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）：本研究工作的目的是利用我们最近开发的亚纳米精密透射电子束烧蚀光刻（TEBAL）的独特功能来证明固态纳米孔与纳米电极、纳米通道的精确集成和其他纳米结构将解决必须克服的关键障碍，以实现基于纳米孔的染色体长度 DNA 分子的低成本高速测序，以及该技术带来的医疗和科学效益。例如，快速、低成本的全基因组 DNA 测序将在疾病的理解、诊断、治疗和预防方面取得重大进展，并在进化研究和细胞运作的理解方面取得重大进展。 该项目将建立在过去十年基于纳米孔的DNA测序方面取得的显着进展的基础上，并计划继续与研究界共享成果、技术和纳米孔设备的传统，以使所开展的工作做出最大的贡献推进最先进的技术。预计所生产的纳米孔-纳米电极装置将为其他小组在各种横向电极传感方法和基于纳米电极的单DNA分子操作方面的进一步工作奠定基础，这将有助于实现基于纳米孔的“1000美元基因组测序仪” 。 该开发（R21）项目将通过展示使用具有集成纳米电极和纳米通道的纳米孔装置可以实现的改进来开始实现上述长期目标。除了开发可靠的纳米孔-纳米电极设备之外，该工作的独特之处还包括集成几何上更复杂的电极图案来操纵 DNA 运动，以及将这些设备与微流体和荧光显微镜设置集成以跟踪 DNA 分子，因此它们可以主动运输到纳米孔。具体任务是要表明： * 通过纳米电极横向传感可以更准确地测量DNA分子长度 * 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，可以提高较长分子的长度测量分辨率 * 单个 DNA 分子可以被选择、运输到纳米孔并通过它易位 这些目标将分几个步骤来实现。首先将制造和表征所需的纳米孔-纳米电极、纳米孔-纳米通道和微流体装置（其中一些已经实现）。接下来，将对这些设备进行实验，以评估其性能并找出问题。最后，通过几个周期的器件细化和进一步的实验将解决这些问题，并将器件性能提高到最佳水平，从而证明目标的实现。 项目健康相关性 这项研究旨在通过开发纳米技术传感器来实现更快、成本更低的 DNA 测序。该传感器的工作原理就像通过手指拨动绳子来找出绳子上的结一样，只不过绳子比绳子细一百万倍！它将使我们能够确定潜在的遗传原因和症状，快速、准确地检测患者的这些原因和症状，并对其进行适当的治疗，从而大大改善对疾病的理解、诊断、治疗和预防。