approval Date, and will expire on the 18-month anniversary of the Stockholder ApprovalDate. Each Placement Agent warrant has an exerice price of $0.32, will become exercisable upon the Stockholder Approval date and willexpire on October 30, 2029.

The Private PlacementWarrants are exercisable, at the option of each holder, in whole or in part by delivering to us a duly executed exercise notice and,at any time a registration statement registering the issuance of the Common Stock underlying the Private Placement Warrants under theSecurities Act of 1933, as amended (the “Securities Act”) is effective and available for the issuance of such shares, oran exemption from registration under the Securities Act is available for the issuance of such shares, by payment in full in immediatelyavailable funds for the number of Common Stock purchased upon such exercise. If at the time of exercise there is no effective registrationstatement registering, or the prospectus contained therein is not available for the issuance of the Common Stock underlying the PrivatePlacement Warrants, then the Private Placement Warrants may also be exercised, in whole or in part, at such time by means of a cashlessexercise, in which case the holder would receive upon such exercise the net number of common shares determined according to the formulaset forth in the Private Placement Warrants.

Under the alternatecashless exercise option of the Series D Warrants, the holder of a Series D Warrant has the right to receive an aggregate numberof shares equal to the product of (x) the aggregate number of shares of Common Stock that would be issuable upon a cash exerciseof the Series D Warrant and (y) 1.0. In addition, the Series D Warrants include a provision that resets their exerciseprice in the event of a reverse split of our Common Stock, to a price equal to the lesser of (i) the then exercise price and (ii) lowestvolume weighted average price (VWAP) during the period commencing five trading days immediately preceding and the five trading days commencingon the date we effect a reverse stock split in the future with a proportionate adjustment to the number of shares underlying the Series DWarrants, subject to a floor of $0.0634.

Subject to limitedexceptions, a holder of Private Placement Warrants does not have the right to exercise any portion of its Private Placement Warrantsif the holder, together with its affiliates, would beneficially own in excess of 4.99% (or, at the election of the purchaser prior toissuance of the Private Placement Warrants, 9.99%) of the number of shares of our Common Stock outstanding immediately after giving effectto such exercise. A holder may increase or decrease the beneficial ownership limitation up to 9.99%, provided, however, that any increasein the beneficial ownership limitation shall not be effective until 61 days following notice of such change to the Company.

Pursuant to the PurchaseAgreement, within 20 calendar days from the date of the Purchase Agreement, we agreed to file a registration statement on Form S-1providing for the resale of the shares issuable upon exercise of the Private Placement Warrants. We agreed to use commercially reasonableefforts to cause such registration statement to become effective within 50 calendar days following the closing date of the Purchase Agreement(or 90 calendar days following the closing date of the Purchase Agreement in the event that the SEC requires the Company to include itsaudited year-end financial statements for the fiscal year ended September 30, 2024 in such registration statement) and to keep suchregistration statement effective at all times until no Selling Stockholder owns any Private Placement Warrants or shares of Common Stockissuable upon exercise thereof.

We also agreed tohold a special meeting of stockholders to obtain the Warrant Stockholder Approval no later than 90 days after the closing of the Offering(the “Special Meeting”). If the Company does not obtain Warrant Stockholder Approval at the first meeting, the Company isobligated to call a meeting every ninety days thereafter to seek Warrant Stockholder Approval until the earlier of the date on whichWarrant Stockholder Approval is obtained or the Series Warrants are no longer outstanding. The Company has agreed to file a preliminaryproxy statement with respect to obtaining Warrant Stockholder Approval at the Special Meeting within 20 days following the closing dateof the Purchase Agreement.

In the event of anyfundamental transaction, as described in the Private Placement Warrants and generally including any merger with or into another entity,sale of all or substantially all of the Company’s assets, tender offer or exchange offer, or reclassification of the shares ofCommon Stock, subject to certain exceptions, then upon any subsequent exercise of a Private Placement Warrant, the holder has the rightto receive as alternative consideration, for each share of Common Stock that would have been issuable upon such exercise immediatelyprior to the occurrence of such fundamental transaction, the number of shares of Common Stock of the successor or acquiring corporationof the Company, if it is the surviving corporation, and any additional consideration receivable upon or as a result of such transactionby a holder of the number of shares of Common Stock for which the Private Placement Warrant is exercisable immediately prior to suchevent. Notwithstanding the foregoing, in the event of a fundamental transaction, the holders of the Private Placement Warrants have theright to require the Company or a successor entity to purchase the Private Placement Warrants for cash in the amount of the Black ScholesValue (as defined in the Private Placement Warrants) of the unexercised portion of the Private Placement Warrants concurrently with orwithin 30 days following the consummation of a fundamental transaction. However, in the event of a fundamental transaction which is notin the Company’s control or in which the consideration payable consists of equity securities of a successor entity that is quotedor listed on a nationally recognized securities exchange, the holders of the Private Placement Warrants will only be entitled to receivefrom the Company or its successor entity, as of the date of consummation of such fundamental transaction the same type or form of consideration(and in the same proportion), at the Black Scholes Value of the unexercised portion of the Private Placement Warrants that is being offeredand paid to the holders of Common Stock in connection with the fundamental transaction, whether that consideration is in the form ofcash, stock or any combination of cash and stock, or whether the holders of Common Stock are given the choice to receive alternativeforms of consideration in connection with the fundamental transaction.

SELLINGSTOCKHOLDERS

The shares of CommonStock being offered by the Selling Stockholders are those issuable to the Selling Stockholders, upon exercise of the Private PlacementWarrants. For additional information regarding the issuances of the Private Placement Warrants, see “Private Placement of Warrants”above. We are registering the shares of Common Stock underlying the Private Placement Warrants in order to permit the Selling Stockholdersto offer the shares for resale from time to time. In addition to the ownership of the shares of Common Stock and the Private PlacementWarrants, the Selling Stockholders have had material relationships with us within the past three years.

