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

• 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
• 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

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

项目摘要 提高DNA测序的准确性、鲁棒性和速度， 开发RNA测序的实用方法，这个NIH R43第一阶段项目的重点是使用 低噪声玻璃芯片上的多层设计固态孔传感器，用于DNA测序 和直接RNA测序。纳米孔背后的基本概念涉及使用应用的 电压驱动单链DNA分子通过一个狭窄的纳米孔， 电解质溶液室。该电压还驱动电解质离子流通过电解质电极。 孔，以电流测量。当分子通过纳米孔时， 离子流和结构信息可以通过分析持续时间和 由此产生的电流减少的幅度。原子级薄2D膜中的纳米孔 提高了分子检测和分析的信噪比， 通过孔隙的离子流随着孔隙厚度线性增加，因此， 离子电流和阻断电流随迁移分子的减少而增加， 纳米孔高度。具体来说，我们寻求使固态离子电流为基础的纳米孔 通过组合多个组件来实现芯片上的模块化多层， 固态超薄孔系统，限制了DNA在传感区域的运动范围， 毛孔。我们通过制造包含第二层氮化硅孔的器件来实现这一点， 包含传感2D孔的初级层，该传感2D孔将装置内的DNA定向到受限的 几何形状，但允许离子的自由运动，以保持高信噪比。我们提出了一个 具有两个独立电连接的特定多层概念以及相应的芯片 设备架构来实现这一目标。在这种方法中，有一个中心的，高度敏感的2D 毛孔第二层是纳米孔阵列（NPA），其与纳米孔阵列共享相同的电极对。 感测2D孔隙。这些孔被构造成平行于“感测”孔，并且用作 “进给”元件将DNA拉伸并进给到感测孔中。我们概述了实际的 利用基于Si的技术实现这一概念，包括DNA的优点（以及 生物分子）测序（分析）。我们的方法消除了任何 酶，并使DNA分子能够被引导通过坚固和持久的纳米孔， 通过定制设计的“阵列芯片”，并在潜在的创纪录的高测序速度促进。 图1：申报的多层器械 这个NIH R43第一阶段提案的概念， 依靠DNA熵的最小化 运动：引导阵列和优化的2D 毛孔 1