石墨烯纳米孔定位和识别DNA损伤位点的分子模拟研究

Nanopore sequencing, as the next generation sequencing technology, can read the gene information from the ionic current blockage induced by the transport of a single DNA molecule in pore. The damaged DNA and unmodified DNA have discrepant physical structures and chemical properties. These differences could induce blockages of ionic current with specificity. However, to locate the damaged sites on a DNA chain and recognize them, we need to break through the limitation of low spatial resolution of traditional nanopores, and then extract the characteristic ionic current signals of different kinds of modifications. Graphene nanopores own a single-atom thickness, promising the single-base spatial resolution. By means of simulations and calculations, in this proposal, we focus on the assessment of graphene nanopores in the locating and recognition of damaged sites on a DNA chain at atomic and molecular level. Firstly, we expect to understand the molecular mechanism dominating the ionic current blockage-- particularly the intermolecular interactions within a graphene nanopore and free energy changes of ions translocation. And then, we will discuss the sensitivity of blocked ionic current towards the inherent structural differences of different kinds of damaged sites on DNA. Finally, the induced ionic current will be predicted during the translocation of damaged DNA in graphene nanopores, and a deep analysis of the characteristic ionic current for different kinds of DNA-damages will be carried out. Based on these investigations, we expect to supply a theoretical foundation for the improvement of the resolution of nanopore experiments further.

纳米孔是新一代基因测序技术，主要根据DNA链在纳米孔内输运时引起的离子电流阻塞来读取基因信息。受损DNA具有与正常DNA不同的物理结构和化学性质，可以对纳米孔内的离子电流产生特异性阻塞效果。但是，定位和识别DNA的损伤位点还需要突破传统纳米孔的低空间分辨率限制，提取各损伤位点在纳米孔内对应的特征离子电流信号。本项目拟利用石墨烯纳米孔的单原子厚度所具备的单碱基分辨潜力，通过模拟计算，在原子、分子尺度上研究石墨烯纳米孔对DNA链上损伤位点的识别和定位能力。重点从受损DNA 分子在石墨烯纳米孔内阻塞离子流的分子机制着手，计算孔内各分子间相互作用、离子输运自由能变化等控制离子阻塞效果的物理化学参量，探讨离子电流阻塞对DNA固有结构差异的敏感性，预测DNA输运过程中损伤位点诱导的阻塞离子电流信号，分析不同类型的DNA损伤引起的特征离子电流，为进一步提高纳米孔实验的分辨率提供理论支撑。

本项目从受损DNA 分子在传统石墨烯纳米孔内阻塞离子流的分子机制着手，计算孔内各分子间相互作用、离子输运自由能变化等控制离子阻塞效果的物理化学参量。我们发现DNA损伤位点在穿过纳米孔过程中有明显的去水化过程并引起分子内氢键重排。利用量子力学/分子力学动力学模拟，我们在类似的去水化过程中观察到了分子内氢键重排伴随的质子迁移动力学。我们探讨了离子电流阻塞对DNA固有结构差异的敏感性，分析了不同类型的DNA损伤引起的特征离子电流。我们发现顺铂-DNA修饰物产生的离子电流阻塞信号最为明显。因此，我们通过增强采样模拟，在原子、分子尺度上进一步研究了实验上已证实的具有特异性识别性质的顺铂-DNA-HMGB1 蛋白复合物的分子间相互作用机理，以望从该自然界存在的特异性识别现象中找到提高纳米孔检测灵敏度的新思路。结果发现在分子识别界面上三维全空间的相互作用协同，在提高特异性结合能力上起关键作用。受此启发，我们与实验合作者合成了三维的类石墨烯纳米孔结构，并探索其对链状生物分子的特异性识别能力。通过本项目的研究，我们为有机-无机界面上分子特异性结合提供了微观理论基础支撑，为新材料在进一步提高纳米孔结构对受损DNA的特异性识别能力的应用提供了前瞻性实验指导。