National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
Phys Chem Chem Phys. 2018 Apr 4;20(14):9063-9069. doi: 10.1039/c7cp07462j.
Fast, low-cost and reliable DNA sequencing is one of the most desirable innovations in recent years, which can pave the way for high throughput, label-free and inexpensive personalized genome sequencing techniques. Although graphene-based nanopore devices hold great promise for next-generation DNA sequencing, it is still a challenging problem to detect different DNA sequences efficiently and accurately. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through the functionalized graphene nanopores is investigated by all-atom molecular dynamic simulations. Interestingly, it is found that the four types of bases could be identified by different ionic currents when they pass through the hydrogenated and hydroxylated pores. For the hydrogenated nanopore, the difference in the ionic current for the four bases is mainly attributed to the different electrostatic interactions between the base and the ion. For the hydroxylated nanopore, apart from the electrostatic interactions, the position of a nucleotide inside the nanopore and the dwell time of an ion around the nucleotide also play an important role in the ionic current. The present study could be helpful to better design a novel device for DNA sequencing in the future.
快速、低成本且可靠的 DNA 测序是近年来最令人向往的创新之一，它为高通量、无标记和廉价的个性化基因组测序技术铺平了道路。尽管基于石墨烯的纳米孔器件为下一代 DNA 测序提供了巨大的潜力，但高效准确地检测不同的 DNA 序列仍然是一个具有挑战性的问题。在本工作中，通过全原子分子动力学模拟研究了四种同源 DNA 链（即 poly(A)20、poly(C)20、poly(G)20 和 poly(T)20）通过功能化石墨烯纳米孔的迁移。有趣的是，研究发现，当四种碱基通过氢化和羟基化的孔时，可以通过不同的离子电流来识别它们。对于氢化纳米孔，四种碱基的离子电流差异主要归因于碱基与离子之间的不同静电相互作用。对于羟基化纳米孔，除了静电相互作用外，核苷酸在纳米孔内的位置和离子在核苷酸周围的停留时间也对离子电流起着重要作用。本研究有助于未来更好地设计用于 DNA 测序的新型设备。
