[Business Transition and Strategy](index=1&type=section&id=Business%20Transition%20and%20Strategy) Applied DNA transitioned to a pure-play synthetic DNA and mRNA solutions provider, focusing on LineaDNA™, LineaRNAP™, and LineaIVT™ - The company has transitioned to a pure-play provider of synthetic DNA and mRNA manufacturing solutions for advanced biotherapeutics and diagnostics[3](index=3&type=chunk) - Commercialization efforts focus on LineaDNA™ (cell-free DNA production), LineaRNAP™ (next-gen T7 RNA polymerase), and LineaIVT™ (an integrated system combining both)[3](index=3&type=chunk) [Management Commentary](index=2&type=section&id=Management%20Commentary) Management confirms operations align with core cell-free DNA and mRNA manufacturing, focusing on shareholder value - Management confirms the company is repositioned as a single business focused on its core competencies in cell-free DNA and mRNA manufacturing solutions[4](index=4&type=chunk) - The company is actively marketing its offerings under the LineaRx brand to deliver value to shareholders[4](index=4&type=chunk) [Recent Corporate and Operational Updates](index=2&type=section&id=Recent%20Corporate%20and%20Operational%20Updates) The company achieved significant operational progress, including reduced cash burn and key commercial milestones - Monthly net cash burn from operations declined approximately **19% sequentially** and **25% year-over-year** due to cost-cutting initiatives[5](index=5&type=chunk) - Received a multi-gram follow-on order for LineaDNA valued at over **$600 thousand** from a global manufacturer of IVDs for a cancer diagnostic application[8](index=8&type=chunk) - Acquired a U.S.-based mRNA contract development manufacturing organization (CDMO) as a new customer for LineaDNA IVT templates[8](index=8&type=chunk) - Launched the LineaRx IVT Discovery Kit to facilitate customer evaluation and initiated industry marketing for LineaRNAP as a standalone product[8](index=8&type=chunk) - Initiated ISO 13485 certification, an international quality management standard, with expected completion in the first quarter of fiscal 2026[13](index=13&type=chunk) [Third Quarter Fiscal 2025 Financial Highlights](index=3&type=section&id=Third%20Quarter%20Fiscal%202025%20Financial%20Highlights) Q3 FY2025 highlights include **$304 thousand** revenue, **$3.7 million** operating loss, and **$4.7 million** cash Q3 FY2025 Key Financial Metrics (vs. Q3 FY2024) | Metric | Q3 FY2025 ($) | Q3 FY2024 ($) | | :--- | :--- | :--- | | Total Revenues | $304 thousand | $473 thousand | | Operating Loss | $3.7 million | $3.3 million | | Adjusted EBITDA | ($3.9 million) | ($3.2 million) | Cash Position and Burn Rate | Metric | Amount ($) | | :--- | :--- | | Cash and Cash Equivalents (as of June 30, 2025) | $4.7 million | | Monthly Net Cash Burn (Q3 FY2025) | $934 thousand | - The company executed two reverse stock splits: a **1-for-50** effective March 14, 2025, and a **1-for-15** effective June 2, 2025[11](index=11&type=chunk) - Financial results have been recast to report the closed MDx Testing Services business as discontinued operations, with the DNA Tagging segment wind-down included in continuing operations[9](index=9&type=chunk)[10](index=10&type=chunk) [Financial Statements](index=6&type=section&id=Financial%20Statements) This section presents unaudited condensed consolidated financial statements and Adjusted EBITDA reconciliation [Condensed Consolidated Balance Sheets](index=6&type=section&id=CONDENSED%20CONSOLIDATED%20BALANCE%20SHEETS) As of June 30, 2025, total assets were **$9.9 million**, cash **$4.7 million**, and liabilities **$2.9 million** Balance Sheet Summary (as of June 30, 2025) | Account | June 30, 2025 ($) | September 30, 2024 ($) | | :--- | :--- | :--- | | Cash and cash equivalents | $4,727,677 | $5,852,363 | | Total current assets | $5,628,902 | $8,047,671 | | Total assets | $9,934,746 | $12,789,040 | | Total current liabilities | $2,035,960 | $2,398,124 | | Total liabilities | $2,946,702 | $3,820,955 | | Total equity | $6,988,044 | $8,968,085 | [Condensed Consolidated Statements of Operations](index=7&type=section&id=CONDENSED%20CONSOLIDATED%20STATEMENTS%20OF%20OPERATIONS) Q3 FY2025 revenues were **$304,393**, operating loss **$3.7 million**, and net loss **$19.4 million** Statement of Operations (Three Months Ended June 30) | Metric | 2025 ($) | 2024 ($) | | :--- | :--- | :--- | | Total Revenues | $304,393 | $472,789 | | Gross Profit | $5,130 | $242,601 | | Loss from Operations | ($3,694,060) | ($3,306,293) | | Net (Loss) Income from Continuing Operations | ($3,647,914) | $1,883,292 | | Net (Loss) Income Attributable to Common Stockholders | ($19,445,607) | $1,879,796 | | Net (Loss) Income Per Share | ($34.00) | $1,170.48 | [Reconciliation of Non-GAAP Measures (Adjusted EBITDA)](index=8&type=section&id=CALCULATION%20AND%20RECONCILIATION%20OF%20ADJUSTED%20EBITDA) Consolidated Adjusted EBITDA loss for Q3 FY2025 was **$3.9 million**, compared to **$3.2 million** prior year Adjusted EBITDA Reconciliation (Three Months Ended June 30) | Metric | 2025 ($) | 2024 ($) | | :--- | :--- | :--- | | Net (Loss) Income | ($3,984,109) | $1,849,501 | | Consolidated Adjusted EBITDA (Loss) | ($3,927,551) | ($3,175,688) |

