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

该项目旨在开发一种工具，可以显著提高核酸的精确度 通过对用于测序应用的生物纳米孔进行合理的工程来进行测序。 尽管纳米孔测序的方法已经有了很大的改进， 关于通过纳米孔传输DNA和RNA分子，样品制备，碱基- 调用算法等，在提高原始精度方面发表的文章相对较少 核苷酸检测，这是纳米孔测序中最常被引用的缺陷 方法。该项目将通过开发一种计算技术来解决这一缺陷 将极大地简化用于RNA和DNA测序的定制纳米孔的设计，潜在地 导致行读取精度的数量级改进。的关键创新之处 该项目利用了最近的方法学进步，使对 仅来自模拟的纳米孔电流水平。改变这一方法论上的突破 成为一个精确的纳米孔设计工具，这个项目将检验和改进模拟 方法论由一系列专门为提供信息而设计的实验指导 需要改进模型。通过设计验证了该方法的实用性。 自定义毛孔以检测具有生物学意义的RNA修改。由此产生的计算量 将以自给自足和完善的形式向研究界提供方法 有文档记录的软件。该项目将由一个跨学科团队来实现，该团队将结合 精通生物纳米孔实验及理论和计算建模 (UIUC)。涉及的两个PI各自具有超过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)和 DNA和离子通过生物纳米孔传输的微观模拟(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).