Scalable Fabrication and Recognition Tunneling Sequencing Study of Gated Nanopore Self-embedded in Transverse Metal Nanojunctions

项目摘要 纳米孔传感已经成为下一代DNA测序技术的焦点。它有 证明了快速单分子DNA测序的巨大潜力，具有长读取长度和简化的 样品制备。然而，现有的纳米孔制备框架仍然面临重大挑战 从离子电流检测的固有分辨率极限和在检测过程中的工程复杂性两者来看， 制造，以便实现两个数量级的更低的错误率和更高的器件成品率/稳定性， 这是人类基因组测序和临床应用所需要的。我们将通过以下方式应对这些挑战： 探索一种独特的制造框架，结合自上而下的光刻和纳米电化学， 制备自嵌入一对横向电极之间的固态纳米孔。这个新 可扩展的平台可以精确控制DNA易位和互补识别隧道 读出，导致更系统的DNA测序研究。 这个探索性的R21项目是基于我们以前对金属尺寸进行线性调整的工作 纳米间隙从30 nm到1 nm的电沉积，和我们的识别隧道测序研究。我们 假设：（1）受控电沉积工艺可应用于一对亚10 nm厚的金属 限制在两个储存室之间的电极，使得差距可以精确地缩小到 超薄隧穿结，用作嵌入在电极之间的纳米孔通道;以及（2） 控制电极能够通过横向电场门控DNA分子的移位， 这也有利于不同碱基的更可再现的识别隧穿记录。 为了检验我们的总体设计和假设，我们将解决两个具体目标：（1）开发鲁棒的 可扩展的制造过程，并制备嵌入金属隧穿内的原型纳米孔器件 连接，和（2）探索使用集成电极和 研究用于具有固有更高分辨率DNA测序的识别隧穿读出。 我们相信，我们的项目具有广泛的和转化的意义，因为简单的平面器件 控制电极的布局、实时制造控制和集成可以实现 具有良好控制的DNA移位的纳米孔装置。此外，根据我们最近的固定结果， 用于阅读DNA碱基的隧穿间隙、具有适当表面的自对准纳米孔和隧穿结 修改将允许更系统地研究识别隧穿电流读出， 更高的带宽和更好的空间分辨率。因此，我们的项目可以发展成一个新的框架， 这导致固态纳米孔阵列的大规模生产，用于低成本，高通量测序， 并作为个体化医疗的负担得起的基因组工具。

PROJECT SUMMARY Nanopore sensing has been the focus of next-generation DNA sequencing technology. It has demonstrated great potential of rapid single-molecule DNA sequencing with long read lengths and simplified sample preparation. However, existing frameworks of nanopore preparation still face significant challenges from both the intrinsic resolution limit of ionic current detection and the engineering complications during fabrication, in order to achieve two-order-of-magnitude lower error rate and higher device yield/stability as required by human genome sequencing and clinical applications. Here we will address these challenges by exploring a unique fabrication framework combining top-down lithography and nanoscale electrochemistry to prepare solid-state nanopores that are self-embedded between a pair of transverse electrodes. This new scalable platform could allow precise control of DNA translocation and complimentary recognition tunneling readout, leading to more systematic DNA sequencing studies. This exploratory R21 project is based on our previous work on linearly tuning the size of a metal nanogap from 30 nm to 1 nm by electrodeposition, and our recognition tunneling sequencing studies. We hypothesize that: (1) the controlled electrodeposition process can be applied to a pair of sub-10 nm thick metal electrodes confined between two reservoir chambers, so that the gap can be precisely narrowed down into an ultra-thin tunneling junction, serving as the nanopore channel embedded between the electrodes; and (2) the control electrodes could enable gating the translocation of the DNA molecules by the transverse electric field, which also facilitates more reproducible recognition tunneling recording of different bases. To test our overall design and hypotheses, we will address two specific aims: (1) to develop robust scalable fabrication procedures and prepare prototype nanopore devices embedded within metal tunneling junctions, and (2) to explore effective control of DNA translocation using the integrated electrodes and investigate recognition tunneling readout for DNA sequencing with intrinsically higher resolution. We believe that our project has broad and translational significance, because the simple planar device layout, real-time fabrication control, and integration of control electrodes could enable reliable preparation of nanopore devices with well-controlled DNA translocation. Moreover, based on our recent results of fixed tunneling gap for reading DNA bases, the self-aligned nanopore and tunneling junction with the proper surface modification would allow more systematic investigation of recognition tunneling current readout with potentially higher bandwidth and better spatial resolution. Therefore our project can be developed into a novel framework that leads to large scale production of solid-state nanopore arrays for low-cost, high throughput sequencing, and serve as an affordable genomic tool for personalized medicine.