On May 28, 2024,the Company entered into the May Placement Agency Agreement with Craig-Hallum and Laidlaw (collectively, the “May PlacementAgents”) pursuant to which the May Placement Agents agreed to serve as the co-placement agents, on a “reasonable bestefforts” basis, in connection with the May 2024 Offering of 9,230,769 units (the “Units”), with eachUnit consisting of either (A) one share of the Company’s Common Stock, one  May 2024 Series A Warrantand one May 2024 Series B Warrant or (B) one pre-funded warrant (each, a “May 2024 Pre-Funded Warrant”)to purchase one share of Common Stock and one May 2024 Series A Warrant and one May 2024Series B Warrant. In connection with the May 2024 Offering, the Company also issued placement agent warrants to purchase upto 461,538 shares of Common Stock. The May 2024 Offering closed on May 29, 2024. The purchase price of each Unitwas $1.30, except for Units which include May 2024 Pre-Funded Warrants, which had a purchase price of $1.2999.

The Company receivednet proceeds from the May Offering, after deducting placement agent fees and other offering expenses payable by the Company, ofapproximately $10.5 million. Each of the Selling Stockholders participated in the May 2024 Offering.

On August 8,2022, the Company completed a best efforts public offering (the “August 2022 Offering”) with respect to the issuanceand sale of: (i) 2,820,000 of shares of the Company’s Common Stock, (ii) 3,000,000 series A common stock purchase warrants,each to purchase one share of Common Stock, (iii) 3,000,000 series B common stock purchase warrants, each to one share of CommonStock, and (iv) 180,000 pre-funded common stock purchase warrants, each to purchase one share of Common Stock. The Company receivednet proceeds of approximately $11.1 million from the August 2022 Offering, after deducting the estimated offering expenses payableby the Company, including placement agent fees. Three of the Selling Stockholders, Sabby Volatility Warrant Master Fund, Ltd.,Anson Master Funds and Michael Bigger, participated in the August 2022 Offering.

The table below liststhe Selling Stockholders and other information regarding the beneficial ownership of the shares of Common Stock by each of the SellingStockholders. The second column lists the number of shares of Common Stock beneficially owned by each Selling Stockholders, based onits ownership of the shares of Common Stock, Priavte Placement Warrants, and other warrants, as of November 15, 2024, assuming exerciseof the warrants held by the Selling Stockholders on that date, without regard to any limitations on exercises. The third and fourth columnsassume the sale of all of the shares offered by the Selling Stockholders pursuant to this prospectus. The third column lists the sharesof Common Stock underlying the Private Placement Warrants offered by this prospectus by the Selling Stockholders.

In accordance withthe terms of the Purchase Agreement with the Selling Stockholders, this prospectus generally covers the resale of the maximum numberof shares of Common Stock issuable upon exercise of the Private Placement Warrants.

Under the terms ofthe Private Placement Warrants, and under the terms of certain other warrants held by the Selling Stockholders, a Selling Stockholdermay not exercise the warrants to the extent such exercise would cause such Selling Stockholder, together with its affiliates and attributionparties, to beneficially own a number of shares of Common Stock which would exceed 4.99% or 9.99%, as applicable, of our then outstandingCommon Stock following such exercise, excluding for purposes of such determination shares of Common Stock issuable upon exercise of suchwarrants which have not been exercised. The number of shares in the table below does not reflect the Private Placement Warrants BeneficialOwnership Limitation. The Selling Stockholder may sell all, some or none of their shares in this offering. See “Plan of Distribution.”

*Less than one percent.

PLANOF DISTRIBUTION

Each Selling Stockholderof the securities and any of their pledgees, assignees and successors-in-interest may, from time to time, sell any or all of their securitiescovered hereby on the principal trading market or any other stock exchange, market or trading facility on which the securities are tradedor in private transactions. These sales may be at fixed or negotiated prices. A Selling Stockholder may use any one or more of the followingmethods when selling securities:

The Selling Stockholdersmay also sell securities under Rule 144 or any other exemption from registration under the Securities Act, if available, ratherthan under this prospectus.

Broker-dealers engagedby the Selling Stockholders may arrange for other brokers-dealers to participate in sales. Broker-dealers may receive commissions ordiscounts from the Selling Stockholders (or, if any broker-dealer acts as agent for the purchaser of securities, from the purchaser)in amounts to be negotiated, but, except as set forth in a supplement to this Prospectus, in the case of an agency transaction not inexcess of a customary brokerage commission in compliance with FINRA Rule 2121; and in the case of a principal transaction a markupor markdown in compliance with FINRA Rule 2121.

Ifat the time of any offering made under this prospectus a member of FINRA participating in the offering has a “conflict of interest”as defined in FINRA Rule 5121 (“Rule 5121”), that offering will be conducted in accordance with the relevant provisionsof Rule 5121.

Our Common Stock islisted the Nasdaq Capital Market under the symbol “APDN.”

In connection withthe sale of the securities or interests therein, the Selling Stockholders may enter into hedging transactions with broker-dealers orother financial institutions, which may in turn engage in short sales of the securities in the course of hedging the positions they assume.The Selling Stockholders may also sell securities short and deliver these securities to close out their short positions, or loan or pledgethe securities to broker-dealers that in turn may sell these securities. The Selling Stockholders may also enter into option or othertransactions with broker-dealers or other financial institutions or create one or more derivative securities which require the deliveryto such broker-dealer or other financial institution of securities offered by this prospectus, which securities such broker-dealer orother financial institution may resell pursuant to this prospectus (as supplemented or amended to reflect such transaction).

The Selling Stockholdersand any broker-dealers or agents that are involved in selling the securities may be deemed to be “underwriters” within themeaning of the Securities Act in connection with such sales. In such event, any commissions received by such broker-dealers or agentsand any profit on the resale of the securities purchased by them may be deemed to be underwriting commissions or discounts under theSecurities Act. Each Selling Stockholder has informed the Company that it does not have any written or oral agreement or understanding,directly or indirectly, with any person to distribute the securities.

