Washington, D.C. 20549 Amendment No. 1 to FORM S-1 As filed with the Securities and Exchange Commission on March 15, 2024. Registration Statement No. 333-277832 UNITED STATES SECURITIES AND EXCHANGE COMMISSION Applied DNA Sciences, Inc. (Exact name of Registrant as specified in its charter) (State or other jurisdiction of incorporation or organization) Delaware 7380 59-2262718 (Primary Standard Industrial Classification Code Number) (I.R.S. Employer Identification Number) 50 Health Sciences Drive Stony Broo ...

As filed with the Securities and Exchange Commission on March 11, 2024. Registration Statement No. 333- UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 Applied DNA Sciences, Inc. (Exact name of Registrant as specified in its charter) (State or other jurisdiction of incorporation or organization) From time to time after this Registration Statement becomes effective. Delaware 7380 59-2262718 (Primary Standard Industrial C ...

The Industrial Products group has plenty of great stocks, but investors should always be looking for companies that are outperforming their peers. Is Applied DNA Sciences (APDN) one of those stocks right now? Let's take a closer look at the stock's year-to-date performance to find out.Applied DNA Sciences is a member of our Industrial Products group, which includes 227 different companies and currently sits at #3 in the Zacks Sector Rank. The Zacks Sector Rank includes 16 different groups and is listed in o ...

Financial Data and Key Metrics Changes - Total revenues for Q1 2024 were approximately $891,000, a decline of $4.4 million compared to $5.3 million in the same period last year [5][6] - Gross profit was $231,000 or 26%, down from $2.4 million or 45% in the prior year, primarily due to a higher percentage of COVID-19 testing service revenue in the previous year [6][7] - Operating loss for the first quarter was $3.8 million compared to $1.2 million in the prior fiscal period [8] - Adjusted EBITDA deteriorated by $2.1 million to a negative $3.2 million compared to a negative $1.1 million in the prior fiscal year period [8] Business Line Data and Key Metrics Changes - Clinical laboratory service revenues decreased significantly, contributing approximately $4.2 million to the total revenue decline [5][6] - Service revenues increased by approximately $15,000 year-over-year, driven by demand for isotopic testing within the DNA Tagging and Security Products and Services segment [6] Market Data and Key Metrics Changes - The company is focusing on the biotherapeutics market, particularly in mRNA therapeutics, with approximately 425 mRNA therapies currently in development [15][17] - The establishment of a GMP capacity is crucial for supporting clinical-grade messenger RNA therapeutics, which is expected to come online in the first half of 2024 [15][16] Company Strategy and Development Direction - The primary objective is the commercialization of the Linea IVT and Linea DNA platforms, with a focus on capital allocation to support biotherapeutic goals [11] - The company aims to transition customers to scale-up agreements for Linea IVT templates and RNA polymerase manufactured under applicable GMPs [14][15] - The partnership with Kudo Bio aims to validate the commercial scale-up of the Linea IVT platform [22] Management's Comments on Operating Environment and Future Outlook - Management expressed optimism about the growing demand for mRNA therapeutics and the company's ability to meet this demand through its unique business model [15][24] - The establishment of a GMP footprint is seen as a significant step towards long-term shareholder value [26] Other Important Information - The company closed a registered direct public offering for gross proceeds of approximately $3.4 million, which will support the establishment of its GMP capacity [9][10] - Cash and cash equivalents totaled $3.4 million as of December 31, 2023, down from $7.2 million on September 30, 2023 [8][9] Q&A Session Summary Question: Can you talk about the CD123 CAR work at the Prague Hematology Institute? - Management highlighted the quality of the scientists involved and the approval process for GMP-grade materials [27] Question: What amount of product is needed for the clinical Phase I trial? - It was estimated that enough material would be needed to treat about 10 patients [29] Question: Can you provide details on Kudo Bio's scale and production? - Kudo Bio is a large player with international facilities and the capability for significant scale in mRNA manufacturing [34][35] Question: What is the customer distribution between the U.S. and international markets? - The majority of customers are currently U.S.-based, with expectations for increased international customer engagement [41][42] Question: What assumptions underlie the projected $15 million annual revenue for Linea IVT? - The projection is based on slightly greater than 100% utilization of the facility, with plans for accommodating increased customer demand [43][44] Question: How does the company benchmark against competitors in production speed? - The company is exceeding turnaround times compared to other enzymatic manufacturers in the scale-up process [48][49]

Applied DNA Sciences (APDN) came out with a quarterly loss of $0.09 per share versus the Zacks Consensus Estimate of a loss of $0.31. This compares to loss of $0.14 per share a year ago. These figures are adjusted for non-recurring items.This quarterly report represents an earnings surprise of 70.97%. A quarter ago, it was expected that this DNA-based security technology company would post a loss of $0.27 per share when it actually produced a loss of $0.26, delivering a surprise of 3.70%.Over the last four ...

