Carbon Nanotubes: A New Synthetic Nanopore for Sequencing

描述（由申请人提供）：纳米孔测序提供了长读数快速单分子测序的可能性，几乎不需要样品制备，并且可以从小型计算机芯片样设备直接进行电子读取。纳米孔是如此之小的孔，以至于DNA的电泳易位必须一次发生一个碱基。所有的纳米孔都需要以原子精度定位DNA以及控制其通过孔的转运速度。在这里，我们介绍了一种全新的用于DNA易位的纳米孔，即单壁碳纳米管（SWCNT）。SWCNTs在原子尺度上相对均匀，易于制造，无需特殊的纳米加工，可以形成优良的电极，简化隧道读出，开启电化学读出的可能性。它们的高宽高比（通道长度/通道直径）可能允许将DNA捕获在管中，为控制易位速度开辟了新的途径。分子动力学模拟预测单链DNA可以被电场驱动通过2nm直径的swcnts。我们已经通过实验证实了这一预测，构建了一个单swcnts连接两个流体储层的装置，并使用PCR验证了DNA易位。亚利桑那州立大学将指导该项目，并专注于设备制造和DNA易位。橡树岭国家实验室将专注于离子和DNA通过SWCNTs运输的多尺度建模。哥伦比亚大学将重点研究纳米尺度的SWCNTs缝隙的构建。在为期两年的项目结束时，我们将：(a)开发出强大的设备制造程序，并将设备提供给研究界；(b)我们将了解控制离子和DNA通过管道运输的因素；(c)我们将确定影响DNA易位速度和一次可传递的聚合物长度的因素；(d)我们将建立一个原型装置，其中一个隧道间隙集成到单个swcnts纳米孔装置中。这些进展将加速纳米孔技术的发展，使其朝着生产廉价、快速和可靠的DNA测序芯片的方向发展。

DESCRIPTION (provided by applicant): Nanopore sequencing offers the possibility of rapid single molecule sequencing with long reads, almost no sample preparation, and direct electronic readout from a small, computer-chip-like device. Nanopores are orifices that are so small that electrophoretic translocation of DNA through them necessarily occurs one base at a time. All nanopores require some means of localizing DNA with atomic precision as well as controlling its speed of translocation through the pore. Here, we introduce an entirely new type of nanopore for the DNA translocation, the single walled carbon nanotube (SWCNT). SWCNTs are relatively homogeneous on an atomic scale, easy to manufacture with no special nanofabrication, and can form excellent electrodes, simplifying tunneling readout and opening the possibility of electrochemical readout. Their high aspect ratio (channel length/channel diameter) might permit trapping of the DNA in the tube, opening a new avenue for control of translocation speed. Molecular dynamics simulations have predicted that single-stranded DNA can be driven through a 2 nm diameter SWCNT by an electric field. We have confirmed this prediction experimentally, building devices in which a single SWCNT connects two fluid reservoirs and using PCR to verify DNA translocation. Arizona State University will direct the project and focus on device fabrication and DNA translocation. Oak Ridge National Laboratory will focus on multiscale modeling of ion and DNA transport through SWCNTs. Columbia University will focus on the construction of nm-scale gaps in SWCNTs. At the end of the two-year project we will: (a) Have developed robust device fabrication procedures and made devices available to the research community; (b) We will have obtained an understanding of the factors controlling the transport of ions and DNA through the tubes; (c) We will have identified factors that affect the speed of DNA translocation and the length of polymers that can be passed in one read; and (d) We will have built prototype devices in which a tunnel gap is integrated into a single SWCNT nanopore device. These developments should accelerate development of nanopore technology towards the production of a cheap, fast, and reliable DNA sequencing chip. PUBLIC HEALTH RELEVANCE: If successful, the new technology could enable ultra-low cost, single molecule sequencing with long reads, making whole-genome studies available to the general population. Making a search of whole genomes for rare variants economically feasible has many implications for medicine.