The Company is requiredto pay certain fees and expenses incurred by the Company incident to the registration of the securities. The Company has agreed to indemnifythe Selling Stockholders against certain losses, claims, damages and liabilities, including liabilities under the Securities Act.

We agreed to keepthis prospectus effective until the earlier of (i) the date on which the securities may be resold by the Selling Stockholders withoutregistration and without regard to any volume or manner-of-sale limitations by reason of Rule 144, without the requirement for theCompany to be in compliance with the current public information under Rule 144 under the Securities Act or any other rule ofsimilar effect or (ii) all of the securities have been sold pursuant to this prospectus or Rule 144 under the Securities Actor any other rule of similar effect. The resale securities will be sold only through registered or licensed brokers or dealers ifrequired under applicable state securities laws. In addition, in certain states, the resale securities covered hereby may not be soldunless they have been registered or qualified for sale in the applicable state or an exemption from the registration or qualificationrequirement is available and is complied with.

Under applicable rules andregulations under the Exchange Act, any person engaged in the distribution of the resale securities may not simultaneously engage inmarket making activities with respect to the Common Stock for the applicable restricted period, as defined in Regulation M, prior tothe commencement of the distribution. In addition, the Selling Stockholders will be subject to applicable provisions of the ExchangeAct and the rules and regulations thereunder, including Regulation M, which may limit the timing of purchases and sales of the CommonStock by the Selling Stockholders or any other person. We will make copies of this prospectus available to the Selling Stockholders andhave informed them of the need to deliver a copy of this prospectus to each purchaser at or prior to the time of the sale (includingby compliance with Rule 172 under the Securities Act).

DESCRIPTIONOF CAPITAL STOCK

The following descriptionof our Common Stock and Private Placement Warrants summarizes the material terms and provisions of the securities that we may issue inconnection with this offering. It may not contain all the information that is important to you. For the complete terms of our CommonStock, please refer to our Certificate of Incorporation and our by-laws (“By-Laws”), which are filed as exhibits to the registrationstatement which includes this prospectus. See “Where You Can Find More Information.” The Delaware General Corporation Law(“DGCL”) may also affect the terms of these securities. The summary below is qualified in its entirety by reference to ourCertificate of Incorporation and By-Laws, each as in effect at the time of any offering of securities under this prospectus.

As of November 15,2024, our authorized capital stock consists of 200,000,000 shares of Common Stock, par value $0.001 per share, of which 50,896,710 shareswere issued and outstanding, and 10,000,000 shares of preferred stock, par value $0.001 per share, of which no shares were issued andoutstanding. In addition, as of November 15, 2024, there were 108,176 shares of Common Stock issuable upon exercise of options outstanding,96,083,181 shares of Common Stock issuable upon exercise of warrants outstanding, and 269,069 shares of Common Stock reserved for futuregrant or issuance. The authorized and unissued shares of Common Stock and preferred stock are available for issuance without furtheraction by our stockholders.

Common Stock

Each stockholder ofour Common Stock is entitled to one vote for each share issued and outstanding held on all matters to be voted upon by the stockholders.Our shares of Common Stock have no preemptive, conversion, or redemption rights. The rights, preferences, and privileges of the holdersof Common Stock are subject to, and may be adversely affected by, the rights of the holders of shares of any series of preferred stock.Upon the sale of substantially all of our stock or assets or dissolution, liquidation or winding up, and after all liquidation preferencespayable to any series of preferred stock entitled thereto have been satisfied, our remaining assets shall be distributed to all holdersof Common Stock and any similarly situated stockholders who are not entitled to any liquidation preference or, if there be an insufficientamount to pay all such stockholders, then ratably among such holders. All of our issued and outstanding shares of Common Stock are fullypaid and non-assessable. The holders of shares of our Common Stock will be entitled to such cash dividends as may be declared from timeto time by our board of directors from funds available therefor.

Our Common Stock islisted the Nasdaq Capital Market under the symbol “APDN.” The transfer agent and registrar for our Common Stock is EquinitiTrust Company, LLC. The transfer agent and registrar’s address is 90 Park Avenue, New York, NY 10016.

Private Placement Warrants

Duration and ExercisePrice

Each Private PlacementWarrant has an exercise price of $0.32 per share of Common Stock and will become exercisable upon the Stockholder Approval Date. TheSeries C Warrants will expire on the five-year anniversary of the Stockholder Approval Date, the Series D Warrants will expireon the 18-month anniversary of the Stockholder Approval Date and the Placement Agent Warrants will expire on October 30, 2029.

Exercisability

The Private PlacementWarrants are exercisable, at the option of each holder, in whole or in part by delivering to us a duly executed exercise notice and,at any time a registration statement registering the issuance of the Common Stock underlying the Private Placement Warrants under theSecurities Act is effective and available for the issuance of such shares, or an exemption from registration under the Securities Actis available for the issuance of such shares, by payment in full in immediately available funds for the number of Common Stock purchasedupon such exercise. Subject to limited exceptions, a holder of Private Placement Warrants will not have the right to exercise any portionof its Private Placement Warrants if the holder, together with its affiliates, would beneficially own in excess of 4.99% (or, at theelection of the purchaser prior to issuance of the Private Placement Warrants, 9.99%) of the number of shares of our Common Stock outstandingimmediately after giving effect to such exercise. A holder may increase or decrease the beneficial ownership limitation up to 9.99%,provided, however, that any increase in the beneficial ownership limitation shall not be effective until 61 days following notice ofsuch change to the Company.

Cashless Exercise

If at the time ofexercise there is no effective registration statement registering, or the prospectus contained therein is not available for the issuanceof the Common Stock underlying the Private Placement Warrants, then the Private Placement Warrants may also be exercised, in whole orin part, at such time by means of a cashless exercise, in which case the holder would receive upon such exercise the net number of commonshares determined according to the formula set forth in the Private Placement Warrant.

