Instrument to Optimize DNA Sequencing by Recognition Tunneling

通过识别隧道优化 DNA 测序的仪器

• 批准号: 8707518
• 负责人: STUART LINDSAY
• 金额: $ 88.43万
• 依托单位: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-15 至 2017-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8707518
• 关键词: Automobile Driving; Base Sequence; Basic Science; Binding; Buffers; Carbon Nanotubes; Chemicals; Clinical; Code; Collaborations; DNA; DNA Sequence; Data; Devices; Electrodes; Electrolytes; Electronics; Electrons; Environment; Epigenetic Process; Future Generations; Genome; Goals; Gold; Grant; Individual; Ions; Kinetics; Laboratories; Letters; Libraries; Liquid substance; Maps; Measurement; Measures; Mechanics; Metals; Modeling; Modification; Nanotechnology; Nature; Nucleosides; Nucleotides; Organic solvent product; Positioning Attribute; Preparation; Process; Production; Reader; Reading; Reagent; Running; Scanning Probe Microscopes; Scheme; Signal Transduction; Single-Stranded DNA; Speed; Surface; Techniques; Testing; Time; Tissues; Water; Water Pollution; Work; analytical tool; aqueous; base; computing resources; cost; data acquisition; design; improved; instrument; multi-scale modeling; nanofluidic; nanopore; nanoscale; news; next generation; quantum; residence; simulation; single molecule; single walled carbon nanotube

DESCRIPTION (provided by applicant): Nanopore sequencing is a technique in which DNA is driven electrophoretically through an orifice so small that each base must pass through one at a time. Translocation of thousands of bases of single stranded DNA has been demonstrated. If such long sequence runs could be read rapidly and accurately with no need for chemical reagents or the preparation of elaborate libraries, costs might be reduced to the point where personal genomes would become available for clinical use. Readouts based on the blockading of ion current have been able to resolve individual nucleotides and a single base trapped at a double-single strand junction in a hairpin but have not been able to read along a DNA molecule continuously. Very recently, we have shown that it is possible to identify individual bases and read along a DNA molecule using a technique we call Recognition Tunneling. Recognition molecules, covalently bound to electrodes, are used to transiently trap each base in turn through noncovalent bonds, giving distinct electronic signatures of all four bases and 5-methyl C. The trapping time with no external force applied to the DNA is long (seconds). However, unbinding is readily accelerated to very short times by the application of small forces, so Recognition Tunneling also provides a straightforward approach to translocation control. Here, we propose to combine Recognition Tunneling with nanopore translocation using metal or graphene nanopores, and metal or carbon nanotube reading electrodes, the probes and pores both being functionalized with recognition molecules. We will study translocation-control in functionalized, conducting nanopores, using both the bias across the pore and the surface potential of the conducting pore as control signals. Using a scanning-tunneling microscope (STM) platform, we will make measurements of Recognition Tunneling signals as DNA emerges from the nanopore. Multiscale (quantum to fluid-mechanical) simulations at Oak Ridge National Laboratory will help us to understand and optimize the translocation and readout processes. This understanding will be shared with collaborators who are developing nanopores with fixed (as opposed to STM) reading schemes with the ultimate goal of producing sequencing chips that are cheap and contain many thousands of devices.

描述（由申请人提供）：纳米孔测序是一种技术，在该技术中，DNA是通过如此小的孔口驱动的，以至于每个底部必须一次穿过一个孔。已经证明了数千种单链DNA碱基的易位。如果可以迅速，准确地读取如此长的序列，而无需化学试剂或精心制作的文库制备，那么成本可能会降低至个人基因组可用于临床使用的程度。基于离子电流封锁的读数已经能够解决单个核苷酸和一个被困在发夹中双环链连接处的单个核苷酸，但无法连续沿DNA分子读取。最近，我们已经表明，可以使用我们称为识别隧道的技术识别单个碱基并沿DNA分子读取。共价结合到电极的识别分子用于迅速通过非共价键瞬时捕获每个碱基，给出了所有四个碱基和5-甲基C的不同电子特征。但是，通过使用小型力，可以将未连接很容易加速到很短的时间，因此识别隧道还提供了一种直接的易位控制方法。在这里，我们建议使用金属或石墨烯纳米孔以及金属或碳纳米管读取电极结合识别隧道与纳米孔易位，探针和孔都用识别分子功能化。我们将使用孔隙孔的偏置和导电孔的表面电势作为对照信号，研究官能化的，导电纳米孔的转运控制。使用扫描接触显微镜（STM）平台，随着DNA从纳米孔出现时，我们将对识别隧道信号进行测量。 Oak Ridge国家实验室的多尺度（与流体机体机械）模拟将有助于我们理解和优化易位和读取过程。这种理解将与正在开发固定（而不是STM）阅读方案的纳米孔的合作者共享，其最终目标是生产便宜且包含数千台设备的测序芯片。