Financial Performance - Total revenues for the three months ended December 31, 2023, were $891,164, a decrease of 83.1% compared to $5,262,752 for the same period in 2022[12]. - Product revenues were $307,317, down 40.4% from $516,396 in the prior year[12]. - Clinical laboratory service revenues significantly dropped to $336,700 from $4,514,295, reflecting a decline of 92.6%[12]. - The company reported a gross profit of $231,097, a significant decline from $2,377,683 in the same quarter last year[12]. - The net loss attributable to Applied DNA Sciences, Inc. was $1,105,100, compared to a net loss of $3,843,372 for the same period in 2022[12]. - The company reported a net loss of $1,130,281 for the three months ended December 31, 2023, compared to a net loss of $3,844,246 for the same period in 2022, indicating an improvement in financial performance[20]. - Operating cash flow was negative at $3,757,679 for the three-month period ended December 31, 2023, compared to negative cash flow of $2,383,106 for the same period in 2022[20]. - The loss from operations for reportable segments in Q4 2023 was $(2,539,861), compared to $(217,084) in Q4 2022[74]. - The company reported a discretionary bonus of $500,000 for the CEO for fiscal 2023, which was declined due to the company's cash position[68]. Cash and Assets - Cash and cash equivalents decreased to $3,359,045 from $7,151,800 as of September 30, 2023[8]. - Total assets as of December 31, 2023, were $9,913,210, down from $13,651,577 at the end of the previous quarter[10]. - The company had cash and cash equivalents of $3,359,045 as of December 31, 2023, down from $15,215,285 at the beginning of the period[20]. - The company reported total current assets of $4,590,046 as of December 31, 2023, down from $8,126,570 as of September 30, 2023, indicating a decrease of approximately 43%[8]. - Cash, cash equivalents, and restricted cash at the end of the period were $4,109,045, down from $12,877,179 at the end of December 2022[20]. - As of December 31, 2023, the company had working capital of $2,002,107 and cash and cash equivalents of $3,359,045[131]. Liabilities and Equity - Total liabilities decreased to $5,784,808 from $8,779,165 as of September 30, 2023[9]. - The company recorded warrant liabilities of $1,646,000 as of December 31, 2023, down from $4,285,000, indicating a decrease of about 62%[9]. - Accounts payable and accrued liabilities totaled $2,023,876 as of December 31, 2023, down from $2,270,388 as of September 30, 2023, representing a decrease of 10.9%[56]. - The company issued 61,200 shares of common stock for net proceeds of approximately $45,480 under an Equity Distribution Agreement, with an aggregate offering price of up to $6,397,939[57][58]. - The balance of warrants outstanding as of December 31, 2023, was 5,213,213, with a weighted average exercise price of $3.32 per share[62]. Revenue Recognition and Segments - The company recognized revenue for its clinical laboratory testing services upon completion of services, with performance obligations satisfied at the point of releasing testing results[141]. - Revenue for research and development contracts is recognized over time, primarily using the cost-to-cost method, reflecting the progress towards completion[142]. - The company has three reportable segments: Therapeutic DNA Production Services, MDx Testing Services, and DNA Tagging and Security Products and Services[46][47]. - For the three-month period ended December 31, 2023, revenues included 25% from one customer in the MDx Testing Services segment and 22% from one customer in the DNA Tagging and Security Products and Services segment[45]. Operational Highlights - The company is focused on expanding its business in the biotechnology sector, particularly in therapeutic DNA production and molecular diagnostics[23]. - The company launched DNA IVT templates in August 2022 and has secured proof of concept contracts with multiple mRNA manufacturing customers, indicating strong market demand[105]. - The acquisition of Spindle in July 2023 is expected to enhance the company's mRNA-related total addressable market (TAM) by approximately 3x compared to selling Linea DNA IVT templates alone[106]. - The company plans to manufacture Linea DNA IVT templates under Good Manufacturing Practices (GMP) with availability expected in the first half of CY2024, and additional GMP materials for drug products planned for 2025[107]. Expenses - Total operating expenses increased to $4,020,163, up 11.8% from $3,596,661 in the same quarter last year[12]. - Selling, general and administrative expenses increased by $458,991 or 17% for the three-month period ended December 31, 2023, totaling $3,084,348[125]. - Research and development expenses decreased by $35,489 or 4% for the three-month period ended December 31, 2023, totaling $935,815[126]. - The total rent expense for the three-month period ended December 31, 2023, was $174,419, compared to $148,826 for the same period in 2022, reflecting an increase of 17.2%[63]. Market Conditions - The effect of inflation on revenue and operating results was not significant, indicating stable operational performance despite economic pressures[146]. - As of Q4 2023, there are 3,951 gene, cell, and RNA therapies in development, almost all utilizing DNA in their manufacturing process, representing a substantial market opportunity for the Linea DNA platform[100]. - The Linea DNA platform offers advantages over plasmid-based DNA manufacturing, including speed, scalability, purity, simplicity, and flexibility, allowing for rapid production of high-fidelity DNA sequences[101][102][103].