Under the alternatecashless exercise option of the Series D Warrants, the holder of a Series D Warrant, has the right to receive an aggregatenumber of shares equal to the product of (x) the aggregate number of shares of Common Stock that would be issuable upon a cash exerciseof the Series D Warrant and (y) 1.0.

Reverse Split

The Series DWarrants include a provision that resets their exercise price in the event of a reverse split of our Common Stock, to a price equal tothe lesser of (i) the then exercise price and (ii) lowest volume weighted average price (VWAP) during the period commencingfive trading days immediately preceding and the five trading days commencing on the date we effect a reverse stock split in the futurewith a proportionate adjustment to the number of shares underlying the Series D Warrants, subject to a floor of $0.0634.

Fundamental Transactions

Inthe event of any fundamental transaction, as described in the Private Placement Warrants and generally including any merger with or intoanother entity, sale of all or substantially all of the Company’s assets, tender offer or exchange offer, or reclassification ofthe shares of Common Stock, subject to certain exceptions, then upon any subsequent exercise of a Private Placement Warrant, the holderwill have the right to receive as alternative consideration, for each share of Common Stock that would have been issuable upon such exerciseimmediately prior to the occurrence of such fundamental transaction, the number of shares of Common Stock of the successor or acquiringcorporation of the Company, if it is the surviving corporation, and any additional consideration receivable upon or as a result of suchtransaction by a holder of the number of shares of Common Stock for which the Private Placement Warrant is exercisable immediately priorto such event. Notwithstanding the foregoing, in the event of a fundamental transaction, the holders of the Private Placement Warrantshave the right to require the Company or a successor entity to purchase the Private Placement Warrants for cash in the amount of theBlack Scholes Value (as defined in the Private Placement Warrants) of the unexercised portion of the Private Placement Warrants concurrentlywith or within 30 days following the consummation of a fundamental transaction. However, in the event of a fundamental transaction whichis not in the Company’s control or in which the consideration payable consists of equity securities of a successor entity thatis quoted or listed on a nationally recognized securities exchange, the holders of the Private Placement Warrants will only be entitledto receive from the Company or its successor entity, as of the date of consummation of such fundamental transaction the same type orform of consideration (and in the same proportion), at the Black Scholes Value of the unexercised portion of the Private Placement Warrantsthat is being offered and paid to the holders of Common Stock in connection with the fundamental transaction, whether that considerationis in the form of cash, stock or any combination of cash and stock, or whether the holders of Common Stock are given the choice to receivealternative forms of consideration in connection with the fundamental transaction.

Transferability

Inaccordance with its terms and subject to applicable laws, a Private Placement Warrant may be transferred at the option of the holderupon surrender of the Private Placement Warrant to us together with the appropriate instruments of transfer and payment of funds sufficientto pay any transfer taxes (if applicable).

FractionalShares

Nofractional shares of Common Stock will be issued upon the exercise of the Private Placement Warrants. Rather, the number of shares ofCommon Stock to be issued will, at our election, either be rounded up to the nearest whole number or we will pay a cash adjustment inrespect of such final fraction in an amount equal to such fraction multiplied by the exercise price.

Trading Market

Thereis no established trading market for the Private Placement Warrants, and we do not expect a market to develop. We do not intend to applyfor a listing for the Private Placement Warrants on any securities exchange or other nationally recognized trading system. Without anactive trading market, the liquidity of the Private Placement Warrant will be limited.

Rightsas a Shareholder

Except as otherwiseprovided in the Private Placement Warrants or by virtue of the holders’ ownership of shares of Common Stock, the holders of PrivatePlacement Warrants do not have the rights or privileges of holders of our shares of Common Stock, including any voting rights, untilsuch Private Placement Warrant holders exercise their warrants.

Possible Anti-TakeoverEffects of Delaware Law and our Certificate of Incorporation and By-Laws

Our Certificate ofIncorporation contains provisions that could make it more difficult to acquire control of our company by means of a tender offer, openmarket purchases, a proxy contest or otherwise. A description of these provisions is set forth below.

Anti-Takeover Effectsof Delaware Law

Companies incorporatedin Delaware are subject to the provisions of Section 203 of the DGCL, or Section 203, unless the corporation has “optedout” of these provisions with an express provision in its original certificate of incorporation or an express provision in itscertificate of incorporation or by-laws resulting from a stockholders’ amendment approved by at least a majority of the outstandingvoting shares. We have opted out of Section 203 with an express provision in our Certificate of Incorporation. Therefore, the anti-takeovereffects of Section 203 do not apply to us.

In general, Section 203prohibits a publicly-held Delaware corporation from engaging in a “business combination” with an “interested stockholder”for a three-year period following the time that this stockholder becomes an interested stockholder, unless the business combination isapproved in a prescribed manner. A “business combination” includes, among other things, a merger, asset or stock sale orother transaction resulting in a financial benefit to the interested stockholder. An “interested stockholder” is a personwho, together with affiliates and associates, owns, or did own within three years prior to the determination of interested stockholderstatus, 15% or more of the corporation’s voting stock.

Under Section 203,a business combination between a corporation and an interested stockholder is prohibited unless it satisfies one of the following conditions:before the stockholder became interested, the board of directors approved either the business combination or the transaction which resultedin the stockholder becoming an interested stockholder; upon consummation of the transaction which resulted in the stockholder becomingan interested stockholder, the interested stockholder owned at least 85% of the voting stock of the corporation outstanding at the timethe transaction commenced, excluding for purposes of determining the voting stock outstanding, shares owned by persons who are directorsand also officers, and employee stock plans, in some instances; or at or after the time the stockholder became interested, the businesscombination was approved by the board of directors of the corporation and authorized at an annual or special meeting of the stockholdersby the affirmative vote of at least two-thirds of the outstanding voting stock which is not owned by the interested stockholder.

