Computational investigation on DNA sequencing using functionalized graphene nanopores
Computational investigation on DNA sequencing using functionalized graphene nanopores
复制标题
使用功能化石墨烯纳米孔进行 DNA 测序的计算研究
DOI：
10.1039/c7cp07462j
复制
发表时间：
2018
影响因子：
3.3
通讯作者：
Ma Yu qiang
中科院分区：
文献类型：
--
作者：
Yu You sheng;Lu Xiang;Ding Hong ming;Ma Yu qiang
快速、低成本和可靠的DNA测序是近年来最令人向往的创新之一，它可以为高通量、无标记和廉价的个性化基因组测序技术铺平道路。尽管基于石墨烯的纳米孔器件为下一代DNA测序带来了巨大的希望，但如何高效、准确地检测不同的DNA序列仍然是一个具有挑战性的问题。本文用全原子分子动力学模拟方法研究了四条均相DNA链(聚(A)20、聚(C)20、聚(G)20和聚(T)20)通过官能化石墨烯纳米孔的移位。有趣的是，当这四种碱通过氢化和羟化的孔时，它们可以通过不同的离子电流来识别。对于氢化纳米孔，四种碱基离子电流的差异主要归因于碱基与离子之间不同的静电相互作用。对于羟基纳米孔，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的作用。本研究有助于更好地设计一种新型的DNA测序装置。
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.