Multilayer Device for Sequencing DNA Through a Solid-State Nanopore

通过固态纳米孔对 DNA 进行测序的多层装置

基本信息

批准号：
10483455
负责人：
David John Niedzwiecki
金额：
$ 14.14万
依托单位：
GOEPPERT, LLC
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-09-23 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10483455
关键词：
3-Dimensional Address Architecture Articular Range of Motion Biological Buffers Caliber Complex Custom DNA DNA Microarray Chip DNA Sequence DNA sequencing Data Analyses Detection Devices Diagnosis Discrimination Electric Capacitance Electrodes Electrolytes Elements Entropy Enzymes Face Finite Element Analysis Freedom Geometry Glass Goals Grant Growth Height Image Ions Length Letters Machine Learning Measurement Measures Mechanics Membrane Methods Modeling Molecular Motion Noise Nucleotides Optics Phase Photons Polymerase Pore Proteins Price Public Health Pythons Research Resistance Running Ships Signal Transduction Single-Stranded DNA Small Business Innovation Research Grant Speed Stochastic Processes Stretching System Techniques Technology Temperature Thick Thinness Time United States National Institutes of Health base cost design detection platform disorder prevention experience feeding fluorophore improved nanopore new technology operation pragmatic implementation sensor sequencing platform silicon nitride single molecule solid state temporal measurement transcriptome sequencing voltage whole genome

项目摘要

Project Summary To improve DNA sequencing capabilities with respect to accuracy, robustness and speed and to develop practical methods of RNA sequencing, this NIH R43 Phase I project focuses on using multilayer-design solid-state pore sensors on low-noise glass chips, towards DNA sequencing and direct RNA sequencing. The basic concept behind nanopores involves using an applied voltage to drive single-stranded DNA molecules through a narrow nanopore, which separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the nanopore they modify the flow of ions, and structural information can be extracted by analysis of the duration and magnitude of the resulting current reductions. Nanopore in atomically-thin 2D membranes improve the signal-to-noise ratio for molecular detection and analysis because the resistance to the ionic flow through a pore increases linearly with the pore thickness, so both the magnitudes of the ionic current and the blocked current with a translocating molecule increase with decreasing nanopore height. Specifically, we seek to make solid-state ionic-current based nanopore sequencing possible by combining several components to make a modular multilayer on-chip solid-state ultrathin-pore system that limits the range of motion for DNA in the sensing region of a pore. We do so by creating devices containing a second layer of silicon nitride holes, parallel to primary layer containing the sensing 2D pore that orient DNA within a device to a restricted geometry, yet allow the free motion of ions to maintain a high signal-to-noise ratio. We propose a specific multilayer concept with two independent electrical connections, and corresponding chip device architecture to achieve this goal. In this method, there is a central, highly sensitive 2D pore. A secondary layer is a nanopore array (NPA) sharing the same electrode pair as the sensing 2D pore. These pores are constructed parallel to the “sensing” pore and serve as “feeding” elements to stretch and feed DNA into the sensing pore. We outline the practical implementation of this concept with Si-based technology, including advantages for DNA (and biomolecule) sequencing (analysis) in solution. Our approach eliminates the need for any enzymes and enables DNA molecules to be guided through robust and long-lasting nanopores, facilitated by the custom-designed “array chip”, and at potentially record high sequencing speeds. Illustration 1: Proposed multilayer device concept for this NIH R43 Phase I proposal, relying on minimization of DNA entropic motion: a guiding array and an optimized 2D pore. 1

项目概要提高 DNA 测序能力的准确性、稳健性和速度，并开发实用的 RNA 测序方法，该 NIH R43 第一阶段项目重点关注使用低噪声玻璃芯片上的多层设计固态孔隙传感器，用于 DNA 测序纳米孔背后的基本概念涉及使用应用程序。电压驱动单链 DNA 分子通过狭窄的纳米孔，该纳米孔将该电压还驱动电解质离子流过电解质溶液的室。孔，以电流测量当分子穿过纳米孔时，它们会发生改变。离子流和结构信息可以通过分析持续时间和原子级薄的二维膜中产生的电流减少的幅度。提高分子检测和分析的信噪比，因为抗通过孔隙的离子流随孔隙厚度线性增加，因此两个量级离子电流和易位分子阻挡电流随着减小而增加具体来说，我们寻求制造基于固态离子电流的纳米孔。通过组合多个组件来实现片上模块化多层的排序固态超薄孔系统，限制DNA在传感区域的运动范围我们通过创建包含第二层氮化硅孔的器件来实现这一点，该孔与孔平行。包含传感 2D 孔的主层，可将设备内的 DNA 定向到受限的位置几何结构，但允许离子自由运动以保持高信噪比。具有两个独立电气连接的特定多层概念以及相应的芯片在该方法中，有一个中央、高度敏感的 2D 设备架构。第二层是与第一层共享相同电极对的纳米孔阵列（NPA）。传感二维孔这些孔平行于“传感”孔构建并用作我们概述了将 DNA 拉伸并送入传感孔的“馈送”元件。利用基于硅的技术实现这一概念，包括 DNA 的优势（以及我们的方法无需任何溶液中的生物分子）测序（分析）。酶并使 DNA 分子能够被引导通过坚固且持久的纳米孔，由定制设计的“阵列芯片”促进，并有可能创纪录的高测序速度。图 1：建议的多层器件 NIH R43 第一阶段提案的概念，依赖于 DNA 熵的最小化运动：引导阵列和优化的 2D 毛孔。 1