Financial Data and Key Metrics Changes - Total revenues for Q4 2023 were $780,000, a decrease from $3.6 million in the same period last year, primarily due to a decline in COVID-19 testing services revenue and a reduction in product revenue [5][6][10] - Gross profit was $79,000 (10% margin) compared to $417,000 (12% margin) in the prior year, with the decline attributed to a higher percentage of COVID-19 testing services and textiles revenue in the previous year [6] - Operating loss for Q4 2023 was $4.2 million, slightly improved from a loss of $4.3 million in the prior year [7] - Cash and cash equivalents totaled $7.2 million on September 30, 2023, down from $10.8 million on June 30, 2023 [8] Business Line Data and Key Metrics Changes - The decline in revenue was largely due to a $2.4 million decrease in COVID-19 testing services, following the expiry of a testing contract [6] - The textiles vertical saw a decrease in cotton tagging revenues, contributing to a reduction in product revenue of $341,000 [6] Market Data and Key Metrics Changes - The company is experiencing strong demand in the cotton industry for traceability technologies due to federal and international legislation related to forced labor [18] - Interest in the linearDNA platform is growing, with several large CDMOs as evaluation customers, indicating a positive market response [25][33] Company Strategy and Development Direction - The company is focusing on biotherapeutic manufacturing, particularly through the linearDNA platform, which aims to provide an alternative to plasmid DNA for genetic medicines [12][32] - Plans for fiscal 2024 include launching GMP manufacturing capacity for mRNA starting materials, which is expected to unlock significant revenue opportunities [30][31] - The company aims to convert existing customers into larger, long-term commercial supply agreements, leveraging the anticipated growth in mRNA manufacturing demand [33] Management's Comments on Operating Environment and Future Outlook - Management anticipates a decline in COVID-19 testing revenues, reflecting a broader trend in the industry as public interest wanes [46] - The approval of the first IND for enzymatically-produced DNA is seen as a positive sign for the industry, indicating regulatory acceptance of enzymatic manufacturing [40] - The company is optimistic about the upcoming fiscal year, expecting to secure larger contracts and capitalize on the growing demand for mRNA starting materials [31][33] Other Important Information - The company filed an 8-K disclosing non-compliance with Nasdaq listing rules regarding minimum bid price requirements, with a 180-day period to regain compliance [10] - The average monthly cash burn for Q4 2023 was $1.2 million, aligning with forecasts post-CUNY contract expiry [8] Q&A Session Summary Question: Can you discuss the Spindle RNA polymerase acquisition and its implications? - The acquisition allowed the company to optimize the polymerase for self-amplifying RNA production, which is promising for the IP portfolio and market demand [38] Question: Who received the first IND approval for enzymatically-produced DNA? - The approval was granted to Touchlight Genetics, indicating FDA's willingness to engage with enzymatically-produced materials, which is a positive sign for the company [40] Question: What is the revenue outlook for clinical laboratory services? - A decline is expected, although local increases in COVID positivity may affect this trend [46] Question: How many customers have ordered from the Linea IVT platform? - There are over 10 customers for IVT templates, with 3 evaluation customers for the Linea IVT platform, expecting to sign more substantive agreements soon [50] Question: What is the cash position after September? - The cash position as of November 30th is approximately $4.5 million [53]

