Genome-scale De Novo DNA Synthesis on Electronic p-Chips with Sorting

电子 p 芯片上的基因组规模 De Novo DNA 分选合成

• 批准号: 9353538
• 负责人: WLODEK MANDECKI
• 金额: $ 7.14万
• 依托单位: PHARMASEQ, INC.
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-07 至 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9353538
• 关键词: Award; Chemistry; Chromosomes; Cloning; Combinatorial Synthesis; Computers; Custom; DNA; DNA Sequence; DNA biosynthesis; Diagnostic; Electronics; Enzymes; Funding; Gene-Modified; Genes; Genome; Genomics; Geometry; Goals; Grant; Health; Large-Scale Sequencing; Lasers; Light; Methods; Microfluidics; Molecular Genetics; Oligonucleotides; Optics; Phase; Polymers; Positioning Attribute; Price; Process; Production; Reaction; Reading; Research; Scientist; Signal Transduction; Small Business Innovation Research Grant; Solid; Sorting - Cell Movement; Speed; System; Technology; Time; Vaccine Design; Work; base; combinatorial; cost; design; drug discovery; genetic variant; genome-wide; innovation; instrument; instrumentation; plasmid DNA; prototype; radio frequency; synthetic construct; synthetic genomics; tool

 DESCRIPTION (provided by applicant): The purpose of the present project is to develop and validate a new method for synthesizing large number of DNA fragments, oligodeoxynucleotides. The method, which is called "sequence-directed DNA synthesis", involves the use of small electronic circuits, "p-Chips", each of which transmits a unique ID number via RF when illuminated with laser light. In a massively parallel format, oligonucleotides are synthesized using p-Chips as the solid phase. The p-Chip ID provides the ability to associate a given DNA sequence with that particular p-Chip as synthesis proceeds. A key part of the system is a high-speed instrument, the sorter, that reads the ID of each p-Chip and then sorts p-Chips into the appropriate reaction vessel based on the p-Chip ID, thus the specific DNA sequence. The system, when completed, will be able to generate synthetic DNA fragments in very short times and at costs that are much lower than current methods. The work plan for the project is to initially, in Phase I, demonstrate the ability to synthesize DNA on currently available 0.5 mm p-Chips and to show feasibility of sorting. Following this, in Phase II, will shift to a new p-Chip design, each of which is one thousandth the volume of the 0.5 mm p-Chip. The main goals will be to build the sorter for these ultra-small chips, and to formulate a working method for large-scale sequence-directed combinatorial DNA synthesis. We will also demonstrate applicability of the method by synthesizing a large number of oligonucleotides on p-Chips and creating a 10 kb long gene fragment. We will obtain the DNA sequence error rate upon cloning and identify the best methods for gene assembly and construction of long segments of chromosomes. The prospect of rapidly producing DNA at low prices has profound implications in a number of fields related to synthetic genomics where new tools are needed. This includes the design of modified genes for enzymes, energy production, vaccine designs and many other applications.

 描述（由适用提供）：本项目的目的是开发和验证一种合成大量DNA片段寡脱氧核苷酸的新方法。该方法称为“序列指导的DNA合成”，涉及使用小型电子电路“ P-Chips”，当用激光光照射时，每种电路都会通过RF传输唯一的ID号。以大量平行的格式，使用P-CHIP作为固相合成寡核苷酸。 P-CHIP ID提供了将给定的DNA序列与该特定P-CHIP相关联的能力。系统的关键部分是一种高速仪器，即混蛋，它读取每个p-chip的ID，然后根据p-Chip ID将p-Chips分类到适当的反应容器中，从而将特定的DNA序列分为适当的反应容器。该系统完成后，将能够在很短的时间内生成合成的DNA片段，并且成本远低于当前方法。该项目的工作计划最初是在第一阶段，证明可以在当前可用的0.5 mm p-chips上合成DNA并显示出排序的可行性。在此之后，在第二阶段，将转移到新的P-CHIP设计，每个设计都是0.5 mm p-chip的千分之一。主要目标是为这些超小芯片构建分隔器，并为大规模序列指导的组合DNA合成制定工作方法。我们还将通过在P-CHIP上合成大量寡核苷酸并创建10 KB长基因片段来证明该方法的适用性。我们将在克隆时获得DNA序列错误率，并确定基因组装和构造染色体长段的最佳方法。以低价格快速生产DNA的前景对与需要新工具的合成基因组学有关的许多领域具有深远的影响。这包括用于酶，能源生产，疫苗设计和许多其他应用的修改基因的设计。