Nanochannel-nanopore based DNA sequencing with DNA motion control and reduced entropic noise

基于纳米通道-纳米孔的 DNA 测序，具有 DNA 运动控制和降低的熵噪声

• 批准号: 10010924
• 负责人: David John Niedzwiecki
• 金额: $ 35万
• 依托单位: GOEPPERT, LLC
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-22 至 2022-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10010924
• 关键词: Ablation; Address; Amplifiers; Area; Buffers; Caliber; Complex; Coupled; Custom; DNA; DNA sequencing; Detection; Development; Devices; Dimensions; Electrodes; Electrolytes; Electronics; Elements; Entropy; Enzymes; Event; Freedom; Genomics; Goals; Image; Ions; Label; Length; Measurement; Measures; Membrane; Methods; Microfluidics; Mission; Molecular Conformation; Monitor; Motion; National Human Genome Research Institute; Noise; Optics; Output; Performance; Phase; Photons; Polymerase; R43 grant; Running; Ships; Signal Transduction; Single-Stranded DNA; Small Business Innovation Research Grant; Speed; Stochastic Processes; Structure; System; Techniques; Technology; Temperature; Thinness; Time; United States National Institutes of Health; Variant; base; cost; feeding; fluorophore; improved; nanochannel; nanoimprint lithography; nanopore; new technology; novel; operation; sensor; sequencing platform; silicon nitride; single molecule; solid state; technology development; temporal measurement; transcriptome sequencing; voltage

Project Summary To improve DNA sequencing and to develop practical methods of RNA sequencing, this NHGRI Phase I project focuses on using solid-state nanopore sensors coupled with sub-30nm wide channels embedded into silicon nitride, with electronics operating at 10 MHz bandwidth for DNA sequencing and direct RNA sequencing. The basic concept 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. The proposed nanochannel system solves two issues relating to DNA sequencing with solid-state nanopores: 1) feeding long strands of DNA to the sensing element in a single-stranded conformation; 2) reducing the variability found in DNA translocation signals by decreasing the conformation variance of DNA within the nanopore interior. Specifically, we seek to make solid-state ionic-current based nanopore sequencing possible by combining three important components: a nanochannel with sufficiently tight dimensions to allow long strands of DNA to enter the sensing nanopore in an ideal conformation, ultra-thin nanopores to increase signal-to-noise and reduce the number of bases within the pore interior, and optimally fast measurement of translocation through these pores with low-noise, high-bandwidth electronics. Our approach aims to eliminate the need for any enzymes and enables DNA molecules to be geometrically constrained and controlled as they are guided to the nanopores.

项目概要 为了改进 DNA 测序并开发 RNA 测序的实用方法，NHGRI 第一阶段项目重点是使用固态纳米孔传感器与亚 30 纳米宽度相结合 嵌入氮化硅的通道，电子器件以 10 MHz 带宽运行 DNA 测序和直接RNA测序。基本概念涉及使用施加的电压 驱动单链 DNA 分子通过狭窄的纳米孔，该纳米孔将不同的室分开 电解质溶液。该电压还驱动电解质离子流过孔隙，测量 作为电流。当分子穿过纳米孔时，它们会改变离子的流动， 结构信息可以通过分析持续时间和幅度来提取 导致电流减少。所提出的纳米通道系统解决了与 DNA 相关的两个问题 使用固态纳米孔进行测序：1) 将长链 DNA 输送至传感元件 单链构象； 2) 通过以下方式减少 DNA 易位信号中发现的变异性 减少纳米孔内部 DNA 的构象变化。具体来说，我们寻求 通过结合三种方法使基于固态离子电流的纳米孔测序成为可能 重要组成部分：具有足够紧密尺寸的纳米通道，以允许长链 DNA以理想构象进入传感纳米孔，超薄纳米孔增加 信噪比并减少孔内部的碱基数量，并且速度最佳 使用低噪声、高带宽电子设备测量通过这些孔隙的易位。 我们的方法旨在消除对任何酶的需求，并使 DNA 分子能够 当它们被引导到纳米孔时受到几何约束和控制。