Election and Removalof Directors

Directors will beelected by a plurality of the voting power of the shares present in person or represented by proxy at the stockholders meeting and entitledto vote on the election of directors. Our Certificate of Incorporation does not provide for a classified board of directors or for cumulativevoting in the election of directors. Under Article VIII of the Certificate of Incorporation and Section 3.13 of the By-Laws,directors may be removed by the stockholders of the Company only for cause, and in such case only by the affirmative vote of the holdersof at least a majority of the voting power of the issued and outstanding shares of capital stock of the Company then entitled to votein the election of directors. On December 21, 2015, the Court of Chancery of the State of Delaware invalidated as a matter of lawcertain provisions of the certificate of incorporation and bylaws of VAALCO Energy, Inc. (“VAALCO”), a Delaware corporation,that permitted the removal of VAALCO’s directors by its stockholders only for cause. In In re VAALCO Energy, Inc.Stockholder Litigation, Consol. C.A. No. 11775-VCL (Del. Ch. Dec. 21, 2015), the Court ruled from the bench to holdthat, in the absence of a classified board of directors or cumulative voting, VAALCO’s “only for-cause” director removalprovisions conflict with Section 141(k) of the DGCL and are therefore invalid. Because the Company’s Certificate of Incorporationand By-Laws contain similar “only for-cause” director removal provisions and the Company does not have a classified boardof directors or cumulative voting, the Company will not attempt to enforce the foregoing “only for-cause” director removalprovision in light of the recent VAALCO decision.

Size of Board andVacancies

The authorized numberof directors may be determined by the Board of Directors, provided the board shall consist of at least one (1) member. No decreasein the number of directors constituting the board shall shorten the term of any incumbent director.

Vacancies occurringon our Board of Directors for any reason and newly created directorships resulting from an increase in the authorized number of directorsmay be filled only by a vote of a majority of the remaining members of the Board of Directors, although less than a quorum, or by a soleremaining director, at any meeting of the Board of Directors.

Amendment

The Certificate ofIncorporation may be amended in the manner prescribed by the DGCL. The Board of Directors is authorized to adopt, amend, alter or repealthe By-Laws by the affirmative vote of at least a majority of the Board of Directors then in office. No amendment to the Certificateof Incorporation or the By-Laws may adversely affect any indemnification right or protection of any director, officer, employee or otheragent existing at the time of such amendment, repeal or adoption of an inconsistent provision for or in respect of any act, omissionor other matter occurring, or any action or proceeding accruing or arising prior to such amendment, repeal or adoption of an inconsistentprovision.

Authorized butUnissued Shares of Common Stock and of Preferred Stock

We believe that theavailability of the “Blank Check” preferred stock under our Certificate of Incorporation provides us with flexibility inaddressing corporate issues that may arise. The Board of Directors has the power, subject to applicable law, to issue series of preferredstock that could, depending on the terms of the series, impede the completion of a merger, tender offer or other takeover attempt thatsome, or a majority, of the stockholders might believe to be in their best interests or in which stockholders might receive a premiumfor their stock over the then prevailing market price of the stock. Our Board of Directors may issue preferred stock with voting rightsor conversion rights that, if exercised, could adversely affect the voting power of the holders of Common Stock.

The authorized sharesof preferred stock, as well as shares of Common Stock, will be available for issuance without further action by our stockholders, unlessaction is required by applicable law or the rules of any stock exchange on which our securities may be listed. Having these authorizedshares available for issuance allows us to issue shares without the expense and delay of a special stockholders’ meeting. We mayuse additional shares for a variety of purposes, including future public offerings to raise additional capital, to fund acquisitionsand as employee compensation. The existence of authorized but unissued shares of Common Stock and preferred stock could render more difficultor discourage an attempt to obtain control of our company by means of a proxy contest, tender offer, merger or otherwise. The above provisionsmay deter a hostile takeover or delay a change in control or management of our company.

Advance NoticeProcedure

Our By-Laws providean advance notice procedure for stockholders to nominate director candidates for election or to bring business before an annual meetingof stockholders. Only persons nominated by, or at the direction of, our Board of Directors or by a stockholder of record who has givenproper and timely notice to our secretary prior to the meeting at which such stockholder is entitled to vote and appears, will be eligiblefor election as a director. In addition, any proposed business other than the nomination of persons for election to our Board of Directorsmust constitute a proper matter for stockholder action pursuant to a proper notice of meeting delivered to us. For notice to be timely,it must generally be delivered to our secretary not less than 90 nor more than 120 calendar days prior to the first anniversary of theprevious year’s annual meeting (or if the date of the annual meeting is more than 30 calendar days before or more than 60 calendardays after the anniversary date of the previous year’s annual meeting, not earlier than the 120th calendar day prior to such meetingand not later than either the 90th calendar day prior to such meeting or the 10th calendar day after public disclosure of the date ofsuch meeting is first made by us). These advance notice provisions may have the effect of precluding the conduct of certain businessat a meeting if the proper procedures are not followed or may discourage or deter a potential acquirer from conducting a solicitationof proxies to elect its own slate of directors or otherwise attempt to obtain control of us.

Special Meetings of Stockholders

Our By-Laws providethat special meetings of stockholders may be called only by the Chairman of the Board, the Chief Executive Officer, or the Board of Directorspursuant to a resolution adopted by a majority of the board.

LEGALMATTERS

The validity of theissuance of our securities offered in this prospectus will be passed upon for us by McDermott Will & Emery LLP, New York, NewYork.

EXPERTS

Marcum LLP, independentregistered public accounting firm, has audited our consolidated financial statements at September 30, 2023 and 2022. We have incorporatedby reference into this prospectus and in the registration statement our financial statements in reliance on Marcum LLP’sreport, which includes an explanatory paragraph as to the Company’s ability to continue as a going conern, given on their authorityas experts in accounting and auditing.