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2025 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-36745 Applied DNA Sciences, Inc. (Exact name of registrant as specified in its charter) | Delaware | 59-2262718 | | --- | ...

Applied DNA Reports Second Quarter Fiscal 2025 Financial Results - Therapeutic DNA Production Services Segment (LineaRx) Revenues Up 44% Y/Y, Contributing to a 6% Increase in Total Revenues - - Intra-Quarter Investor Conference Call and Webcast Scheduled for June 3, 2025, at 4:30 PM ET - STONY BROOK, N.Y. – May 15, 2025 - Applied DNA Sciences, Inc. (NASDAQ: APDN) ("Applied DNA" or the "Company"), a leader in PCR-based DNA technologies, today reported financial results for its second quarter of fiscal 2025 e ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2025 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-36745 Applied DNA Sciences, Inc. (Exact name of registrant as specified in its charter) | Delaware | 59-2262718 | | --- ...

Applied DNA Sciences, Inc. (NASDAQ:APDN) Q1 2025 Earnings Conference Call February 13, 2025 4:30 PM ET Company Participants Sanjay Hurry - Executive Director, IR & Corporate Communications Beth Jantzen - CFO James Hayward - Chairman & CEO Clay Shorrock - Chief Legal Officer & Executive Director, Business Development Judith Murrah - President & Secretary Conference Call Participants Eduardo Arce - H.C. Wainwright & Co Operator Good day, and welcome to the Applied DNA Sciences First Quarter Fiscal 2025 Financ ...

