基于超薄二维材料纳米孔DNA测序的理论设计与研究

项目名称： 基于超薄二维材料纳米孔DNA测序的理论设计与研究

项目编号： No.21673101

项目类型： 面上项目

立项/批准年度： 2017

项目学科： 数理科学和化学

项目作者： 刘海英

作者单位： 济南大学

项目金额： 30万元

中文摘要： 由于在遗传学各个领域都有着重要意义，DNA测序备受关注。近年来研究者认为纳米孔测序技术很有前景，有望实现低成本、快速测序。本项目拟基于超薄二维纳米材料，设计一套固态纳米孔测序方案。该类材料的单层厚度，与DNA双螺旋中碱基的层间距相当，利于实现单分子检测。利用拉伸分子动力学(SMD)，模拟处于电解质溶液中的DNA在合适电压驱动下通过纳米孔的行为。探索纳米孔的尺寸、形状和膜材料对DNA移位的影响。从SMD轨迹中，在原子水平上抽取DNA穿过纳米孔时的准确位型。将带孔的二维材料与置于其中的碱基构建分子结。采用密度泛函并结合非平衡格林函数的方法进行电荷输运计算。利用沿纳米条带的横向电流来识别DNA分子。揭示DNA分子与纳米孔的相互作用机制。该工作将为设计DNA测序传感器提供有用信息。

中文关键词： 量子化学；电荷输运；纳米孔；DNA测序；二维纳米材料

英文摘要： DNA sequencing has attracted much attention due to its significant importance in various subfields of genetics. Nanopore sequencing is believed to be one of the most promising technologies that can lower the cost and speed up DNA sequencing. In this proposal, we will design a novel solid-state nanopore scheme for DNA sequencing based on ultrathin two-dimensional (2D) nanomaterials. The single layer of these 2D materials is only one-atom-thick, so that the entire thickness of the nanopore is comparable to the dimensions of DNA nucleotides. Therefore, these materials are becoming potential sensor candidates to achieve single-base resolution for DNA sequencing. DNA molecules in electrolytic solution will be driven through the nanopore under a suitable bias voltage by steered molecular dynamics (SMD) simulation. The effects of pore sizes, pore shapes and membrane materials on the rapid motion of DNA will be explored. On the basis of the resulting SMD trajectories, exact translocation geometries of the threaded DNA will be captured with atomic-scale details. A two-terminal molecular device will be built using 2D nanoribbon with a drilled pore and the nucleobase, which placed into the most probable position inside the nanopore according to SMD trajectories. Charge transport calculations will be carried out by means of density functional theory (DFT) combined with the nonequilibrium Green’s function method (NEGF). The calculated transverse sheet current across 2D material nanoribbons will provide another opportunity to identity DNA. The interaction mechanism of DNA-nanopore will be revealed. We believe that this work may provide important information for the design of promising DNA sequencing sensors.

英文关键词： quantum chemistry;charge transport;nanopore;DNA sequencing;two-dimensional nanomaterials