WHEREYOU CAN FIND ADDITIONAL INFORMATION

We have filed withthe SEC a registration statement on Form S-1 under the Securities Act with respect to the securities offered by this prospectus.This prospectus, which constitutes a part of the registration statement, does not contain all of the information set forth in the registrationstatement, as permitted by the rules and regulations of the SEC. For further information with respect to us and our securities,we refer you to the registration statement, including the exhibits filed as a part of the registration statement. Statements containedin this prospectus concerning the contents of any contract or any other document are not necessarily complete. If a contract or documenthas been filed as an exhibit to the registration statement, please see the copy of the contract or document that has been filed. Eachstatement in this prospectus relating to a contract or document filed as an exhibit is qualified in all respects by the filed exhibit.The SEC also maintains an Internet website that contains the registration statement of which this prospectus forms a part, as well asthe exhibits thereto. These documents, along with future reports, proxy statements and other information about us, are available at theSEC’s website, www.sec.gov.

We are subject tothe information and reporting requirements of the Exchange Act, and, in accordance with this law, file periodic reports and other informationwith the SEC. These periodic reports and other information are available at the SEC’s website, www.sec.gov. We also maintain awebsite at http://www.adnas.com. You may access these materials free of charge as soon as reasonably practicable after they are electronicallyfiled with, or furnished to, the SEC. Information contained on our website is not a part of this prospectus, and the inclusion of ourwebsite address in this prospectus is an inactive textual reference only.

MATERIALCHANGES

None.

Incorporationof Certain Information by Reference.

We have elected toincorporate certain information by reference into this prospectus. By incorporating by reference, we can disclose important informationto you by referring you to other documents we have filed or will file with the SEC. The information incorporated by reference is deemedto be part of this prospectus, except for information incorporated by reference that is superseded by information contained in this prospectus.This means that you must look at all of the SEC filings that we incorporate by reference to determine if any statements in the prospectusor any document previously incorporated by reference have been modified or superseded. This prospectus incorporates by reference thedocuments listed below and any future information filed (rather than furnished) with the SEC under Sections 13(a), 13(c), 14, or15(d) of the Exchange Act between the date of this prospectus and the termination of this offering, provided, however, that we arenot incorporating any information furnished under Item 2.02 or Item 7.01 of any current report on Form 8-K:

Upon written or oralrequest, we will provide without charge to each person, including any beneficial owner, to whom a copy of the prospectus is delivereda copy of the documents incorporated by reference in this prospectus (other than exhibits to such documents unless such exhibits arespecifically incorporated by reference in this prospectus). You may request a copy of these filings, at no cost, by writing or telephoningus at the following address: Applied DNA Sciences, Inc., 50 Health Sciences Drive, Stony Brook, New York 11790, c/o Investor Relations,telephone: 631-240-8800. You may also access these documents on our website at www.adnas.com.

Information on our website, including subsections,pages, or other subdivisions of our website, or any website linked to by content on our website, is not part of this prospectus and youshould not rely on that information unless that information is also in this prospectus or incorporated by reference in this prospectus.

Up to 20,312,500shares of Common Stock underlying the Series C Warrants

Up to 20,312,500shares of Common Stock underlying the Series D Warrants

Up to 1,015,625shares of Common Stock underlying the Placement Agent Warrants

Applied DNA Sciences, Inc.

PRELIMINARY PROSPECTUS

,2024

PART II

INFORMATION NOTREQUIRED IN THE PROSPECTUS

The following tablesets forth the expenses to be incurred in connection with the offering described in this Registration Statement. All amounts are estimatesexcept the SEC’s registration fee.

Section 145 ofthe Delaware General Corporation Law empowers a corporation to indemnify its directors and officers and to purchase insurance with respectto liability arising out of their capacity or status as directors and officers, provided that the person acted in good faith and in amanner the person reasonably believed to be in our best interests, and, with respect to any criminal action, had no reasonable causeto believe the person’s actions were unlawful. The Delaware General Corporation Law further provides that the indemnification permittedthereunder shall not be deemed exclusive of any other rights to which the directors and officers may be entitled under the corporation’sbylaws, any agreement, a vote of stockholders or otherwise. The amended and restated certificate of incorporation of the registrant providesfor the indemnification of the registrant’s directors and officers to the fullest extent permitted under the Delaware General CorporationLaw. In addition, the amended and restated bylaws of the registrant require the registrant to fully indemnify any person who was or isa party or is threatened to be made a party to any threatened, pending or completed action, suit or proceeding (whether civil, criminal,administrative or investigative) by reason of the fact that such person is or was a director or officer of the registrant, or is or wasa director or officer of the registrant serving at the registrant’s request as a director, officer, employee or agent of anothercorporation, partnership, joint venture, trust or other enterprise, against expenses (including attorney’s fees), judgments, finesand amounts paid in settlement actually and reasonably incurred by such person in connection with such action, suit or proceeding, tothe fullest extent permitted by applicable law.

Section 102(b)(7) ofthe Delaware General Corporation Law permits a corporation to provide in its certificate of incorporation that a director of the corporationshall not be personally liable to the corporation or its stockholders for monetary damages for breach of fiduciary duty as a director,except (i) for any breach of the director’s duty of loyalty to the corporation or its stockholders; (ii) for acts oromissions not in good faith or which involve intentional misconduct or a knowing violation of law; (iii) for payments of unlawfuldividends or unlawful stock repurchases or redemptions; or (iv) for any transaction from which the director derived an improperpersonal benefit. The registrant’s amended and restated certificate of incorporation provides that the registrant’s directorsshall not be personally liable to it or its stockholders for monetary damages for breach of fiduciary duty as a director and that ifthe Delaware General Corporation Law is amended to authorize corporate action further eliminating or limiting the personal liabilityof directors, then the liability of the registrant’s directors shall be eliminated or limited to the fullest extent permitted bythe Delaware General Corporation Law, as so amended.