Financial Performance - Total revenues for the three months ended December 31, 2024, increased to $1,196,617, representing a 34.3% growth compared to $891,164 in the same period of 2023[12] - Product revenues rose to $495,847, up 61.2% from $307,317 year-over-year, while service revenues increased to $374,444, a 51.5% increase from $247,147[12] - Gross profit for the quarter was $684,107, significantly higher than $231,097 in the prior year, indicating improved operational efficiency[12] - The net loss attributable to common stockholders for the quarter was $(17,546,635), compared to $(1,182,857) in the same quarter of 2023, reflecting increased expenses and warrant modifications[12] - The Company incurred a net loss of $2,668,713 and generated negative operating cash flow of $3,326,074 for the three-month period ended December 31, 2024[21] - The company reported a consolidated loss before provision for income taxes of $2,668,713 for the three-month period ended December 31, 2024, compared to a loss of $1,130,281 in 2023, indicating a significant increase in losses[87] Cash and Liquidity - Cash and cash equivalents at the end of the period were $10,044,365, up from $4,109,045 at the end of December 2023, showing improved liquidity[14] - Cash and cash equivalents increased to $9,294,365 as of December 31, 2024, up from $6,431,095 as of September 30, 2024[36] - Cash and cash equivalents as of December 31, 2024, were $9,294,365, with working capital of $8,889,342[146] Assets and Liabilities - Total assets increased to $15,970,701 as of December 31, 2024, compared to $12,789,040 at September 30, 2024, indicating growth in the company's asset base[11] - Total liabilities decreased to $3,421,056 from $3,820,955, reflecting a reduction in financial obligations[11] - Accounts payable and accrued liabilities totaled $1,610,972 as of December 31, 2024, down from $1,793,427 on September 30, 2024, indicating a decrease of about 10.1%[59] Capital and Financing - The company reported a significant increase in additional paid-in capital, rising to $339,918,754 from $318,805,058, indicating successful capital raising efforts[13] - The Company closed a registered direct offering on October 31, 2024, raising approximately $5.7 million in net proceeds after deducting fees and expenses[61] - The Company entered into a purchase agreement on October 30, 2024, to issue and sell 19,247,498 shares of Common Stock, along with various warrants, raising approximately $6.5 million in gross proceeds before expenses[170][171] Operational Changes - The Company completed a workforce reduction of approximately 20% of its total headcount and approximately 13% in annual payroll costs due to the strategic review of its DNA Tagging and Security Products and Services segment[15] - The Company plans to exit its DNA Tagging and Security Products and Services business segment, which will incur one-time personnel-related charges of approximately $300,000[15] - The company is restructuring its business model with an emphasis on Therapeutic DNA Production Services, aiming to enhance operational efficiency and market positioning[95] Segment Performance - The Company has three reportable segments: Therapeutic DNA Production Services, MDx Testing Services, and DNA Tagging and Security Products and Services[44] - Revenues from one customer within the MDx Testing Services segment accounted for 19% of total revenues for the three-month period ended December 31, 2024[42] - Two customers accounted for 61% of the Company's accounts receivable as of December 31, 2024[43] Future Outlook - The company anticipates future growth in demand for Therapeutic DNA Production Services, which is a key focus of its business strategy[95] - The company expects future demand for COVID-19 testing to continue to decline, potentially leading to the termination of COVID-19 testing services[129] Compliance and Regulatory - The Company received a notification from Nasdaq regarding non-compliance with the minimum bid price requirement, with a deadline of May 12, 2025, to regain compliance[74] - The Company intends to implement a reverse stock split to regain compliance with Nasdaq's Bid Price Rule if necessary[76] - The company is currently evaluating the impact of adopting new accounting standards related to income tax disclosures and segment reporting, effective for fiscal years beginning after December 15, 2024[55][56] Research and Development - Research and development expenses increased by $79,195 or 8% to $1,015,010 for the three-month period ended December 31, 2024, compared to $935,815 in the same period of 2023[141] - As of Q4 2024, there are 4,238 gene, cell, and RNA therapies in development, almost all utilizing DNA in their manufacturing process, representing a substantial market opportunity for the LineaDNA platform[111] Miscellaneous - The total rent expense for the three-month periods ended December 31, 2024, and 2023 was $188,558 and $180,916, respectively[79] - There were no changes in internal control over financial reporting that materially affected the company's financial reporting during the fiscal quarter ended December 31, 2024[166] - The company has no ongoing legal proceedings that could materially impact its financial condition[168]

Exhibit 99.1 Applied DNA Reports First Quarter Fiscal 2025 Financial Results and Highlights Operational Progress - Announces Exit of DNA Tagging and Security Products and Services Business Segment - - Workforce Reduction of 20% of Headcount Implemented in January - - GMP Site 1 Facility Complete and Certified for Commercial Operation in January - - Webcast and Conference Call Scheduled for today at 4:30 PM ET - STONY BROOK, N.Y. – February 13, 2025 - Applied DNA Sciences, Inc. (NASDAQ: APDN) ("Applied DNA" ...

Applied DNA Sciences (APDN) came out with a quarterly loss of $0.32 per share versus the Zacks Consensus Estimate of a loss of $0.33. This compares to loss of $5.20 per share a year ago. These figures are adjusted for non-recurring items.This quarterly report represents an earnings surprise of 3.03%. A quarter ago, it was expected that this DNA-based security technology company would post a loss of $0.64 per share when it actually produced earnings of $0.47, delivering a surprise of 173.44%.Over the last fo ...

