DNA 3.0: Development of a novel, efficient and cost-effective enzymatic process for synthesis of DNA oligonucleotides

DNA 3.0：开发一种新颖、高效且​​具有成本效益的 DNA 寡核苷酸合成酶法

• 批准号: 10614066
• 负责人: Helge Zieler
• 金额: $ 98.38万
• 依托单位: PRIMORDIAL GENETICS, INC
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-04-15 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10614066
• 关键词: Artificial Intelligence; Back; Bacteria; Bioinformatics; Biological; Biological Sciences; Biotechnology; Birth; Chemicals; Chemistry; Clinical; Clinical Trials; Communicable Diseases; Computational Biology; Coupled; Coupling; Cystic Fibrosis; DNA; DNA biosynthesis; DNA-Directed DNA Polymerase; Development; Diagnosis; Diagnostic; Diagnostic Reagent; Environment; Enzymes; Friends; Genetic; Genetic Diseases; Healthcare; Heart Diseases; Immobilization; In Vitro; Industrialization; Industry; Information Storage; Length; Machine Learning; Malignant Neoplasms; Manuals; Manufacturer; Medicine; Methods; Molecular Evolution; Molecular Genetics; Nucleic Acids; Nucleotides; Oligonucleotides; Organic solvent product; Pharmaceutical Preparations; Pharmacologic Substance; Phase; Prevention; Process; Production; Property; RNA; RNA chemical synthesis; Reagent; Research Project Grants; Route; Small Business Innovation Research Grant; Solid; Technology; Therapeutic; Time; Vaccines; Validation; Variant; Virus Diseases; Work; chemical synthesis; commercialization; computational platform; cost; cost effective; enzyme activity; experience; flexibility; human disease; improved; in vitro testing; innovation; manufacture; novel; nucleic acid-based therapeutics; prototype; research and development; screening; supply chain; synthetic biology; synthetic construct; therapeutic RNA; timeline

Project Summary/Abstract Since the birth of biotechnology in the 1980s, efficient nucleic acid synthesis has been a key driver of biological discovery and bio-product development, culminating in the recent emergence of the ‘synthetic biology’ field and rapid development of nucleic acid therapeutics. Sequence-specific RNA and DNA manufacturing is having an especially strong impact in healthcare, where FDA approval of the first oligonucleotide-based therapeutics in 2018 quickly led to many hundreds of similar drugs entering clinical trials. Despite these positive developments, new DNA and RNA synthesis technologies are urgently needed to meet the rapidly rising demand for clinical-grade oligonucleotides, because the current chemical synthesis strategies are costly, difficult to scale, inefficient and limited to molecules of 200 nucleotides or less in length. In the past decade, enzymatic oligonucleotide synthesis (EOS) strategies have been explored and developed for this purpose. In a Phase I feasibility project, Primordial Genetics Inc. demonstrated the use of novel template- independent DNA polymerases (TIDPs) for controlled addition of natural, unmodified nucleotides to a growing DNA strand in a simple process that does not require a chemical deblocking step. This innovation has the potential to enable a robust, inexpensive, flexible, environmentally friendly and easily scalable enzymatic route to manufacturing DNA and RNA used in therapeutics, vaccines, diagnostics and R&D products. In this Phase II Small Business Innovation Research (SBIR) project, Primordial Genetics proposes to continue the Phase I work to optimize the already discovered TIDPs to enable a high rate (99%) of single nucleotide addition in each synthesis cycle that is needed for an industrial EOS process. The company’s genetic improvement and screening platform, specifically the Function Generator™ technology, will be applied together with the artificial intelligence and machine learning capabilities of our computational biology collaborator Koliber Biosciences to improve these enzymes to the desired level of efficiency. A prototype EOS process will be developed using the optimized enzymes acting on oligonucleotides immobilized on a solid support. The prototype EOS process has the potential to enable more efficient DNA and RNA synthesis and remove the manufacturing bottlenecks that are currently holding back the development of nucleic acid medicines. Over time, we will adapt the TIDPs to allow synthesis of all modified nucleotides currently being incorporated into DNA- and RNA-based therapeutics, vaccines, as well as reagents for diagnostics, R&D and DNA-based information storage.

项目概要/摘要 自20世纪80年代生物技术诞生以来，高效的核酸合成一直是关键 生物发现和生物产品开发的驱动力，最终导致最近出现的 “合成生物学”领域和核酸疗法的快速发展。序列特异性 RNA 和 DNA 制造对医疗保健领域产生了特别强烈的影响，FDA 2018 年第一个基于寡核苷酸的疗法获得批准，迅速导致数百个 同类药物进入临床试验。尽管有这些积极的进展，新的 DNA 和 RNA 迫切需要合成技术来满足快速增长的临床级需求 寡核苷酸，因为目前的化学合成策略成本高昂，难以规模化， 效率低且仅限于长度为 200 个核苷酸或更短的分子。近十年来，酶法 为此目的已经探索和开发了寡核苷酸合成（EOS）策略。 在一期可行性项目中，Primordial Genetics Inc. 展示了新型模板的使用- 独立的 DNA 聚合酶 (TIDP)，用于控制添加天然的、未修饰的核苷酸 通过简单的过程生长 DNA 链，不需要化学解封闭步骤。这 创新有潜力实现稳健、廉价、灵活、环保和 易于扩展的酶法路线，用于制造用于治疗、疫苗、 诊断和研发产品。 在这个第二阶段小企业创新研究 (SBIR) 项目中，Primordial Genetics 建议继续第一阶段工作，以优化已发现的 TIDP，以实现高 工业 EOS 所需的每个合成周期中单核苷酸添加率 (99%) 过程。该公司的遗传改良和筛选平台，特别是功能 Generator™技术，将与人工智能和机器学习一起应用 我们的计算生物学合作者 Koliber Biosciences 改进这些酶的能力 达到所需的效率水平。将使用优化的 EOS 流程开发原型 作用于固定在固体支持物上的寡核苷酸的酶。 原型 EOS 工艺有潜力实现更高效的 DNA 和 RNA 合成 消除目前制约核材料发展的制造瓶颈 酸性药物。随着时间的推移，我们将调整 TIDP 以允许合成所有修饰的核苷酸 目前正被纳入基于 DNA 和 RNA 的疗法、疫苗以及试剂中 用于诊断、研发和基于 DNA 的信息存储。