DNA sequencing using nanopore-nanoelectrode devices for sensing and manipulation

使用纳米孔-纳米电极装置进行 DNA 测序以进行传感和操作

• 批准号: 7928701
• 负责人: Marija Drndic
• 金额: $ 28.14万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-19 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7928701
• 关键词: Ablation; Achievement; Address; Arts; Caliber; Communities; Complement; Complex; Computers; DNA; DNA Sequence; Development; Devices; Diagnosis; Electric Capacitance; Electrodes; Electron Beam; Electrons; Electrostatics; Fingers; Genetic; Genome; Goals; Hemolysin; Individual; Length; Measurement; Measures; Medical; Membrane; Metals; Methodology; Microfluidic Microchips; Microfluidics; Mole the mammal; Motion; Nanostructures; Noise; Operative Surgical Procedures; Patients; Pattern; Performance; Process; Research; Resolution; Running; Seeds; Signal Transduction; Solutions; Speed; Staging; Structure; Study Section; Symptoms; Techniques; Technology; Time; Validation; Vestibule; Work; base; cost; disorder prevention; ds-DNA; electric impedance; fluorescence microscope; improved; lithography; nano; nanochannel; nanofluidic; nanometer; nanopore; nanoscale; prototype; research study; sensor; silicon nitride; simulation; single molecule; solid state; transmission process

DESCRIPTION (provided by applicant): The aim of this research effort is to leverage the unique capabilities of our recently developed sub-nanometer precision transmission electron beam ablation lithography (TEBAL) to demonstrate that the precise integration of solid-state nanopores with nanoelectrodes, nanochannels and other nanostructures will address key obstacles that must be overcome to achieve nanopore-based low-cost high-speed sequencing of chromosomal length DNA molecules, and the resultant medical and scientific benefits enabled by this technology. Fast and low cost full genome DNA sequencing will allow, for example, major improvements in the understanding, diagnosis, treatment and prevention of disease, and significant advances in evolutionary research and the understanding of cellular operation. This project will build on the remarkable progress towards nanopore-based DNA sequencing over the past decade, and it is planned to continue the tradition of sharing results, techniques and nanopore devices with the research community so that the work carried out will make the maximal contribution to advancing the state of the art. It is expected that the nanopore-nanoelectrode devices produced will seed further work by other groups on a variety of transverse electrode sensing methodologies and nanoelectrode-based single DNA molecule manipulation, which will contribute to the achievement of a nanopore-based "$1000 genome sequencer". This development (R21) project will begin work on the long term goals described above by demonstrating the improvements that can be achieved using nanopore devices with integrated nanoelectrodes and nanochannels. Beyond developing reliable nanopore-nanoelectrode devices, the unique aspects of the proposed work include the integration of geometrically more complex electrode patterns to manipulate DNA motion, and the integration of these devices with microfluidics and a fluorescent microscope setup to allow tracking of DNA molecules, so that they can be actively transported to the nanopore. The specific tasks are to show that: * DNA molecule length can be measured more accurately by transverse sensing with nanoelectrodes * the translocation speed of double stranded DNA can be reduced by applying forces via nanoelectrodes * by constraining DNA molecules, length measurement resolution improves for longer molecules * individual DNA molecules can be selected, transported to a nanopore and translocated through it These objectives will be accomplished in several steps. The required nanopore-nanoelectrode, nanopore-nanochannel and microfluidics devices will first be fabricated and characterized (some of this has already been achieved). Next, experiments with these devices will be conducted to evaluate their performance and identify problems. Finally, several cycles of device refinement and further experiments will resolve these problems and improve device performance to optimal levels, so that achievement of the objectives can be demonstrated. PROJECT HEALTH RELEVANCE This research aims to achieve much faster and lower-cost DNA sequencing by developing a nanotechnological sensor. This sensor works just like picking out the knots on a string by running it through one's fingers, except the string is a million times thinner! It will enable major improvements in the understanding, diagnosis, treatment and prevention of disease, by allowing us to determine the underlying genetic causes and symptoms, detect these rapidly and accurately in patients, and treat them appropriately.

描述（由申请人提供）：这项研究工作的目的是利用我们最近开发的我们最近开发的子纳米精度传播电子束片段烧蚀光刻（TEBAL）的独特功能，以证明，固态纳米孔的精确整合与纳米电极与纳米电极的确切整合在一起染色体长度的DNA分子以及该技术所产生的医学和科学益处。快速和低成本的全基因组DNA测序将允许例如，对疾病的理解，诊断，治疗和预防以及进化研究的重大进展以及对细胞运作的理解的重大进展。 该项目将基于过去十年来基于纳米孔的DNA测序的显着进步，并计划继续与研究界共享结果，技术和纳米孔设备的传统，以便进行这项工作将为推进艺术状况做出最大的贡献。预计所生产的纳米纳米纳米电极设备将在其他组上对各种横向电极传感方法进行进一步的工作，而基于纳米电极的单个DNA分子操作将有助于基于纳米孔的“基于纳米孔”的“ $ 1000基因组序列”。 该开发项目（R21）项目将通过证明使用具有集成纳米电极和纳米渠道的纳米孔设备来实现的改进来开始在上述长期目标上进行工作。除了开发可靠的纳米纳米纳米电极设备外，提出的工作的独特方面包括将几何电极模式整合到操纵DNA运动中，以及将这些设备与微功能和荧光显微镜设置整合在一起，以允许对DNA分子进行跟踪，从而可以将它们的运输型运输到Nanopore上。具体任务是表明： * DNA分子长度可以通过用纳米电极横向感测得更准确地测量 *通过纳米电极施加力可以降低双链DNA的易位速度 *通过限制DNA分子，长度测量分辨率可以改善更长的分子 *可以选择单个DNA分子，运输到纳米孔并通过它转移 这些目标将通过几个步骤实现。所需的纳米纳米电极，纳米纳米渠道和微流体设备将首先制造和表征（其中一些已经实现）。接下来，将对这些设备进行实验，以评估其性能并确定问题。最后，设备改进和进一步实验的几个周期将解决这些问题并将设备性能提高到最佳水平，以便可以证明目标的实现。 项目健康相关性本研究旨在通过开发纳米技术传感器来实现更快，更低的成本DNA测序。该传感器的工作方式就像通过用手指伸出弦上的结上的结，只是弦较薄一百万倍！它将通过允许我们确定潜在的遗传原因和症状，在患者中迅速，准确地检测这些原因，并适当治疗它们，从而实现对疾病的理解，诊断，治疗和预防疾病的重大改善。