GenSyn: A Cycle for Serial Assembly of Very Large DNA Molecules

GenSyn：非常大的 DNA 分子的串行组装循环

• 批准号: 10369379
• 负责人: DAVID C. SCHWARTZ
• 金额: $ 26.55万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-19 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10369379
• 关键词: Adsorption; Attenuated; Bacterial Artificial Chromosomes; Binding; Biological Assay; Buffers; Cells; Charge; Chemicals; Chromosomes; Complement; Computer Models; Computer Simulation; Coupling; DNA; DNA Binding; DNA biosynthesis; Device Designs; Diffuse; Dimensions; Engineering; Fluorescence; Genome; Genomic DNA; Genomics; Glass; Grain; Health; Human; Human Genome; Hybrids; Image; Image Analysis; In Vitro; Ionic Strengths; Laboratories; Length; Ligation; Liquid substance; Measurement; Mediating; Methods; Microscopy; Modality; Modeling; Modification; Molecular; Molecular Conformation; Names; Oligonucleotides; Optics; Pathway interactions; Peptide Nucleic Acids; Performance; Periodicity; Phase; Physical condensation; Polyamines; Process; Reagent; Reproducibility; Research; Scheme; Seeds; Solid; Stretching; Surface; System; Techniques; Technology; Validation; base; design; electric field; foot; microscopic imaging; molecular modeling; monomer; novel; operation; physical property; polyacrylamide; polyacrylamide hydrogels; research and development; response; single molecule; synthetic construct; synthetic nucleic acid; technology development

Abstract The broad, long-term objectives of the proposed research are development of a system for direct, cell-free, validated fabrication of very large DNA assemblies, for applications in synthetic applications and genome assembly. This system – “GenSyn” – will harness the advantages of large DNAs for synthesis on supports in ways that will complement and synergize cell-based techniques for the serial assembly of very large DNA molecules. The proposed research is based on i) binding approaches supporting chemical and enzymatic processes; ii) shear-free fluidic operations; iii) new methods for enhancing hybridization/ligation yields and iv) validations. The devices are designed for gentle fluidic operations supporting assembly and image analysis of large DNA constructs by epifluorescence microscopy. The first step in the GenSyn cycle will be binding DNA molecules to a support by hybridization with oligonucleotides that are bound to a derivatized glass surface. The hybridization and ligation steps will be optimized using physical and chemical manipulations. Modified large DNAs will be used as coupler molecules, supporting GenSyn cycles. Overall cycle performance metrics (coupling yields as a function of cycle number, molecule breakage, reagent retention, timings and enzymatic activity) will be assessed in ways that will inform and be guided by computer models. This research will help advance fundamental studies on genomes and human health.

摘要 拟议研究的广泛的长期目标是开发一个系统， 直接，无细胞，验证非常大的DNA组装的制造，用于合成 应用和基因组组装。该系统-“GenSyn”-将利用 大的DNA在支持物上合成的方式，将补充和协同细胞为基础的 非常大的DNA分子的串联组装技术。拟议的研究是 基于i）支持化学和酶过程的结合方法; ii）无剪切 流体操作; iii）提高杂交/连接产率的新方法和iv）验证。 这些设备设计用于温和的流体操作，支持组装和图像分析 大的DNA构建体的荧光显微镜。GenSyn周期的第一步将 通过与结合到载体上的寡核苷酸杂交， 衍生的玻璃表面。杂交和连接步骤将使用物理方法进行优化。 和化学操作。修饰的大DNA将被用作偶联分子， GenSyn周期。整体循环性能指标（耦合产量作为循环的函数 数量、分子断裂、试剂保留、时间和酶活性）进行评估 以计算机模型为指导。这项研究将有助于推动 基因组和人类健康的基础研究。