The Assemblatron

组装机

• 批准号: 10564169
• 负责人: Jef D BOEKE
• 金额: $ 102.92万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-02-01 至 2026-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10564169
• 关键词: Affect; Agriculture; Algorithms; Area; Automation; Bacterial Artificial Chromosomes; Biological Assay; Biomedical Research; Bypass; Characteristics; Circular DNA; DNA; Development; Devices; Diagnosis; Dryness; Ecosystem; Environment; Environment Design; Environmental Science; Evolution; Excision; Exonuclease; Frequencies; Genes; Genomics; Genotype; Goals; Human; International; Length; Letters; Link; Machine Learning; Measures; Mentors; Methods; Modification; National Human Genome Research Institute; Nucleic Acids; Oligonucleotides; Persons; Probability; Process; Productivity; Protocols documentation; Reproducibility; Research; Research Personnel; Series; Short Tandem Repeat; Software Design; Source; Structure; System; Techniques; Testing; Transcriptional Regulation; Tube; Untranslated RNA; Work; Yeasts; biological research; cost; dark matter; design; disorder prevention; homologous recombination; improved; programs; rapid technique; remediation; synthetic construct; synthetic genomics; synthetic nucleic acid; vector; yeast genome

Project Summary Methods for rapidly generating synthetic nucleic acid constructs have dramatically changed biological and biomedical research. Improvements in these arenas will continue to impact varied areas of genomics and biomedicine such as synthetic genomics and associated functional screens. Enabling significant advances with new nucleic acid synthesis and synthetic construct capabilities has the potential to lead to remarkable improvements in the understanding, diagnosis, treatment and prevention of disease; advances in agriculture, environmental science and remediation; and our understanding of evolution and ecological systems. Current abilities to work with a variety of synthetic constructs have been enabled by cost reductions in oligonucleotide synthesis along with vastly improved techniques for hierarchal assembly of larger constructs, largely in yeast. Our group has led the way both in assembling the yeast genome (i.e. the international Sc2.0 project) and in a NHGRI-sponsored CEGS that has launched the “Dark Matter Project”, aiming to functionally dissect noncoding DNA and its contribution to human/mammalian transcriptional regulation. We have also developed an in-house design software application environment linked to our LIMS called MenDEL (Mentored Design Environment and LIMS). But we need to do much more to make such projects ever easier to do – ultimately, in any lab. In this project we plan to develop the “Assemblatron”, a workflow/Design platform/Host vector system that systematically optimizes the “Yeast assembly” process, and is capable of producing very large DNA molecules of up to a megabase in size. We will develop a system in which one person can assemble 1-2 Megabases of 20-30 kb DNA pieces in a few days’ work, and 1-2 Mb of ~100 kb pieces in 2-4 weeks. The specific goal is >10X improvement in Big DNA assembly efficiency, manifested as the ability of a single researcher, starting with 3 kb starting materials, to do the following: 1) Assemble 1-2 Mb of DNA in 1-2 weeks and 2) Finalize assembly into 10 to 20 100+ kb pieces in 2-4 weeks. Ultimately this research program will lead to development of an Assemblatron device that automates much or all of the process. We plan to achieve this improvement in efficiency, which is currently limited by a series of bottlenecks that exist throughout the workflow using a combination of dry lab and wet lab methods, outlined below.

项目概要 快速生成合成核酸构建体的方法已经极大地改变了生物学和 这些领域的进步将继续影响基因组学和生物医学的各个领域。 生物医学，例如合成基因组学和相关的功能筛选，实现了重大进展。 新的核酸合成和合成构建能力有潜力带来显着的成果 提高对疾病的认识、诊断、治疗和预防； 环境科学和修复；以及我们对进化和生态系统的理解。 目前使用各种合成结构的能力是通过降低成本来实现的 寡核苷酸合成以及更大结构的分级组装技术的大幅改进， 主要是在酵母方面。我们的团队在组装酵母基因组（即国际 Sc2.0）方面处于领先地位。 项目），并在 NHGRI 赞助的 CEGS 中启动了“暗物质项目”，旨在从功能上 我们还剖析了非编码 DNA 及其对人类/哺乳动物转录调控的贡献。 开发了一个与我们的 LIMS 相连的内部设计软件应用环境，称为 MenDEL（Mentored 设计环境和 LIMS），但我们需要做更多的工作来使此类项目变得更容易完成 – 最终，在任何实验室中。 在这个项目中，我们计划开发“Assemblatron”，一个工作流程/设计平台/主机矢量系统， 自然优化“酵母组装”过程，能够产生非常大的DNA分子 我们将开发一个系统，一个人可以组装 1-2 个巨型基地。 几天内获得 20-30 kb DNA 片段，并在 2-4 周内获得 1-2 Mb 约 100 kb 片段。 大 DNA 组装效率提高了 10 倍以上，表现为单个研究人员的能力，开始 使用 3 kb 起始材料，执行以下操作：1) 在 1-2 周内组装 1-2 Mb DNA，2) 完成 最终，该研究计划将在 2-4 周内组装成 10 至 20 个 100+ kb 的片段。 我们计划使用 Assemblatron 设备来实现大部分或全部流程的自动化。 效率，目前受到整个工作流程中存在的一系列瓶颈的限制，使用 干实验室和湿实验室方法的组合，概述如下。