Electronic Sequencing in Nanopores

描述(由申请人提供)：长期目标是一种用于通用仪器的纳米孔探测器芯片，能够进行廉价的从头测序，也可以用于重新测序项目。该仪器直接产生碱基依赖的电子信号，因为数千个碱基长度的单链基因组DNA片段被顺序驱动通过与电接触的单壁碳纳米管探针连接的纳米孔。最终的系统旨在提供相对高质量的序列，使用不到100万个细胞的DNA覆盖6.5倍的基因组，而不需要扩增或标记。具体目标是：1)表征离子溶液中含有和不含DNA分子的无间隙纳米管铰接式纳米孔探测器，建立器件模型；2)控制无间隙纳米管铰接纳米孔中单链DNA的结合、移位和滑动；3)研究和优化DNA分子感应场效应对无间隙纳米管铰接纳米孔中纳米管电极电导的调制；4)分析和优化第一代探测器中间隙纳米管电极之间的隧道电流调制；5)设计和制造嵌入‘T’纳米管几何结构的第二代探测器，实现1Kb/s长度的DNA测序；6)设计了用于高通量10Kb/s/纳米孔测序的第三代纳米孔探测器。如果我们能够像这里建议的那样，以104个碱基/秒的速度解析每个碱基通过纳米孔，那么一个由100个这样的纳米孔阵列组成的仪器可以在大约20小时内产生一个哺乳动物基因组的高质量草稿序列，成本大约为每个哺乳动物基因组1,000美元。以这些降低的成本进行基因组测序将在许多方面为改善人类健康做出重要贡献，包括对疾病的理解、诊断、治疗和预防；环境科学和补救；以及人类健康和疾病的遗传学，这些都源于对进化的理解。健康相关项目我们正在开发一种仪器的核心探测器，它可以在大约20小时内产生一个哺乳动物基因组的高质量草稿序列，每个哺乳动物基因组的成本约为1,000美元。以这些降低的成本进行基因组测序将在许多方面为改善人类健康做出重要贡献，包括对疾病的理解、诊断、治疗和预防；环境科学和补救；以及人类健康和疾病的遗传学，这些都源于对进化的理解。

DESCRIPTION (provided by applicant): The long-term objective is a nanopore detector chip for a general utility instrument capable of inexpensive de novo sequencing that can also be used for re-sequencing projects. The instrument directly generates base-dependent electronic signals as multi-kilobase length fragments of single stranded genomic DNA is driven sequentially through nanopores articulated with electrically contacted single walled carbon 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 or labeling. The specific aims are: 1) Characterize ungapped nanotube articulated nanopore detectors in ionic solution with and without DNA molecules to establish a device model; 2) Control ssDNA binding, translocation, and sliding on the nanotube surface exposed in ungapped nanotube articulated nanopores; 3) Study and optimize DNA molecule induced field effect modulation of nanotube electrode conductance in ungapped nanotube articulated nanopores as a function of nanotube bias, gate voltage, and solution properties; 4) Analyze and optimize tunneling current modulations between gapped nanotube electrodes in the first generation detector; 5) Design and fabricate a second generation detector with embedded 'T' nanotube geometry and achieve 1 Kb/sec sequencing on Kb length strands of DNA; 6) Design a third generation nanopore detector for high throughput 10 Kb/sec/nanopore sequencing. If we are able to resolve each base as it passes through a nanopore at the rate of 104 bases/sec as proposed here, an instrument with an array of 100 such nanopores could produce a high quality draft sequence of one mammalian genome in ~20 hours at a cost of approximately $1,000/mammalian genome. Genomic sequencing at these reduced costs would make vital contributions to improved human health on many fronts, including the understanding, diagnosis, treatment, and prevention of disease; environmental science and remediation; and the genetics of human health and disease derived from the understanding of evolution. PROJECT HEALTH RELEVANCE We are developing the core detector of an instrument that could produce a high-quality draft sequence of one mammalian genome in ~20 hours at a cost of approximately $1,000/mammalian genome. Genomic sequencing at these reduced costs would make vital contributions to improved human health on many fronts, including the understanding, diagnosis, treatment, and prevention of disease; environmental science and remediation; and the genetics of human health and disease derived from the understanding of evolution.