Modeling macromolecular transport through protein and solid-state nanopores

模拟通过蛋白质和固态纳米孔的大分子运输

• 批准号: 8728977
• 负责人: MURUGAPPAN MUTHUKUMAR
• 金额: $ 26.29万
• 依托单位: UNIVERSITY OF MASSACHUSETTS AMHERST
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-06-06 至 2017-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8728977
• 关键词: Address; Base Sequence; Behavior; Charge; Chemicals; Computer Simulation; Coupled; Coupling; DNA; DNA Sequence; Development; Devices; Diffusion; Disease; Electrolytes; Electrophoresis; Electrostatics; Environment; Enzymes; Equation; Genome; Goals; Healthcare; High-Throughput Nucleotide Sequencing; Human; Ions; Laboratories; Length; Maintenance; Massive Parallel Sequencing; Mediating; Methods; Modeling; Pattern; Physics; Polymerase; Polymers; Pore Proteins; Proteins; Public Health; Reading; Research; Sodium Chloride; Specificity; Speed; Statistical Mechanics; Surface; System; Techniques; Technology; Temperature; Time; Work; base; cost; design; genome sequencing; nanopore; public health relevance; research study; solid state; statistics; stem; theories; voltage

DESCRIPTION (provided by applicant): The urgent need to develop low-cost and high-quality revolutionary technologies for sequencing mammalian-sized genomes has inspired many experimental strategies. Chief among these is the nanopore-based electrophoresis. While excellent progress is continuously being made with this technique, there are many challenges in reaching the goals of very high quality sequencing and fabricating massively parallel sequencing devices. These challenges stem from the physics of nanopore-based electrophoresis of DNA which needs to be understood from a fundamental scientific point of view. The proposed research deals with fundamental understanding of the behavior of DNA in nanopore environments under the influence of electric and hydrodynamic forces, and ratcheting forces from enzymes. We will investigate the challenges underlying several key system components in the goal of reducing the cost, increasing the speed, and increasing the accuracy of sequencing mammalian-sized genomes. The major challenges deal with slowing down DNA through nanopore, effects of specific ions, conformational fluctuations of DNA, effects of flow fields arising from hydrodynamics, salt concentration gradients, and electroosmotic flow, and fluctuations in the processivity of enzymes. We will use a combination of concepts from polymer physics, statistical mechanics theory, computer simulations, and numerical computation of coupled nonlinear equations to address polyelectrolyte statistics and dynamics, electrostatics, and hydrodynamics in the phenomena of DNA translocation. The proposed research, while being generally relevant to all nanopore-based experiments, will be hinged specifically on: (a) slowing down DNA and fundamental understanding of translocation, mediated by voltage, temperature, identity and amount of electrolyte, salt concentration gradient, and patterns on pore surface, (b) controlling the stochasticity in enzyme-ratcheted translocation and fundamental understanding of coupling among fluctuations in enzyme processivity, DNA conformational fluctuations, and electrophoretic drift-diffusion, and (c) designing optimum configuration of compact arrays of thousands of nanopores for massively parallel DNA sequencing without crosstalk between the units.

描述（由申请人提供）：迫切需要开发低成本和高质量的革命性技术，用于测序人类大小的基因组，这激发了许多实验策略。其中最主要的是基于纳米孔的电泳。虽然该技术不断取得了很好的进展，但在达到非常高质量的测序和制造大规模并行测序装置的目标方面存在许多挑战。这些挑战来自于基于纳米孔的DNA电泳的物理学，需要从基础科学的角度来理解。拟议的研究涉及对DNA在纳米孔环境中在电力和水动力以及酶的棘轮力影响下的行为的基本理解。我们将研究几个关键系统组件的挑战，以降低成本，提高速度，并提高测序的准确性。主要的挑战涉及减缓DNA通过纳米孔，特定离子的影响，DNA的构象波动，流体力学，盐浓度梯度和电渗流产生的流场的影响，以及酶的持续合成能力的波动。我们将使用聚合物物理，统计力学理论，计算机模拟和耦合非线性方程的数值计算的概念的组合，以解决DNA易位现象中的静电统计和动力学，静电学和流体力学。拟议的研究，而一般相关的所有纳米孔为基础的实验，将具体取决于：（a）减慢DNA和对易位的基本理解，所述易位由电压、温度、电解质的身份和量、盐浓度梯度和孔表面上的图案介导，（B）控制酶棘轮移位中的随机性和基本理解酶持续合成能力波动之间的耦合，DNA构象波动和电泳漂移扩散，以及（c）设计用于大规模并行DNA测序的数千个纳米孔的紧凑阵列的最佳配置，而单元之间没有串扰。