[Forward-looking Information](index=3&type=section&id=Forward-looking%20Information) This section outlines forward-looking statements in the Annual Report on Form 10-K, emphasizing inherent risks and uncertainties that may cause actual results to differ materially - Forward-looking statements are subject to **known and unknown risks, uncertainties, and other factors** that may cause actual results to differ materially from projections[8](index=8&type=chunk)[10](index=10&type=chunk)[13](index=13&type=chunk) - Key areas of forward-looking statements include **future revenues, expenditures, capital requirements, ability to continue as a going concern, need for additional financing, business strategy, demand for services (Therapeutic DNA, MDx Testing, DNA Tagging), regulatory approvals**, and **profitability**[11](index=11&type=chunk)[12](index=12&type=chunk) - The company assumes **no obligation to update** any forward-looking statement or risk factor unless required by law[14](index=14&type=chunk) [ITEM 1. BUSINESS](index=6&type=section&id=ITEM%201.%20BUSINESS) Applied DNA Sciences is a biotechnology company focused on DNA and RNA production and detection across three markets, prioritizing Therapeutic DNA Production and MDx Testing Services [Overview](index=6&type=section&id=Overview) Applied DNA Sciences develops and commercializes DNA and RNA production and detection technologies, focusing on Therapeutic DNA Production and MDx Testing Services - The company operates in three primary business markets: **Therapeutic DNA Production Services, MDx Testing Services**, and **DNA Tagging and Security Products and Services**[18](index=18&type=chunk) - Current growth strategy focuses on developing and commercializing **Therapeutic DNA Production Services** and expanding **MDx Testing Services** through genetic testing[19](index=19&type=chunk) [Corporate History](index=6&type=section&id=Corporate%20History) The company was formed in 1983, reincorporated in Delaware in 2008, and is headquartered in Stony Brook, New York - The company was initially formed in **1983**, reincorporated in **Delaware in 2008**, and is headquartered in **Stony Brook, New York**[20](index=20&type=chunk)[21](index=21&type=chunk) [Industry Background and Markets](index=8&type=section&id=Industry%20Background%20and%20Markets) This section details the company's three main business segments, highlighting their technologies, market opportunities, and strategic focus [Therapeutic DNA Production Services](index=8&type=section&id=Therapeutic%20DNA%20Production%20Services) The company develops Linea DNA and Linea IVT platforms for enzymatic DNA and mRNA production, offering advantages over traditional methods for nucleic acid-based therapeutics - The **Linea DNA platform** enables rapid, efficient, and large-scale cell-free manufacture of high-fidelity DNA sequences, offering advantages over plasmid-based methods in **speed, scalability, purity, simplicity**, and **flexibility**[24](index=24&type=chunk)[26](index=26&type=chunk)[27](index=27&type=chunk) - The **Linea IVT platform**, combining Linea DNA IVT templates and Linea RNAP (from Spindle acquisition), aims to improve mRNA production by preventing dsRNA contamination, offering faster delivery (**14-30 days**), and reducing manufacturing complexities[31](index=31&type=chunk) - The acquisition of Spindle in **July 2023** is expected to increase the company's mRNA-related Total Addressable Market (TAM) by approximately **3x**[32](index=32&type=chunk) Linea DNA Quality Grades and Availability | Quality Grade | Permitted Use | Company Status | | :------------------------- | :------------------------------------------------------------------- | :------------------------------------------- | | GLP | Research and pre-clinical discovery | Currently available | | GMP for Starting Materials | DNA critical starting materials for the production of mRNA therapies | Planned availability first half of CY2024 (1) | | GMP | DNA biologic, drug substance and/or drug product | Planned availability first half of CY 2025 (1) | (1) Dependent on the availability of future financing - The company plans to develop **Linea DNA-based therapeutic or prophylactic vaccines** for high-value veterinary health indications, leveraging LNP encapsulation for intramuscular administration[36](index=36&type=chunk)[37](index=37&type=chunk)[38](index=38&type=chunk) [MDx Testing Services](index=12&type=section&id=MDx%20Testing%20Services) ADCL provides MDx testing services, including PGx testing pending NYSDOH approval, with historical revenue largely from safeCircle™ COVID-19 testing - ADCL offers **MDx testing services**, including pharmacogenomics (PGx) testing, which is currently pending **NYSDOH approval**[39](index=39&type=chunk)[40](index=40&type=chunk)[41](index=41&type=chunk) - The majority of historical MDx revenue came from **safeCircle™ COVID-19 testing**, but demand has significantly decreased, resulting in reduced revenues[42](index=42&type=chunk) - Upon **NYSDOH approval**, the company plans to leverage **PGx Testing Services** for large entities and self-insured employers, citing potential healthcare cost reductions and improved patient wellbeing[41](index=41&type=chunk) [DNA Tagging and Security Products and