High-bandwidth DNA sequencing using graphene nanoribbon-nanopore devices

使用石墨烯纳米带-纳米孔装置进行高带宽 DNA 测序

• 批准号: 8755887
• 负责人: Marija Drndic
• 金额: $ 44万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-01 至 2016-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8755887
• 关键词: Address; Amplifiers; Base Sequence; Caliber; Carbon; Cells; Charge; Custom; DNA; DNA Sequence; Detection; Development; Devices; Diagnosis; Discrimination; Electrolytes; Electronics; Electrostatics; Enzymes; Exhibits; Fiber Optics; Genetic; Geometry; Goals; Grant; Individual; Ion Channel; Lead; Length; Letters; Location; Measurement; Measures; Methods; Microscope; Motion; Noise; Nucleotides; Patients; Reading; Relative (related person); Reporting; Research; Resolution; Shapes; Side; Signal Transduction; Single-Stranded DNA; Sodium Chloride; Solutions; Speed; Symptoms; Techniques; Technology; Testing; Thick; Variant; Vision; Width; base; cost; density; design; disorder prevention; electrical property; nano; nanopore; nanoscale; next generation; prevent; public health relevance; screening; sensor; voltage

DESCRIPTION (provided by applicant): We propose to sequence DNA by harnessing the one-atom thickness (as thin as the separation between nucleotides) and electrical properties of graphene. A direct readout of the DNA sequence is possible by measuring the modulation of the current flowing through a single-layer graphene nanoribbon (GNR), induced by each base in a single-stranded DNA molecule as it passes through a nanopore (NP) in that GNR. This geometry is anticipated to exhibit large changes in the charge density and electrical current levels in the GNR for each nucleotide base translocating due to the unique electrostatic potential associated with each nucleotide. The major benefit of this approach is that the GNR operating currents (1-10 mA) are orders of magnitude higher than the signals in ionic-current-based sequencing, enabling much higher signal-to-noise ratio and sequencing speeds of 106 bases/s. Important feasibility tests have already been realized in our group. We tested 20 - 200 nm-wide single-layer GNRs with NPs at the GNR edges carrying up to 10 mA in 1 mM to 1M KCl solution at bandwidths as high as 100 MHz. We also developed a method to drill NPs without lowering the GNR conductance and observed correlated GNR and ionic signals during dsDNA translocation. We anticipate that single- base resolution will be achievable at currently reported DNA translocation speeds. This eliminates the need for custom high-speed ultralow noise electronics, as many off-the-shelf photodiode amplifiers for fiber-optics are designed for these current and bandwidth ranges. It also removes the need to slow down or constrain the DNA molecule as it translocates, since the measurement speed is high enough to prevent Brownian fluctuations of the molecule from blurring the GNR signal. The aims of our proposed research are as follows: 1. Optimize GNR device parameters and measurement conditions to achieve sequencing with an error rate less than 0.1% at 10 MHz bandwidth. 2. Demonstrate proof-of-principle multiplexing with ten GNRs on a single chip. 3. Develop the GNR nucleotide sensing mechanism towards an ultrafast, low cost DNA sequencing solution.

描述（由申请人提供）：我们建议利用石墨烯的单原子厚度（与核苷酸之间的间隔一样薄）和电学性质对DNA进行测序。通过测量流过单层石墨烯纳米带（GNR）的电流调制，DNA序列的直接读出是可能的，当单链DNA分子通过纳米孔（NP）时，单链DNA分子中的每个碱基都会引起电流调制。由于与每个核苷酸相关的独特静电电位，这种几何形状预计会在每个核苷酸碱基易位时显示出GNR中电荷密度和电流水平的巨大变化。这种方法的主要优点是GNR工作电流（1-10 mA）比基于离子电流的测序信号高几个数量级，从而实现更高的信噪比和106碱基/s的测序速度。我们组已经完成了重要的可行性测试。我们测试了20 - 200纳米宽的单层GNR， GNR边缘的NPs在带宽高达100 MHz的1mm至1M KCl溶液中携带高达10 mA。我们还开发了一种在不降低GNR电导的情况下钻取NPs的方法，并观察了dsDNA易位过程中GNR和离子的相关信号。我们预计单碱基分辨率将在目前报道的DNA易位速度下实现。这消除了对定制高速超低噪声电子器件的需求，因为许多现成的光纤光电二极管放大器都是针对这些电流和带宽范围设计的。由于测量速度足够高，可以防止分子的布朗波动使GNR信号变得模糊，因此它也不需要在DNA分子易位时减慢或限制DNA分子。我们提出的研究目的如下：1。优化GNR器件参数和测量条件，实现在10mhz带宽下错误率小于0.1%的测序。2. 演示在单个芯片上使用十个gnr的原理验证复用。3. 开发GNR核苷酸传感机制，以实现超快，低成本的DNA测序解决方案。