Improving biological nanopores for precision nucleic acid sequencing using a computational microscope

该项目旨在开发一种工具，可以大大提高核酸的精确度 通过使生物纳米孔的合理工程化以用于测序应用来进行测序。 尽管纳米孔测序的方法学已经经历了重大改进， 关于通过纳米孔运输DNA和RNA分子，样品制备，碱基- 调用算法等，相对较少发表关于提高原始精度的文章， 核苷酸检测，这是纳米孔测序最常引用的缺陷 法该项目将通过开发一种计算技术来解决这一缺陷， 将大大简化用于RNA和DNA测序的定制纳米孔的设计， 导致行读取精度的数量级改进。的关键创新 该项目利用了最近的方法学进展，这些进展对 纳米孔电流水平单独模拟。将这一方法上的突破 一个精确的纳米孔设计工具，该项目将检查和改进模拟 由一组专门设计的实验指导的方法学， 需要改进模型。该方法的实际效用将通过设计 定制孔来检测生物学上显著的RNA修饰。由此产生的计算 方法将提供给研究界的形式，自足和良好的， 文档化软件。该项目将由一个跨学科的团队实现， 生物学（UMass）纳米孔实验与理论和计算建模的专业知识 （UIUC）。参与的两名PI均具有超过15年的纳米孔研究经验 技术，包括生物纳米孔的合成和表征（Chen）， DNA和离子通过生物纳米孔的微观模拟（Aksimentiev）。

This project aims to develop a tool that can considerably increase the precision of nucleic acid sequencing by enabling rational engineering of biological nanopores for sequencing applications. Although the methodology of nanopore sequencing has undergone major improvement with regard to transporting DNA and RNA molecules through the nanopore, sample preparation, base- calling algorithms, etc., relatively little has been published on improving the raw accuracy of nucleotide detection, which is the most commonly quoted deficiency of the nanopore sequencing method. This project will address this deficiency by developing a computational technology that will greatly simplify the design of custom nanopores for RNA and DNA sequencing, potentially leading to orders-of-magnitude improvement in row read accuracy. The key innovation of the project exploits recent methodological advances that have made plausible de novo prediction of nanopore current levels from simulations alone. To transform this methodological breakthrough into an accurate nanopore design tool, this project will examine and improve the simulation methodology guided by a set of experiments designed specifically to provide the information needed to improve the model. The practical utility of the method will be demonstrated by designing custom pores to detect biologically significant RNA modifications. The resulting computational method will be made available to the research community in the form of self-contained and well- documented software. This project will be realized by an interdisciplinary team that combines expertise in biological (UMass) nanopore experiment with theoretical and computation modeling (UIUC).The two PIs involved each have over 15 years of experience with research on nanopore technology, which includes synthesis and characterization of biological nanopores (Chen) and microscopic simulations of DNA and ion transport through biological nanopores (Aksimentiev).