Sequencing a DNA molecule using a Synthetic Nanopore

使用合成纳米孔对 DNA 分子进行测序

基本信息

批准号：
7647467
负责人：
GREGORY LOUIS TIMP
金额：
$ 35.46万
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：
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/7647467
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

项目摘要

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，该硅集成电路将纳米孔机制与分子陷阱结合在一起。其基本组成部分是金属氧化物半导体 (MOS) 电容器形成的坚固纳米厚膜中的单个纳米直径孔。为了对分子进行测序，当 DNA 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感应的电压。 1 nm 的孔径是一个关键规格，因为它迫使与每个碱基相关的独特偶极矩在易位过程中几乎横向于电极，同时最大限度地减少热波动并排除大部分水。另一个关键规格是分隔形成电容器的电极的 SiO2 绝缘体的厚度。测序的空间分辨率本质上由SiO2 厚度决定。利用直径为 1 nm 的孔隙和 0.7 nm 厚的氧化物，我们期望能够测量易位期间与跨越绝缘体的单个碱基相关的电信号。为了促进信号恢复，我们打算在分子通过孔的易位过程中捕获分子，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）来提高电信噪比水平，而不会影响吞吐量，并有效地平均掉与 DNA 构象变化相关的噪声。 DNA 和离子分布。我们计划制造和测试结合纳米孔电容器机制和分子陷阱的集成电路，并对其进行优化以用于单分子DNA测序，同时我们还计划模拟性能并测试该机制的理论分辨率将分子动力学与自洽 3D 泊松解算器结合使用。

项目成果

期刊论文数量（7）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

DNA base-calling from a nanopore using a Viterbi algorithm.

使用维特比算法从纳米孔进行 DNA 碱基识别。

DOI：
10.1016/j.bpj.2012.04.009
发表时间：
2012-05-16
期刊：
Biophysical journal
影响因子：
3.4
作者：
W. Timp;J. Comer;A. Aksimentiev
通讯作者：
A. Aksimentiev

Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations.

使用固态纳米孔检测 DNA 结合蛋白：来自计算机模拟的见解。

DOI：
发表时间：
2012-12
期刊：
影响因子：
2.9
作者：
Comer, Jeffrey;Ho, Anthony;Aksimentiev, Aleksei
通讯作者：
Aksimentiev, Aleksei

p-n Semiconductor membrane for electrically tunable ion current rectification and filtering.

p-n 半导体膜，用于电可调离子电流整流和过滤。

DOI：
10.1021/nl0707104
发表时间：
2007-05-22
期刊：
Nano letters
影响因子：
10.8
作者：
M. Gracheva;J. Vidal;J. Leburton
通讯作者：
J. Leburton

Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes.

多价电解质中 DNA 电荷的电和电泳反转。

DOI：
10.1039/b917973a
发表时间：
2010-01-01
期刊：
Soft matter
影响因子：
3.4
作者：
Luan B;Aksimentiev A
通讯作者：
Aksimentiev A

Small-Signal Performance and Modeling of sub-50nm nMOSFETs with f above 460-GHz.

f 高于 460 GHz 的 50 nm 以下 nMOSFET 的小信号性能和建模。

DOI：
10.1016/j.sse.2008.01.025
发表时间：
2008-06-01
期刊：
Solid-state electronics
影响因子：
1.7
作者：
V. Dimitrov;J. Heng;K. Timp;O. Dimauro;R. Chan;M. Hafez;J. Feng;T. Sorsch;W. Mansfield;J. Miner;A. Kornblit;F. Klemens;J. Bower;R. Cirelli;E. Ferry;A. Taylor;M. Feng;G. Timp
通讯作者：
G. Timp