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

• 批准号: 8719765
• 负责人: Kenneth L Shepard
• 金额: $ 47.16万
• 依托单位: COLUMBIA UNIV NEW YORK MORNINGSIDE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-14 至 2017-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8719765
• 关键词: Address; Amplifiers; Biological; Caliber; Charge; Complex; Custom; DNA; DNA Sequence; DNA analysis; DNA-Directed DNA Polymerase; Detection; Development; Devices; Diagnosis; Diffusion; Electronics; Frequencies; Generations; Genome; Image; Length; Lipid Bilayers; Measurement; Measures; Membrane; Noise; Operating System; Optics; Photons; Post Technic; Process; Reaction; Reading; Research; Semiconductors; Signal Transduction; Sodium Chloride; Speed; System; Techniques; Technology; Testing; Time; Transducers; base; cost; design; detector; disorder prevention; fluorophore; improved; instrumentation; millisecond; nanofabrication; nanopore; operation; silicon nitride; single molecule; solid state

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（由申请人提供）：对第三代DNA测序系统的需求很强，即单分子，大量平行和实时。但是，对于单分子光学技术，来自单个荧光团的信号通常<2500个光子/秒（相当于50 FA阶的电流水平）。这导致复杂的光学器件试图收集发出的每个光子，并使平台的缩放变得困难。另外，必须将合成反应有意减慢至1 Hz（或较慢），以便为这些弱嘈杂的光学信号提供足够的成像时间。 单分子的局限性 光学技术突出了电化学检测方法的关键优势，这些方法具有明显较高的信号水平（通常高三个数量级），从而有可能使用适当的传感器，检测器和放大器的适当共同设计进行高带宽检测。作为一种潜在的生物电子转导机制，已大力将纳米孔技术的开发发展为开发。然而，纳米孔被证明受到相对较短的生物分子在孔的电荷敏感区域所花费的相对较短的限制。受货架电子产品的使用限制，纳米孔测量的噪声限宽通常小于100 kHz，限制了可用的感应和驱动策略，并违背了任何测序应用所需的多重整合。 在这四年的工作中，我们专注于显着改善纳米孔检测电子的噪声限制带宽，从而使其具有全部潜力 通过在同一检测底物上与多个纳米孔的高水平并行支持，同时支持高水平的并行性。我们考虑以众多平行方式（特定的目标2）来考虑将固态（特定目标1）和生物孔（特定目标3）（特定目标3）（特定目标3）（特定目标3）（特定目标2）纳入这些测量底物的技术。我们提出的利用商品CMOS技术和协整检测电子的技术是完全笼统的，并且对所有其他单分子生物电子转导方法都具有重要意义。这些高带宽的集成电子设备还将实现“闭环”感应和致动（特定目标4），从而可以在微秒（或更好的）时间表上对捕获和易位动力学进行动态操纵。

项目成果

Hybrid integrated biological-solid-state system powered with adenosine triphosphate.

• DOI: 10.1038/ncomms10070
• 发表时间: 2015-12-07
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Roseman JM;Lin J;Ramakrishnan S;Rosenstein JK;Shepard KL
• 通讯作者: Shepard KL

Single ion channel recordings with CMOS-anchored lipid membranes.

使用 CMOS 锚定脂质膜进行单离子通道记录。

• DOI: 10.1021/nl400822r
• 发表时间: 2013
• 期刊: Nano letters
• 影响因子: 10.8
• 作者: Rosenstein,JacobK;Ramakrishnan,Siddharth;Roseman,Jared;Shepard,KennethL
• 通讯作者: Shepard,KennethL

Single-Stranded DNA Translocation Recordings through Solid-State Nanopores on Glass Chips at 10 MHz Measurement Bandwidth

• DOI: 10.1021/acsnano.9b04626
• 发表时间: 2019-09-01
• 期刊: ACS NANO
• 影响因子: 17.1
• 作者: Chien, Chen-Chi;Shekar, Siddharth;Drndic, Marija
• 通讯作者: Drndic, Marija

Single-molecule bioelectronics.

单分子生物电子学。

• DOI: 10.1002/wnan.1323
• 发表时间: 2015
• 期刊: Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology
• 作者: Rosenstein,JacobK;Lemay,SergeG;Shepard,KennethL
• 通讯作者: Shepard,KennethL

Measurement of DNA Translocation Dynamics in a Solid-State Nanopore at 100 ns Temporal Resolution.

• DOI: 10.1021/acs.nanolett.6b01661
• 发表时间: 2016-07-13
• 期刊: Nano letters
• 影响因子: 10.8
• 作者: Shekar S;Niedzwiecki DJ;Chien CC;Ong P;Fleischer DA;Lin J;Rosenstein JK;Drndić M;Shepard KL
• 通讯作者: Shepard KL