Services](index=12&type=section&id=DNA%20Tagging%20and%20Security%20Products%20and%20Services) The CertainT® platform uses non-biologic DNA tags for supply chain security and product authentication, primarily for cotton, with increased interest due to UFLPA - The **CertainT® platform** uses non-biologic DNA tags for supply chain security and product authentication, with a primary focus on **cotton**[43](index=43&type=chunk)[44](index=44&type=chunk) - The **Uyghur Forced Labor Prevention Act (UFLPA)** has increased interest in DNA tagging, fiberTyping, and isotopic analysis services as evidence for product origin[45](index=45&type=chunk) [Sales and Marketing](index=14&type=section&id=Sales%20and%20Marketing) The company has a small sales and marketing team consisting of five employees, with three directly involved in sales - The sales and marketing team comprises **five employees**, with **three directly engaged in sales**[46](index=46&type=chunk) [Research and Development](index=14&type=section&id=Research%20and%20Development) R&D efforts focus on optimizing LineaDNA and Linea IVT platforms, developing veterinary vaccines, validating PGx testing, and incorporating DNA tags - R&D efforts are focused on optimizing **LineaDNA** and **Linea IVT platforms**, developing **LineaDNA-based veterinary vaccines**, validating **PGx testing services**, and incorporating/authenticating DNA tags in various products[48](index=48&type=chunk)[49](index=49&type=chunk)[50](index=50&type=chunk) Research and Development Expenses | Fiscal Year Ended September 30 | R&D Expenses (Millions) | | :----------------------------- | :---------------------- | | 2023 | $3.7 | | 2022 | $3.9 | [Raw Materials and Suppliers](index=14&type=section&id=Raw%20Materials%20and%20Suppliers) The company relies on DNA polymerase and synthesized DNA templates, but Linea RNAP is from a single third-party CDMO, posing supply risks - Key raw materials include **DNA polymerase (DNAP)** and **synthesized DNA templates**, generally available from multiple sources[51](index=51&type=chunk) - **Linea RNAP** for **Therapeutic DNA Production Services** is currently manufactured by a single third-party CDMO, creating a risk of production delays if this supplier's production ceases[51](index=51&type=chunk) [Manufacturing](index=15&type=section&id=Manufacturing) The company manufactures GLP grade Linea DNA at Stony Brook, with plans for GMP grades, while Linea RNAP is produced by a third-party CDMO - **Linea DNA** is manufactured at the Stony Brook facility, currently at **GLP grade**, with plans for **GMP non-drug substance grade in CY2024** and **GMP drug substance grade in CY2025**[52](index=52&type=chunk) - **Linea RNAP** is produced by a third-party CDMO in the United States[52](index=52&type=chunk) - In-house authentication capabilities for **DNA Tagging and Security** are available in **Stony Brook** and **India**[52](index=52&type=chunk) [Distribution of our Products/Services and Commercial Agreements](index=15&type=section&id=Distribution%20of%20our%20Products%2FServices%20and%20Commercial%20Agreements) The company distributes its products and services directly to customers, through channel partners, and via licensed distributors - Products and services are distributed directly to customers, through channel partners, and via licensed distributors[52](index=52&type=chunk) [Collaboration and Licensing Agreements](index=15&type=section&id=Collaboration%20and%20Licensing%20Agreements) The company partners with CLEARED4 for COVID-19 testing and Cornell University for veterinary health LNP formulations and LineaDNA expression vectors - Partnership with **CLEARED4** for **COVID-19 testing solutions**, integrating **safeCircle™** with their digital health platform[53](index=53&type=chunk) - Collaboration with **Cornell University College of Veterinary Medicine** to develop LNP formulations and **LineaDNA expression vectors** for veterinary health, specifically equine infectious diseases[54](index=54&type=chunk) [Customers](index=15&type=section&id=Customers) The company experienced significant customer concentration, with two MDx Testing Services customers accounting for 65% and 14% of FY2023 revenue Revenue Concentration from MDx Testing Services Customers | Fiscal Year | Customer 1 Revenue Share | Customer 2 Revenue Share | | :---------- | :----------------------- | :----------------------- | | 2023 | 65% | 14% | - The **COVID-19 testing contract with CUNY**, which accounted for **65% of FY2023** and **58% of FY2022 revenues**, terminated in **June 2023**, resulting in a significant revenue reduction[55](index=55&type=chunk) - Three customers accounted for **60% of accounts receivable** at **September 30, 2023**, and two customers accounted for **89%** at **September 30,

Third Quarter Fiscal 2023 Financial Results 10 August 2023 ...

Applied DNA Sciences, Inc. (NASDAQ:APDN) Q3 2023 Earnings Conference Call August 10, 2023 4:30 PM ET Company Participants Sanjay Hurry - Head of IR Beth Jantzen - CFO James Hayward - Chairman, President and CEO Clay Shorrock - Chief Legal Officer and Head of Business Development Conference Call Participants Jason McCarthy - Maxim Group Operator Good day, and welcome to the Applied DNA Sciences Inc. Fiscal Third Quarter 2023 Financial Results Conference Call. [Operator Instructions] Please note, this event i ...