SEQUENCING DNA USING MSPA

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 该项目旨在通过对用于纳米孔测序应用的膜通道MspA进行基因工程改造，大大加快低成本人类基因组测序技术的开发。使用Anton，我们将获得一个50微秒的全原子分子动力学轨迹，其特征在于电场驱动的单DNA链通过MspA的渗透和与DNA运输相关的MspA的离子电导的调制。对所获得的轨迹的分析将确定限制在MspA收缩部中的DNA核苷酸序列如何调节通过MspA的离子电流在实验中用于确定DNA序列的物理效应。此外，相同的MD轨迹将揭示单个DNA链通过MspA的典型渗透途径，这是MspA的进一步基因工程所需的，目的是降低DNA运输的速度，从而从简单的离子电流测量中检测DNA序列。这个项目是一个千载难逢的机会，通过高性能计算从根本上推进个人基因组学和医学时代的关键技术。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. This project aims to dramatically accelerate the development of a low-cost technology for sequencing human genomes by genetically engineering the membrane channel MspA for nanopore sequencing applications. Using Anton, we will obtain a 50-microsecond all-atom molecular dynamics trajectory characterizing the electric field-driven permeation of a single DNA strand through MspA and the modulation of the ionic conductance of MspA associated with DNA transport. Analysis of the obtained trajectory will determine how the sequence of DNA nucleotides confined in the constriction of MspA modulates the ionic current through MspAthe physical effect used to determine the DNA sequence in experiment. Furthermore, the same MD trajectory will reveal a typical permeation pathway of a single DNA strand through MspA, which is required for further genetic engineering of MspA with the aim of reducing the velocity of DNA transport and thus detecting the DNA sequence from a simple ionic current measurement. This project is truly a once-in-a-lifetime opportunity to radically advance the key technology of the approaching era of personal genomics and medicine through high-performance computing.