Integrated, multiplexed high-frequency electronic analysis of DNA in nanopores

纳米孔中 DNA 的集成、多重高频电子分析

基本信息

批准号：
8545205
负责人：
Kenneth L Shepard
金额：
$ 46.87万
依托单位：
COLUMBIA UNIV NEW YORK MORNINGSIDE
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-14 至 2015-07-31
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): There is strong demand for third-generation DNA sequencing systems to be single-molecule, massively- parallel, and real-time. For single-molecule optical techniques, however, the signal from a single fluorophore is typically < 2500 photons/sec (equivalent to electrical current levels on the order of 50 fA). This leads to complex optics to try to collect every photon emitted and makes scaling of the platforms difficult. Additionally, synthesis reactions must be intentionally slowed to 1 Hz (or slower) to allow sufficient imaging times for these weak, noisy optical signals. The limitations of single-molecule optical techniques highlight key advantages of electrochemical detection approaches, which have significantly higher signal levels (typically three orders of magnitude higher), allowing for the possibility for high-bandwidth detection with the appropriate co-design of transducer, detector, and amplifier. Significant effort has been directed toward the development of nanopore technology as one potential bioelectronic transduction mechanism. Nanopores, however, have proved to be extremely limited by the relatively short time biomolecules spend in the charge-sensitive region of the pore. Restricted by the use of off- the-shelf electronics, the noise-limite bandwidth of nanopore measurements is typically less than 100 kHz, limiting the available sensing and actuation strategies and defying multiplexed integration which would be required for any sequencing application. In this four-year effort, we focus on improving significantly the noise-limited bandwidth of the detection electronics for nanopores allowing their full potential to be realized through close integration of the electronics and the pore while simultaneously supporting high levels of parallelism with multiple nanopores on the same detection substrate. We consider techniques for integrating both solid-state (Specific Aim 1) and biological pores (Specific Aim 3) onto these measurement substrates in a massively parallel manner (Specific Aim 2). The techniques we propose for leveraging commodity CMOS technology and co-integrating detection electronics are completely general and have significance to all other single-molecule bioelectronic transduction approaches. These high-bandwidth integrated electronics will also enable "closed-loop" sensing and actuation (Specific Aim 4), allowing dynamic manipulation of capture and translocation dynamics at microsecond (or better) timescales.

描述（申请人提供）：人们对第三代DNA测序系统的单分子、大规模并行和实时性有着强烈的需求。然而，对于单分子光学技术，来自单个荧光团的信号通常 < 2500 光子/秒（相当于 50 fA 数量级的电流水平）。这导致需要复杂的光学器件来尝试收集发射的每个光子，并使平台的扩展变得困难。此外，必须有意将合成反应减慢至 1 Hz（或更慢），以便为这些微弱、嘈杂的光信号提供足够的成像时间。单分子的局限性光学技术凸显了电化学检测方法的关键优势，其信号水平显着提高（通常高出三个数量级），从而可以通过传感器、检测器和放大器的适当协同设计进行高带宽检测。纳米孔技术作为一种潜在的生物电子转导机制的发展已付出了巨大的努力。然而，事实证明，纳米孔受到生物分子在孔的电荷敏感区域停留相对较短的时间的极大限制。受使用现成电子设备的限制，纳米孔测量的噪声限制带宽通常小于 100 kHz，限制了可用的传感和驱动策略，并且无法满足任何测序应用所需的多重集成。在这四年的努力中，我们致力于显着提高纳米孔检测电子器件的噪声限制带宽，从而充分发挥其潜力通过电子器件和孔的紧密集成来实现，同时支持同一检测基板上多个纳米孔的高水平并行性。我们考虑以大规模并行方式（具体目标 2）将固态（具体目标 1）和生物孔（具体目标 3）集成到这些测量基板上的技术。我们提出的利用商品 CMOS 技术和共集成检测电子学的技术是完全通用的，并且对所有其他单分子生物电子转导方法具有重要意义。这些高带宽集成电子器件还将实现“闭环”传感和驱动（具体目标 4），从而允许在微秒（或更好）时间尺度上动态操纵捕获和易位动态。