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.

项目摘要 快速产生合成核酸构建体的方法已经发生了巨大变化的生物学和 生物医学研究。这些领域的改进将继续影响基因组学的各个领域和 生物医学（例如合成基因组学和相关功能筛选）。通过 新的核酸合成和合成构造能力有可能导致显着 改善疾病的理解，诊断，治疗和预防；一致的进步， 环境科学和补救；以及我们对进化和生态系统的理解。 当前与各种合成结构合作的能力已通过降低成本启用 寡核苷酸的合成以及较大构建体的层次组装的技术大大改进， 主要在酵母中。我们的小组在组装酵母基因组方面都领先（即国际SC2.0 项目）和在启动“暗物质项目”的NHGRI赞助的CEG中，旨在在功能上 解剖非编码DNA及其对人/哺乳动物转录调控的贡献。我们也有 开发了一个内部设计软件应用程序应用程序环境，与我们的LIMS相关称为Mendel（指导 设计环境和LIM）。但是，我们需要做更多的事情来使此类项目更容易做到 - 最终，在任何实验室中。 在这个项目中，我们计划开发“汇编”，这是一个工作流/设计平台/主机向量系统，该系统 系统地优化“酵母组装”过程，并能够产生非常大的DNA分子 最多的巨大大小。我们将开发一个系统，一个人可以组装1-2个兆巴 在几天的工作中，有20-30 kb的DNA零件，在2-4周内1-2 MB的碎片约为100 kb。具体目标 大DNA组装效率的提高> 10倍，表现为单个研究人员的能力，开始 使用3 kb的起始材料，进行以下操作：1）在1-2周内组装1-2 MB的DNA和2）最终确定 在2-4周内组装成10至20个100 kb的零件。最终，该研究计划将导致发展 汇编设备的大部分或全部过程。我们计划实现这一改进 效率，目前受到整个工作流程中存在的一系列瓶颈的限制 干燥实验室和湿实验室方法的组合，以下概述。