Large-Scale Nanopore Arrays for DNA Sequencing

用于 DNA 测序的大规模纳米孔阵列

• 批准号: 7192249
• 负责人: Carlos H Mastrangelo
• 金额: $ 29.49万
• 依托单位: CASE WESTERN RESERVE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-26 至 2009-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7192249
• 关键词: DNA; electrodes; macromolecule; measurement; nucleic acid sequence; silicon

DESCRIPTION (provided by applicant): Today, synthetic nanopore devices are the subject of intense investigation as intriguing candidate devices for high-speed non-enzymatic interrogation of individual biological macromolecules. Such functionality is required for example in order to sequence individual DNA fragments of unknown composition at high speeds. While many theoretical aspects regarding macromolecule translocation physics and novel readout schemes are presently under investigation by several NIH-funded groups, the practical utilization of nanopores in sequencing systems also requires large arrays of nanopores working in parallel, each of these connected to high-sensitivity electronic amplifiers/detectors. Such degree of parallelism and systems integration is necessary in order to achieve significant improvements in throughput compared with today's state-of-the-art massively-parallel enzymatic sequencing by synthesis schemes (SBS) (such as those offered by 454 Life Sciences which reports high-fidelity sequencing of bacterial genomes at 20 Mb/day). To illustrate the need for arrays one may consider for example, a 100- nanopore array with average nanopore translocation rate of 100b/ms/pore could in principle sequence fragments at (high-fidelity, 100 repeats) rates of 10 Gb/day, allowing an entire human genome to be sequenced in a day, 500 times faster than SBS. The aims of this proposal are (a) the development of highly-integrated arrays of nanopores that can be fabricated by lithographic methods along with on-chip silicon-based electronic circuits and circuit techniques that amplify and isolate their various electrical signals, and (b) the exploration of a dipole sensing methodology which in principle can distinguish signals from each of the DNA bases. A quadrature capacitance sensor will be incorporated in some of the fabricated nanopores. Arrays of nanopores will be constructed on silicon substrates using a self-aligned compositional approach. Quadrature dipole moment detectors will be constructed that yield a signal independent of the rotation of the DNA molecule relative to the electrodes.

描述（由申请人提供）：如今，合成纳米孔装置作为对单个生物大分子进行高速非酶询问的有趣候选装置而成为深入研究的主题。例如，为了对未知组成的单个 DNA 片段进行高速测序，就需要这种功能。 虽然许多关于大分子易位物理和新颖读出方案的理论方面目前正在由几个 NIH 资助的小组进行研究，但纳米孔在测序系统中的实际应用还需要大量并行工作的纳米孔阵列，每个纳米孔阵列都连接到高灵敏度电子放大器/检测器。 与当今最先进的大规模并行酶促合成测序方案 (SBS)（例如 454 Life Sciences 提供的方案，该方案报告以 20 Mb/天的速度对细菌基因组进行高保真测序）相比，这种程度的并行性和系统集成对于实现吞吐量的显着提高是必要的。为了说明对阵列的需求，人们可以考虑，例如，平均纳米孔易位率为 100b/ms/孔的 100 纳米孔阵列原则上可以以 10 Gb/天（高保真，100 次重复）的速率对片段进行测序，从而可以在一天内对整个人类基因组进行测序，比 SBS 快 500 倍。 该提案的目的是（a）开发高度集成的纳米孔阵列，可以通过光刻方法以及片上硅基电子电路和电路技术来放大和隔离各种电信号，以及（b）探索偶极子传感方法，该方法原则上可以区分来自每个 DNA 碱基的信号。正交电容传感器将被纳入一些制造的纳米孔中。 纳米孔阵列将使用自对准组合方法构建在硅基底上。 正交偶极矩检测器将被构造为产生与 DNA 分子相对于电极的旋转无关的信号。