Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study
Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study
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DOI：
10.1016/j.bpj.2012.08.012
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发表时间：
2012-09-05
影响因子：
3.4
通讯作者：
Khalid, Syma
中科院分区：
文献类型：
--
作者：
Guy, Andrew T.;Piggot, Thomas J.;Khalid, Syma
工程蛋白纳米孔，例如那些基于金黄色葡萄球菌的a-溶血素的纳米孔，已经显示出作为下一代DNA测序设备的组件的巨大前景。然而，在这种蛋白质纳米孔能够被充分利用之前，必须在单个分子水平上表征其中DNA的构象动力学和转位途径。在这里，我们使用原子分子动力学模拟单链DNA在外加电场作用下通过模型α-溶血素孔的运动。这些模拟能够表征单链DNA采用的构象，并允许探索构象如何影响野生型模型孔和一些突变体内的易位。我们的结果表明，蛋白质纳米孔和DNA之间的特定相互作用可以对DNA构象产生重大影响，通常导致局部卷曲，这反过来又可以改变DNA碱基离开纳米孔的顺序。因此，我们的模拟表明，控制蛋白质纳米孔内DNA构象的策略对于DNA测序来说将是一个明显的优势。
Engineered protein nanopores, such as those based on a-hemolysin from Staphylococcus aureus have shown great promise as components of next-generation DNA sequencing devices. However, before such protein nanopores can be used to their full potential, the conformational dynamics and translocation pathway of the DNA within them must be characterized at the individual molecule level. Here, we employ atomistic molecular dynamics simulations of single-stranded DNA movement through a model a-hemolysin pore under an applied electric field. The simulations enable characterization of the conformations adopted by single-stranded DNA, and allow exploration of how the conformations may impact on translocation within the wildtype model pore and a number of mutants. Our results show that specific interactions between the protein nanopore and the DNA can have a significant impact on the DNA conformation often leading to localized coiling, which in turn, can alter the order in which the DNA bases exit the nanopore. Thus, our simulations show that strategies to control the conformation of DNA within a protein nanopore would be a distinct advantage for the purposes of DNA sequencing.