As permitted by theDelaware General Corporation Law, the registrant intends to enter into separate indemnification agreements with each of the registrant’sdirectors and certain of the registrant’s officers which require the registrant, among other things, to indemnify them againstcertain liabilities which may arise by reason of their status as directors, officers or certain other employees.

The registrant hasobtained and maintains insurance policies under which its directors and officers are insured, within the limits and subject to the limitationsof those policies, against certain expenses in connection with the defense of, and certain liabilities which might be imposed as a resultof, actions, suits or proceedings to which they are parties by reason of being or having been directors or officers. The coverage providedby these policies may apply whether or not the registrant would have the power to indemnify such person against such liability underthe provisions of the Delaware General Corporation Law.

These indemnificationprovisions and the indemnification agreements the registrant intends to enter into between the registrant and the registrant’sofficers and directors may be sufficiently broad to permit indemnification of the registrant’s officers and directors for liabilities(including reimbursement of expenses incurred) arising under the Securities Act of 1933, as amended.

February 2022Offering

On February 21,2022, concurrently with a registered direct offering of 1,496,400 shares of our Common Stock and/or pre-funded warrants (the “February 2022Pre-Funded Warrants”) to an institutional investor (the “February 2022 Purchaser”), we  issued to the February 2022Purchaser in a private placement (together with the registered direct offering, the “February 2022 Offerings”) unregisteredwarrants (“February 2022 Common Warrants”) to purchase up to 1,496,400 shares of Common Stock. Each February 2022Common Warrant has an exercise price of $2.84 per share, is exercisable six months from the date of issuance and will expire five yearsfrom the initial exercise date.

Roth Capital Partners,LLC (the “February 2022 Placement Agent”) acted as the exclusive placement agent for the February 2022 Offerings,pursuant to a placement agency agreement (the “February 2022 Placement Agreement”), dated February 21, 2022, byand between the Company and the February 2022 Placement Agent.

The closing of theFebruary 2022 Offerings took place on February 24, 2022. The February 2022 Common Warrants and shares of Common Stockissuable upon exercise thereof were issued in reliance on the exemptions from registration provided by Section 4(a)(2) underthe Securities Act and Regulation D promulgated thereunder for transactions not involving a public offering.

The net proceeds fromthe February 2022 Offerings were approximately $3.7 million. Net proceeds are what we received after paying the placement agent’sfees and other expenses of the offering. The net proceeds exclude the proceeds, if any, from the exercise of the February 2022 Pre-FundedWarrants and the February 2022 Common Warrants sold in the February 2022 Offerings.

Each of the abovesecurities were not registered under the Securities Act and were issued in reliance on the exemptions from registration provided by Section 4(a)(2) underthe Securities Act and Regulation D promulgated thereunder, for transactions not involving a public offering.  The Company fileda registration statement for the resale of the February 2022 Common Warrants on July 19, 2022, and the registration statementwas declared effective on July 27, 2022.

January 2024Offering

OnJanuary 31, 2024, the Company entered into a Placement Agreement (the “January 2024 Placement Agreement”) withMaxim Group (“Maxim”) pursuant to which Maxim agreed to serve as the sole placement agent, on a “reasonable best efforts”basis, in connection with the an offering (the “January 2024 Offering”) of 3,228,056 shares of the Company’sCommon Stock and pre-funded warrants to purchase up to 2,416,005 shares of Common Stock, and in a concurrent private placement,unregistered common warrants (the “January 2024 Common Warrants”) to purchase up to 41,640,625 shares of Common Stock.Also on January 31, 2024, in connection with the Offering, the Company entered into purchase agreements with the purchasers in theJanuary 2024 Offering (the “January 2024 Purchase Agreements”).

TheJanuary 2024 Offering closed on February 2, 2024. The Company received gross proceeds from the January 2024 Offering,before deducting placement agent fees and other estimated offering expenses payable by the Company, of approximately $3.4 million.

Eachof the above securities were not registered under the Securities Act and were issued in reliance on the exemptions from registrationprovided by Section 4(a)(2) under the Securities Act and Regulation D promulgated thereunder, for transactions not involvinga public offering.

Pursuantto the January 2024 Purchase Agreements, within 45 calendar days from the date of the January 2024 Purchase Agreements,the Company agreed to file a registration statement on Form S-3 (or other appropriate form if the Company is not then S-3 eligible)providing for the resale by the Purchasers of the Shares issuable upon exercise of the Private Common Warrants. The Company agreed touse commercially reasonable efforts to cause such registration statement to become effective within 90 days following the closingdate of the Purchase Agreements and to keep such registration statement effective at all times until no Purchaser owns any January 2024Common Warrants or shares of Common Stock issuable upon exercise thereof. The Company filed the registration statement for this transactionon March 12, 2024, and the registration statement was declared effective on March 20, 2024.

October 2024 Offering

On October 30,2024, the Company entered into the Purchase Agreement with certain institutional investors, pursuant to which the Company agreed to issueand sell in the Offering (i) 19,247,498 shares Company’s Common Stock and Pre-Funded Warrants to purchase up to 1,065,002shares of Common Stock, and (ii) Series C Warrants to purchase up to 20,312,500 shares of Common Stock, Series D Warrantsto purchase up to 20,312,500 shares of Common Stock and (iii) Placement Agent Warrants to purchase up to 1,015,625.

The Company receivedgross proceeds from the Offering, before deducting placement agent fees and other estimated offering expenses payable by the Company,of approximately $6.5 million.

Each of the abovesecurities were not registered under the Securities Act and were issued in reliance on the exemptions from registration provided by Section 4(a)(2) underthe Securities Act and Regulation D promulgated thereunder, for transactions not involving a public offering.

