Sequencing DNA by transverse electrical measurements in Nanochannels

通过纳米通道中的横向电测量对 DNA 进行测序

• 批准号: 7477746
• 负责人: Robert Riehn
• 金额: $ 21.93万
• 依托单位: NORTH CAROLINA STATE UNIVERSITY RALEIGH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7477746
• 关键词: DNA; DNA Sequence; Data; Detection; Development; Devices; Dimensions; Electrochemistry; Electrodes; Environment; Enzymes; Exploratory/Developmental Grant; Fission Yeast; Fluorescence Microscopy; Fungal DNA; Genome; Genomics; Grant; Guanine + Cytosine Composition; Investigation; Lateral; Location; Maintenance; Maps; Measurement; Measures; Methods; Molecular Motors; Monitor; Motion; Nature; Performance; Phase; Philosophy; Polymers; Reading; Reading Frames; Research; Resolution; Saccharomyces cerevisiae; Sampling; Semiconductors; Signal Transduction; Specificity; Speed; Standards of Weights and Measures; Stretching; Structure; Techniques; Technology; Testing; Today; Vertebral column; Viral; anticancer research; base; cost; ds-DNA; electric field; electrical measurement; interest; lithography; nanochannel; nanoelectronics; nanofabrication; nanofluidic; nanopore; point of care

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.

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，并使用纳米电极进行检测。纳米通道平台将实现>100 kbp的超长读码框，这将极大地帮助整个基因组的组装。纳米通道处理还将使得能够对同一分子进行多次读取，并且对易位速度进行良好控制。我们希望该技术最终能够满足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的方法的基本原理是可行的。这将构成开发符合规定品质因数的器械的基础。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，由于DNA存在电信号，并且所获得的信号是序列特异性的。我们将研究信号产生的机制，特别是研究隧道效应、电化学或反离子的极化。为了理解信号的性质及其对测序的有用性，我们将制备间隙在亚5 nm（1 nm）和50 nm之间的电极配置。将使用单链和双链DNA对器械进行评价。我们将通过合成嵌段寡聚物和基因组DNA样品的测序或GC含量图谱评估所获得数据的分辨率和质量。