Sequencing a DNA molecule using a Synthetic Nanopore

使用合成纳米孔对 DNA 分子进行测序

• 批准号: 7235399
• 负责人: GREGORY LOUIS TIMP
• 金额: $ 61.66万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-08-01 至 2010-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7235399
• 关键词: Affect; Amplifiers; Area; Back; Bioinformatics; Biosensor; Caliber; Charge; Chemical Structure; Chemistry; Compatible; DNA; DNA Sequence; Data; Dependence; Deposition; Detection; Development; Dimensions; Electric Capacitance; Electrodes; Electrolytes; Electron Beam; Elements; Event; Feedback; Frequencies; Image; In Situ; Ions; Left; Length; Localized; Measurement; Measures; Membrane; Membrane Proteins; Methodology; Microfluidics; Miniaturization; Molecular; Molecular Conformation; Nanotechnology; Noise; Nucleotides; Oxides; Performance; Polynucleotides; Positioning Attribute; Program Development; Range; Recovery; Research; Resistance; Resolution; Right-On; Scheme; Semiconductors; Signal Transduction; Silicon; Simulate; Single-Stranded DNA; Slice; Solutions; Specific qualifier value; Surface; System; Techniques; Testing; Thick; Time; Vertebral column; Water; base; design; dipole moment; ds-DNA; electric field; improved; innovation; inorganic phosphate; lithography; metal oxide; molecular dynamics; nanometer; nanopore; nanoscale; oxidation; performance tests; programs; research study; response; sensor; simulation; single molecule; stem; three dimensional structure; tool; voltage

DESCRIPTION (provided by applicant): We plan to explore the feasibility of sequencing a DNA molecule using a revolutionary type of silicon integrated circuit that incorporates a nanopore mechanism with a molecular trap. The essential component is a single, nanometer-diameter pore in a robust, nanometer-thick membrane formed from a Metal Oxide Semiconductor (MOS) capacitor. To sequence the molecule, the voltage induced by the dipole moment associated with each base is measured using the electrodes on the capacitor as the DNA translocates through the pore. The 1 nm diameter of the pore is a key specification since it forces the unique dipole moment associated with each base to be nearly transverse to electrodes during a translocation, while minimizing thermal fluctuations and excluding most of the water. Another crucial specification is the thickness of the SiO2 insulator separating the electrodes forming the capacitor. The spatial resolution for sequencing is essentially determined by the SiO2 thickness. With a 1 nm diameter pore and a 0.7nm thick oxide, we expect to be able to measure the electrical signal associated with a single base spanning the insulator during a translocation. To facilitate signal recovery, we intend to trap the molecule during the translocation through the pore, forcing it to oscillate back-and-forth between the electrodes. The oscillation in the position of the DNA allows for narrow-band synchronous detection (lock-in techniques) to be used to improve the electrical signal-to-noise level without compromising the throughput and effectively averages out the noise associated with conformational changes in the DNA and the ion distribution. While we plan to fabricate and test an integrated circuit incorporating a nanopore-capacitor mechanism with a molecular trap and optimize it for sequencing a single molecule of DNA, at the same time we also plan to simulate the performance and test the theoretical resolution of the mechanism using molecular dynamics in conjunction with a self-consistent 3D Poisson solver.

描述（由申请人提供）：我们计划探索使用革命性类型的硅集成电路对DNA分子进行测序的可行性，所述硅集成电路将纳米孔机制与分子陷阱结合。其基本组成部分是由金属氧化物半导体（MOS）电容器形成的坚固的纳米厚膜中的单个纳米直径孔。为了对分子进行测序，当DNA易位通过孔时，使用电容器上的电极测量由与每个碱基相关的偶极矩诱导的电压。孔的1 nm直径是一个关键规格，因为它迫使与每个碱基相关的独特偶极矩在移位期间几乎横向于电极，同时最小化热波动并排除大部分水。另一个关键的规格是分隔形成电容器的电极的SiO2绝缘体的厚度。测序的空间分辨率基本上由SiO2厚度决定。利用1 nm直径的孔和0.7 nm厚的氧化物，我们期望能够测量与移位期间跨越绝缘体的单个碱基相关的电信号。为了促进信号恢复，我们打算在通过孔的易位期间捕获分子，迫使其在电极之间来回振荡。DNA位置的振荡允许使用窄带同步检测（锁定技术）来改善电信号-噪声水平而不损害通量，并有效地平均与DNA和离子分布中的构象变化相关的噪声。虽然我们计划制造和测试一个集成电路，将纳米孔电容器机制与分子陷阱相结合，并对其进行优化，用于对单个DNA分子进行测序，但同时我们还计划使用分子动力学结合自洽的3D泊松求解器来模拟性能并测试该机制的理论分辨率。