Nanopore sequencing of DNA with MspA

使用 MspA 进行 DNA 纳米孔测序

• 批准号: 8134493
• 负责人: Aleksei Aksimentiev
• 金额: $ 72.81万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-23 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8134493
• 关键词: Alabama; Amplifiers; Characteristics; Charge; Communities; Computers and Advanced Instrumentation; DNA; DNA Sequence; Data; Detection; Development; Devices; Electronics; Engineering; Ensure; Genes; Genus Mycobacterium; Goals; Human Genome; Hydrophobicity; Individual; Laboratories; Length; Lipid Bilayers; Location; Measures; Microfluidics; Modeling; Molecular Biology; Motion; Mutate; Mutation; Mycobacterium smegmatis; National Human Genome Research Institute; Noise; Nucleotides; Pore Proteins; Preparation; Proteins; Reader; Reading; Regulation; Research; Resolution; Resources; Sampling; Science; Shapes; Speed; Stream; Structure; System; Techniques; Technology; Testing; Time; Universities; Washington; Work; base; constriction; cost; design; design and construction; improved; instrumentation; link protein; molecular dynamics; mutant; nanopore; next generation; novel; nucleobase; porin; prototype; public health relevance; reconstitution; reconstruction; research study; response; simulation; single molecule

DESCRIPTION (provided by applicant): The objective of this project is to engineer a new protein pore, MspA, for nanopore DNA sequencing. MspA's short and narrow constriction, its extreme stability against denaturation and its tolerance to mutations make this protein an ideal, inexpensive and novel nanopore sequencing development platform. We have obtained exciting results that demonstrate the feasibility of our proposal. We designed and made MspA mutants that pass DNA. Importantly, mutated MspA can already nearly resolve single nucleotides using co-passing current alone. Molecular dynamics simulation of MspA agrees excellently with experiment. A prototype fast, low-noise current amplifier was built specifically for nanopore sequencing experiments. Our specific aims are to (i) rationally design, produce and test MspA mutants to improve DNA base recognition and reduce translocation speed; (ii) use molecular dynamics simulation to understand how DNA interacts with MspA and to optimize MspA for nanopore sequencing; (iii) construct a single chain protein to further improve DNA base sensitivity and control of DNA motion in an asymmetric MspA pore; (iv) construct a highly sensitive electronic amplifier and a practical bilayer apparatus. We have formed a team of three outstanding labs with complementary expertise in protein science, protein simulation, single-channel experiments, molecular biology, and instrumentation to realize these aims. It is our goal to develop a system that can sequence a human genome for under $1000. PUBLIC HEALTH RELEVANCE: This three university team is engineering a novel pore from mycobacteria, MspA, for nanopore DNA sequencing. MspA has an ideal shape for nanopore sequencing. The protein pore is remarkably tolerant of mutations so that it can be exactly tailored to be sensitive to individual nucleotides when DNA passes through it.

描述（由申请人提供）：该项目的目标是设计一种新的蛋白质孔 MspA，用于纳米孔 DNA 测序。 MspA 的短而窄的收缩、其对变性的极端稳定性以及对突变的耐受性使该蛋白质成为理想、廉价且新颖的纳米孔测序开发平台。 我们获得了令人兴奋的结果，证明了我们建议的可行性。我们设计并制造了可传递 DNA 的 MspA 突变体。重要的是，突变的 MspA 几乎可以仅使用共通电流来解析单个核苷酸。 MspA 的分子动力学模拟与实验结果非常吻合。专门为纳米孔测序实验构建了快速、低噪声电流放大器原型。 我们的具体目标是（i）合理设计、生产和测试MspA突变体，以提高DNA碱基识别并降低易位速度； (ii) 使用分子动力学模拟来了解 DNA 如何与 MspA 相互作用并优化 MspA 以进行纳米孔测序； (iii)构建单链蛋白以进一步提高DNA碱基敏感性和对不对称MspA孔中DNA运动的控制； (iv) 构建高灵敏度电子放大器和实用的双层装置。 我们组建了一个由三个优秀实验室组成的团队，在蛋白质科学、蛋白质模拟、单通道实验、分子生物学和仪器方面具有互补的专业知识，以实现这些目标。我们的目标是开发一种能够以 1000 美元以下的价格对人类基因组进行测序的系统。 公共健康相关性：这三个大学团队正在从分枝杆菌 MspA 中设计出一种新型孔，用于纳米孔 DNA 测序。 MspA 具有适合纳米孔测序的理想形状。蛋白质孔对突变具有显着的耐受性，因此当 DNA 通过它时，它可以精确地定制以对单个核苷酸敏感。