Electronic Sequencing in Nanopores

纳米孔中的电子测序

• 批准号: 7238487
• 负责人: JENE A GOLOVCHENKO
• 金额: $ 168.58万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-08-01 至 2008-08-18
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7238487
• 关键词: Adsorption; Agreement; Agriculture; Algorithms; Base Composition; Biophysics; Carbon Nanotubes; Cells; Characteristics; Collaborations; Computer-Assisted Image Analysis; Copy Number Polymorphism; DNA; DNA Sequence; Detection; Development; Devices; Diagnosis; Disease; Ecology; Electrodes; Electronics; Engineering; Evolution; Future; Genome; Genomics; Goals; Health; Hour; Human; Human Genetics; Individual; Ions; Joints; Label; Length; Licensing; Link; Localized; Measurement; Mechanics; Membrane; Methods; Microfluidics; Molecular; Nanotubes; Neck; Noise; Nucleic Acids; Nucleotides; Oranges; Performance; Phase; Physics; Polymers; Process; Production; Property; Quality Control; RNA; Rate; Reading; Research; Resolution; Rights; Risk; Scheme; Science; Services; Side; Signal Transduction; Single-Stranded DNA; Solutions; Speed; Surface; System; Technology; Temperature; Testing; Time; Variant; Work; akeson; base; computerized data processing; cost; data acquisition; detector; disorder prevention; electrical property; improved; instrument; interest; mammalian genome; monomer; nanopore; nanoscale; quantum; remediation; research study; response; scale up; sensor; single molecule; solid state; theories; voltage

DESCRIPTION (provided by applicant): The long-term objective is to develop a general utility instrument capable of inexpensive de novo sequencing that can also be used for re-sequencing projects to recognize genome variation in heterozygous genomes. The system being developed will sequentially, and directly, identify the nucleotides in very long fragments of genomic DNA from a base-dependent electronic signal produced by a nanopore articulated with nanotube probes. The final system is intended to provide a relatively high quality sequence from 6.5-fold coverage of a genome using DNA from fewer than 1 million cells, with no amplification and minimal preparative steps. The specific aims for the initial 5 year period of this project are: 1. Improve nanopore surfaces to reduce nonspecific adsorption, pore clogging, and electrical noise; 2. Fabricate and test a nanopore detector articulated with integrated nanotubes for molecular identification; 3. Investigate and optimize the electronic properties of nanotube-DNA interactions to control DNA translocation, orientation and nucleotide contrast; 4. Develop new enzymatic methods to better control and limit the rate of DNA translocation through articulated nanopores; 5. Develop algorithms for feature detection and identification of signals from articulated nanopores; 6. Demonstrate single base sensitivity and resolution on single-stranded DNA translocating through a nanopore. If, as proposed here, we are able to resolve each base as it passes through a nanopore at the rate of 104 bases/sec, an instrument with an array of 100 such nanopores could produce a high-quality draft sequence of 1 mammalian genome in ~20 hours at a cost of approximately $1,000/mammalian genome. Genomic sequencing at these sharply reduced costs would make vital contributions to improved human health on many fronts, including the understanding, diagnosis, treatment, and prevention of disease; advances in agriculture, environmental science and remediation; and the genetics of human health and disease derived from the understanding of evolution.

描述（由申请人提供）：长期目标是开发一种能够廉价的从头测序的通用式仪器，该工具也可用于重新测试项目以识别杂合基因组中的基因组变异。正在开发的系统将依次，直接地鉴定出非常长的基因组DNA片段中的核苷酸，该核苷酸是由由纳米管探针表达的纳米孔产生的基础依赖性电子信号。最终系统旨在使用少于100万个细胞的DNA提供相对较高的质量序列，而没有扩增和最小的准备步骤。该项目最初5年的特定目的是：1。改善纳米孔表面以减少非特异性吸附，孔隙堵塞和电噪声； 2。制造并测试用整合纳米管表达的纳米孔检测器，以进行分子鉴定； 3。研究和优化纳米管-DNA相互作用的电子特性，以控制DNA易位，方向和核苷酸对比度； 4。开发新的酶方法，以更好地控制和限制通过铰接的纳米孔的DNA易位速率； 5。开发用于特征检测和识别信号纳米孔信号的算法； 6。证明了通过纳米孔转移的单链DNA上的单碱基灵敏度和分辨率。如果在这里提出的那样，我们能够以104个碱基/秒的速度通过纳米孔来解决每个碱基，则具有100个这样的纳米孔的仪器可以在20个小时内以约20小时的成本产生1,000美元/哺乳动物的基因组的高质量草稿序列。以这些急剧降低的成本进行基因组测序将对改善许多方面的人类健康做出至关重要的贡献，包括对疾病的理解，诊断，治疗和预防；农业，环境科学和补救的进步；人类健康和疾病的遗传学源于对进化的理解。