Business Development and Strategy - The company is focusing on the development and commercialization of its Therapeutic DNA Production Services, particularly expanding its contract development and manufacturing operation (CDMO) for synthetic DNA[24]. - The company is exploring the potential divestiture of its DNA Tagging and Security Products and Services business segment to reduce expenses and achieve cost savings[25]. - The company is engaged in a strategic review of its business segments, which may lead to workforce reductions and management changes[25]. - The company announced a multi-year commercialization agreement for its CertainT platform with Indus Group in July 2024, focusing on product traceability in the cotton supply chain[63]. - The company is exploring the potential divestiture of its DNA Tagging and Security Products and Services segment[125]. Market Opportunities and Product Development - As of Q3 2024, there are 4,099 gene, cell, and RNA therapies in development, almost all utilizing DNA in their manufacturing process, representing a substantial market opportunity for the company's LineaDNA platform[32]. - The LineaDNA platform offers significant advantages over traditional plasmid-based DNA manufacturing, including speed, scalability, purity, simplicity, and flexibility[34][35][38]. - The company launched its Linea IVT platform in July 2023, combining its LineaDNA IVT templates with proprietary RNAP, potentially increasing its mRNA-related total addressable market (TAM) by approximately 3-5 times[44][45]. - The company plans to manufacture GMP non-drug substance grade DNA in January 2025 and GMP drug substance grade DNA in the first half of calendar year 2026[72]. - The company has filed or intends to file patent applications for its technologies, with a patent portfolio that includes 8 issued patents and 11 pending applications in the Therapeutic DNA Production Services segment[86]. Financial Performance and Challenges - Revenue decreased from $18.2 million in fiscal 2022 to $13.4 million in fiscal 2023, and further declined to $3.4 million in fiscal 2024[121]. - The company reported a net loss of $7,088,306 for the fiscal year ended September 30, 2024, with an accumulated deficit of $309,672,755[122]. - Cash and cash equivalents as of September 30, 2024, were $6,431,095, which raised substantial doubt about the company's ability to continue as a going concern[122]. - The company closed a registered direct offering on October 31, 2024, receiving net proceeds of approximately $5.8 million, increasing the consolidated cash balance to approximately $10.1 million as of November 30, 2024[122]. - The company may require additional financing, which could lead to the issuance of additional shares, resulting in dilution for existing stockholders[126]. Regulatory and Compliance Issues - The company is subject to extensive regulations by the FDA and other authorities, which may delay product approvals and require substantial financial resources[93]. - The FDA's final rule on Laboratory Developed Tests (LDTs) will require compliance with various phases starting from May 6, 2025, impacting clinical laboratories significantly[98]. - The company is monitoring legislative developments, including the VALID Act, which could clarify the FDA's authority over LDTs and impact its business[101]. - The FDA's new regulations on Laboratory Developed Tests (LDTs) could lead to substantial costs and delays for the company in obtaining pre-market clearance or approval[167]. - Regulatory compliance is critical, and failure to comply could result in the inability to manufacture synthetic DNA products, adversely affecting revenue generation[216]. Operational Risks and Market Competition - The company faces substantial competition in the markets for drug and biologic candidates and synthetic DNA, which may hinder its ability to compete effectively[119]. - The competitive landscape for synthetic DNA and MDx Testing Services is intensifying, with many competitors having greater capital resources and market experience[179][183]. - The company must secure stable supplies of components and raw materials to avoid production delays and increased operating costs[174]. - The market for biologics and drug components is rapidly evolving, with significant competition from well-capitalized companies that may develop superior products[187]. - The company faces risks of obsolescence as competitors may develop more effective or less costly products[188]. Research and Development - The company incurred approximately $3.6 million and $3.7 million on research and development activities for the fiscal years ended September 30, 2024, and 2023, respectively[70]. - The company incurs research and development expenses to develop new products and technologies, which may face unanticipated delays and expenses, potentially leading to a total loss of investment in these new products[190]. - The success of the company's Therapeutic DNA Production Services is highly dependent on collaborators and customers obtaining regulatory approval for their pharmaceutical and biotherapeutic product candidates[204]. Customer and Market Dynamics - The company’s MDx Testing Services, which include COVID-19 testing, have seen a significant decline in revenue following the termination of a major contract with CUNY[184]. - Customer spending on pharmaceutical and biologic development will significantly impact the company's sales and profitability, influenced by factors such as available resources and access to capital[166]. - The company is dependent on consumer demand for products utilizing its technology, which could be adversely affected by various market factors[206]. Human Resources and Organizational Structure - As of September 30, 2024, the company had a total of 48 employees, including 46 full-time and 2 part-time[107]. - The company has been working with Insperity Inc. since June 2012 to manage back-end administrative human resources responsibilities[107]. - The company is engaged in a strategic review that may result in divestitures or workforce reductions, impacting its operational capabilities[141]. Risk Management and Compliance - The company is exposed to risks of fraud and misconduct by employees and third parties, which could lead to significant penalties and impact business operations[220]. - Compliance costs may increase significantly if customers obtain FDA approval and begin commercializing their products in the U.S.[221]. - The company has adopted a code of business conduct and ethics, but it may not effectively prevent misconduct or manage risks[221]. - Failure to comply with healthcare laws could result in substantial penalties, adversely affecting the company's financial conditions[222].

Exhibit 99.1 Applied DNA Announces Fourth Quarter and Fiscal Year 2024 Financial Results, Announces Strategic Restructuring to Prioritize the Manufacture of Critical Starting Materials for Genetic Medicines - Pursuing Divestiture of CertainT® Platform, Implements Changes to Corporate Leadership - - Buildout of GMP Manufacturing Facility to be Completed by January 9, 2025 - - Webcast and Conference Call Scheduled for Thursday, January 9, 2025, at 4:30 PM ET - STONY BROOK, N.Y. – December 17, 2024 - Applied D ...