基于超薄二维材料纳米孔DNA测序的理论设计与研究

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.

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。

二维材料纳米孔测序是最具前景的单分子测序方式之一。相比于传统测序方法，其具有测速更快、准确率更高、成本更低的优势。课题组采用分子动力学和非平衡态格林函数结合密度泛函的方法，对二维材料纳米孔DNA测序进行了详细地理论研究。各项研究任务基本按照计划得以执行。已经完成的主要研究内容如下：（1）寻找到了三种适合DNA测序的新型二维材料，构建了纳米孔模型。我们在早期选择石墨烯做纳米孔材料的基础上，又选择了二硫化钼、三磷化锗和硅烯作为测序的基础材料，对这些材料的结构和电子性质进行了深入研究。（2）掌握了构建二维材料的拓扑文件和力场文件的方法，解决了项目申请时提出的关键技术问题。在外加电场作用下，用分子动力学模拟了DNA链穿过二维材料纳米孔的迁移过程，已经掌握了分析穿孔动力学数据的基本方法。（3）利用实验上可测的纵向离子电流，进行了DNA测序和甲基化的识别。在详细研究DNA碱基分子各种甲基化形式的基础上，采用分子动力学方法，通过二硫化钼纳米孔，利用垂直于二维材料的离子电流数据，初步做到了识别DNA甲基化重要形式5mC碱基的目的。相对于只对天然DNA测序来说，能够进行甲基化的探测也是该项目实施的一大创新点。（4）利用实验上可测的横向电流，进行了DNA的测序。利用密度泛函并结合非平衡态格林函数的方法，通过三磷化锗纳米孔，利用沿膜材料方向的横向电荷输运性质，选择胞嘧啶作为探针分子，对天然DNA进行了单碱基的识别。（5）课题组还在DNA的氨基修饰和二维材料的储氢方面进行了深入研究，后续我们还会开展异质结纳米孔和利用二维材料与DNA的吸附进行测序方面的研究。.在项目执行期内，课题组共发表论文3篇，均被SCI收录。课程组成员参加了5场国内大型学术会议，发表了3篇会议摘要论文，并开展了国际学术交流，到韩国成均馆大学进行了旨在推进分子动力学研究进程的学术访问。