Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores
Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores
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DOI：
10.1063/1.2746246
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发表时间：
2007-07-07
影响因子：
4.4
通讯作者：
Muthukumar, M.
中科院分区：
文献类型：
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作者：
Forrey, Christopher;Muthukumar, M.
我们已经实现了一个粗粒度模型来研究通过位于合成膜纳米孔的电压驱动的as-DNA易位。利用朗格万动力学计算了DNA通过纳米孔的模拟轨迹。我们提出了基于超过12万个个体易位的结果。我们特别感兴趣的是这项工作，探索各种实验观察到的物理基础，但知之甚少的现象。值得注意的是，我们在模拟中观察到ds-DNA发夹的形成，这被广泛怀疑是量化堵塞的基础。我们研究了易位时间，一个在聚电解质表征中至关重要的可测量量，作为沿聚合物主链发夹顶点位置的函数，发现这种行为可以通过模拟参数在一定程度上调整。我们还研究了发夹倾向作为易位事件启动器的电压依赖性。令人惊讶的是，我们发现所得的概率在很大程度上取决于所计算的事件最终是否成功。进一步的细节使我们提出，实验易位研究中的失败尝试可能比通常认识到的更常见，也更具有欺骗性。我们发现单个文件成功易位所花费的时间与链长度与施加电压的比例成正比。最后，我们解决了易位实验中一个常见但令人困惑的现象：在易位事件中，通过孔的电流高度但不完全受阻。我们提出的研究结果为这些事件提供了新的解释。
We have implemented a coarse-grained model to study voltage-driven as-DNA translocation through nanopores located in synthetic membranes. The simulated trajectory of the DNA through the nanopores was calculated using Langevin dynamics. We present the results based on more than 120 000 individual translocations. We are particularly interested in this work in probing the physical basis of various experimentally observed-yet poorly understood-phenomena. Notably, we observe in our simulations the formation of ds-DNA hairpins, widely suspected to be the basis for quantized blockage. We study the translocation time, a measurable quantity crucially important in polyelectrolyte characterization, as a function of hairpin vertex location along the polymer backbone, finding that this behavior can be tuned to some degree by simulation parameters. We also study the voltage dependence of the tendency of hairpins to serve as the initiators of translocation events. Surprisingly, we find that the resulting probability depends vitally upon whether the events counted are ultimately successful or not. Further details lead us to propose that failed attempts in experimental translocation studies may be more common-and deceptive-than is generally recognized. We find the time taken by successful single file translocations to be directly proportional to the ratio of chain length to the applied voltage. Finally, we address a common yet puzzling phenomenon in translocation experiments: translocation events in which the current through the pore is highly, yet incompletely, blocked. We present the findings that offer a new explanation for such events.