The full potential of solid state nanopores is yet to be realized for genome sequencing. Due to its robustness it can handle strong voltage amplitude and frequency. The effect of strong alternating voltage on the dynamics of nucleotides during translocation has been explored. We proposed a setup consisting of single stranded DNA covalently linked with symmetric polycations at both ends fashioned after the proposal of Kasianowicz. ¹ Such a setup allows for repeated back and forth motion of the DNA along the nanopore (1.45 nm diameter and 1.53 nm thick) by simply switching the voltage polarity if the polycation tail is sufficiently long (≥ 10) and the applied voltage is below 0.72 volts, but the average residence time of the nucleotides are too small to be of any practical use (6-30 ns). When alternating voltage of higher frequency is applied, it enhances the average residence time of the nucleotides by an order of magnitude to ∼ 0.1 µs relative to direct voltage but the individual trajectories are too stochastic. Since, we are able to collect repeated read on the dynamics of individual nucleotides, we obtained the most probable time of appearance of a nucleotide within the nanopore. With such construct we were able to get almost linear dependence of most probable time versus nucleotide index, after gaussian fitting.

中文翻译：

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使用分子动力学通过纳米孔对聚阳离子-DNA-聚阳离子进行牙线冲洗期间的核苷酸动力学

固态纳米孔在基因组测序方面的全部潜力尚未实现。由于其稳健性，它可以处理强电压幅度和频率。已经探索了强交流电压对易位过程中核苷酸动力学的影响。我们提出了一种由单链 DNA 组成的设置，该设置由在 Kasianowicz 的提议后形成的两端对称聚阳离子共价连接。¹如果聚阳离子尾足够长（≥ 10）且施加的电压低于 0.72，则这种设置允许 DNA 沿着纳米孔（1.45 nm 直径和 1.53 nm 厚）重复来回运动，只需切换电压极性伏特，但核苷酸的平均停留时间太小，没有任何实际用途（6-30 ns）。当施加更高频率的交流电压时，相对于直流电压，它会将核苷酸的平均停留时间提高一个数量级，达到 ~ 0.1 µs，但单个轨迹过于随机。由于我们能够收集单个核苷酸动力学的重复读数，我们获得了纳米孔内核苷酸出现的最可能时间。使用这样的构建体，在高斯拟合之后，我们能够获得最可能的时间与核苷酸指数的几乎线性相关性。