Pursuant to the PurchaseAgreement, within 20 calendar days from the date of the Purchase Agreement, the Company agreed to file a registration statement on Form S-1providing for the resale by the purchasers in the Offering of the shares of Common Stock issuable upon exercise of the Private PlacementWarrants. The Company agreed to use commercially reasonable efforts to cause such registration statement to become effective within 50calendar days following the closing date of the Purchase Agreement (or 90 calendar days following the closing date of the Purchase Agreementin the event that the Commission requires the Company to include its audited year-end financial statements for the fiscal year endedSeptember 30, 2024 in such registration statement) and to keep such registration statement effective at all times until no Purchaserowns any Private Placement Warrants or shares of Common Stock issuable upon exercise thereof.

(a) Exhibits.

The exhibit indexattached hereto is incorporated herein by reference.

(b) Financial Statement Schedules.

Schedules have beenomitted because the information required to be set forth therein is not applicable or is shown in the financial statements or notes thereto.

The undersigned registranthereby undertakes:

(1) To file,during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

(i) To includeany prospectus required by Section 10(a)(3) of the Securities Act of 1933;

(ii) To reflectin the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effectiveamendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in the registrationstatement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securitiesoffered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering rangemay be reflected in the form of prospectus filed with the U.S. Securities and Exchange Commission pursuant to Rule 424(b) if,in the aggregate, the changes in volume and price represent no more than a 20% change in the maximum aggregate offering price setforth in the “Calculation of Registration Fee” table in the effective registration statement; and

(iii) To includeany material information with respect to the plan of distribution not previously disclosed in the registration statement or any materialchange to such information in the registration statement; provided, however, that paragraphs (1)(i), (1)(ii) and (1)(iii) abovedo not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in reports filedwith or furnished to the Securities and Exchange Commission by the registrant pursuant to Section 13 or Section 15(d) ofthe Securities Exchange Act of 1934 that are incorporated by reference in the registration statement.

(2) That, forthe purpose of determining any liability under the Securities Act of 1933, each such post-effective amendment shall be deemed to be anew registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemedto be the initial bona fide offering thereof.

(3) To removefrom registration by means of a post-effective amendment any of the securities being registered which remain unsold at the terminationof the offering.

(4) That, forthe purpose of determining liability under the Securities Act of 1933 to any purchaser, each prospectus filed pursuant to Rule 424(b) aspart of a registration statement relating to an offering, other than registration statements relying on Rule 430B or other thanprospectuses filed in reliance on Rule 430A, shall be deemed to be part of and included in the registration statement as of thedate it is first used after effectiveness. Provided, however, that no statement made in a registration statement or prospectus thatis part of the registration statement or made in a document incorporated or deemed incorporated by reference into the registration statementor prospectus that is part of the registration statement will, as to a purchaser with a time of contract of sale prior to such firstuse, supersede or modify any statement that was made in the registration statement or prospectus that was part of the registration statementor made in any such document immediately prior to such date of first use.

(5) That forthe purpose of determining liability of the registrant under the Securities Act of 1933 to any purchaser in the initial distributionof securities, the undersigned registrant undertakes that in a primary offering of securities of the undersigned registrant pursuantto this registration statement, regardless of the underwriting method used to sell the securities to the purchaser, if the securitiesare offered or sold to such purchaser by means of any of the following communications, the undersigned registrant will be a seller tothe purchaser and will be considered to offer or sell such securities to such purchaser:

(i) Any preliminaryprospectus or prospectus of the undersigned registrant relating to the offering required to be filed pursuant to Rule 424;

(ii) Any freewriting prospectus relating to the offering prepared by or on behalf of the undersigned registrant or used or referred to by the undersignedregistrant;

(iii) The portionof any other free writing prospectus relating to the offering containing material information about the undersigned registrant or itssecurities provided by or on behalf of the undersigned registrant; and

(iv) Any othercommunication that is an offer in the offering made by the undersigned registrant to the purchaser.

(6) Insofar asindemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling personsof the registrant pursuant to any charter provision, by law or otherwise, the registrant has been advised that in the opinion of theU.S. Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act of 1933 andis, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than payment by the registrantof expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action,suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, theregistrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriatejurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will begoverned by the final adjudication of such issue.

(7) The undersignedregistrant hereby undertakes that:

(i) For purposesof determining any liability under the Securities Act of 1933, the information omitted from the form of prospectus filed as part of thisregistration statement in reliance upon Rule 430A and contained in a form of prospectus filed by the registrant pursuant to Rule 424(b)(1) or(4) or 497(h) under the Securities Act shall be deemed to be part of this registration statement as of the time it was declaredeffective; and

(ii) For thepurpose of determining any liability under the Securities Act of 1933, each post-effective amendment that contains a form of prospectusshall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities atthat time shall be deemed to be the initial bona fide offering thereof.

EXHIBIT INDEX

SIGNATURES

Pursuant to the requirementsof the Securities Act of 1933, as amended, the registrant has duly caused this registration statement to be signed on its behalf by theundersigned, thereunto duly authorized, in the Town of Stony Brook, State of New York, on the 18^th day of November, 2024.

POWEROF ATTORNEY

KNOW ALL MEN BY THESEPRESENTS, that each officer and director of Applied DNA Sciences, Inc. whose signature appears below constitutes and appoints BethM. Jantzen his or her true and lawful attorney-in-fact and agent, with full power of substitution and revocation, for him or her andin his or her name, place and stead, in any and all capacities, to execute any or all amendments including any post-effective amendmentsand supplements to this Registration Statement, and any additional Registration Statement filed pursuant to Rule 462(b), and tofile the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, grantingunto said attorney-in-fact and agent full power and authority to do and perform each and every act and thing requisite and necessaryto be done, as fully to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that saidattorney-in-fact and agent, or his substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

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Pursuant to the requirementsof the Securities Act of 1933, as amended, this registration statement has been signed by the following persons in the capacities andon the dates indicated.