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

使用计算显微镜改进生物纳米孔以进行精确核酸测序

基本信息

批准号：
10214806
负责人：
Aleksei Aksimentiev
金额：
$ 27.9万
依托单位：
UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-06-01 至 2024-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10214806
关键词：
Accounting Address Algorithms Amino Acid Sequence Biological Case Study Communities Computer Models Computer software Computing Methodologies Consumption Custom DNA DNA Sequence DNA sequencing Data Detection Development Diagnostic Disease Documentation Engineering Exclusion Genetic Individual Ion Transport Mainstreaming Measures Medical Methodology Methods Microscope Microscopic Modeling Modification Molecular Molecular Conformation Mutagenesis Mutation Nucleic acid sequencing Nucleotides Outcome Preparation Publishing RNA RNA Sequences Research Resolution Resources Sampling Screening for cancer Signal Transduction Software Tools Source Statistical Methods System Technology Testing Theoretical model Time Work base blind constriction cost design drug development experience experimental study genetic makeup improved in silico innovation instrumentation molecular dynamics mutant nanopore portability programs sequencing platform simulation tool transcriptome sequencing

项目摘要

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).

该项目旨在开发一种可以显着提高核酸检测精度的工具通过对生物纳米孔进行合理的工程设计以用于测序应用来进行测序。尽管纳米孔测序的方法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，关于提高原始精度的文章相对较少核苷酸检测，这是纳米孔测序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导致行读取精度提高几个数量级。该技术的关键创新在于该项目利用了最新的方法论进展，使从头预测变得合理纳米孔电流水平仅来自模拟。转变这一方法论突破转化为精确的纳米孔设计工具，该项目将检查和改进模拟以一组专门为提供信息而设计的实验为指导的方法需要改进模型。该方法的实用性将通过设计来证明定制孔来检测具有生物学意义的 RNA 修饰。由此产生的计算结果该方法将以独立且完善的形式提供给研究界记录的软件。该项目将由一个跨学科团队来实现，该团队结合了生物（麻省大学）纳米孔实验的理论和计算建模专业知识（UIUC）。参与的两位PI均拥有超过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)。