Different nucleotides generate specific ionic currents that discriminate between the nucleotides while they are passing through the nanopore constriction. MspA is a commonly used nanopore for DNA sequencing. However, the reasons of the current variation remain ambiguous. Our work unveils the microscopic mechanism of current variation for an ssDNA passing through the MspA nanopore by all-atom molecular dynamic simulations. Besides the physical rigidity and dimensions of the nucleotides, nucleotide orientation is observed to induce nonignorable current variation. Besides the generally considered MspA nanopore constriction, it is also found that the region below constriction could be used to detect and differentiate single nucleotides when the single-stranded DNA translocates in the form of base–constriction–base meshing and ratcheting across the nanopore constriction compared to other regions. The work provides a novel insight into facilitating the development of low-cost and high-throughput nanopore DNA sequencing.

中文翻译：

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揭示用于 DNA 测序的 MspA 纳米孔传感区电流变化的微观机制

不同的核苷酸会产生特定的离子电流，当它们通过纳米孔收缩时，可以区分这些核苷酸。MspA 是 DNA 测序常用的纳米孔。然而，当前变化的原因仍然不明确。我们的工作通过全原子分子动力学模拟揭示了通过 MspA 纳米孔的 ssDNA 电流变化的微观机制。除了核苷酸的物理刚性和尺寸外，还观察到核苷酸方向会引起不可忽视的电流变化。除了普遍认为的 MspA 纳米孔收缩，还发现，与其他区域相比，当单链 DNA 以碱基-收缩-碱基啮合和棘轮穿过纳米孔收缩的形式易位时，收缩下方的区域可用于检测和区分单个核苷酸。这项工作为促进低成本和高通量纳米孔 DNA 测序的发展提供了新的见解。