Sequencing DNA by transverse electrical measurements in Nanochannels

描述（由申请人提供）：我们建议开发一种基于分子横向电测量的DNA测序方法。我们的平台将围绕在纳米流体通道中操纵拉伸和线性化的DNA，以及使用纳米电极进行检测。纳米通道平台将实现> - 100kbp的超长读帧，这将极大地帮助全基因组的组装。纳米通道处理还可以实现对同一分子的多次读取，并对易位速度进行良好的控制。我们期望这项技术最终能满足1000美元基因组的成本和性能要求。在这个探索性的R21阶段，我们的目标是通过实验确定所提出方法的基本原理是可行的。这将构成开发符合定义的优点数字的设备的基础。对于这项探索性资助（R21），我们的目标是证明我们可以使用成熟的半导体和纳米电子学制造技术（电子束光刻，电迁移，纳米电镀）制造功能性纳米电极/纳米通道器件，并且由于DNA存在电信号，并且获得的信号是序列特异性的。我们将研究信号产生的机制，并将特别研究隧道，电化学或反离子极化作为可能的候选。为了了解信号的性质及其对测序的有用性，我们将准备在亚5 nm （1nm）和50 nm之间间隙的电极配置。设备将使用单链和双链DNA进行评估。我们将通过测序或合成片段低聚物和基因组DNA样本的gc含量图谱来评估所获得数据的分辨率和质量。

DESCRIPTION (provided by applicant): We propose to develop a sequencing method for DNA that is based on transverse electrical measurements through the molecule. Our platform will be built around manipulating stretched and linearized DNA in nanofluidic channels, and detection using nanoelectrodes. The nanochannel platform will enable ultralong read frames of >100 kbp, which will greatly help assembly of whole genomes. Nanochannel handling will also enable multiple reads of the same molecule, and good control over the translocation speed. We expect that the technique will ultimately fulfill the cost and performance demands of the $1000- genome. In this exploratory R21 phase we aim to experimentally establish that the basic principles underlying the propose method are viable. This will form the basis of the development of a device that meets the defined figures of merit. For this exploratory grant (R21) we aim to demonstrate that we can fabricate functional nanoelectrodes/nanochannel device using proven semiconductor and nanoelectronics fabrication techniques (ebeam lithography, electromigration, nanoplating), that an electrical signal due to the DNA exists, and that the obtained signal is sequence specific. We will investigate the mechanism by which the signal arises, and will in particular examine tunneling, electrochemistry, or polarization of counterions as possible candidates. In order to understand the nature of the signal and its usefulness to sequencing, we will prepare electrode configurations with gaps between sub-5 nm (1nm) and 50 nm. Devices will be evaluated using both single and double stranded DNA. We will assess the resolution and quality of the obtained data by sequencing or GC-content mapping of synthetic block oligomers and genomic DNA samples.