Yu Meng, Si Wei, Zeng Tao, Chen Chang, Lin Xiaojing, Ji Zhouxiang, Guo Fei, Li Yuxiang, Sha Jingjie, Dong Yuliang
Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
BGI-ShenZhen, Shenzhen 518103, China.
J Phys Chem Lett. 2021 Sep 23;12(37):9132-9141. doi: 10.1021/acs.jpclett.1c02414. Epub 2021 Sep 15.
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.
不同的核苷酸在通过纳米孔收缩区时会产生特定的离子电流，从而区分这些核苷酸。MspA是一种常用于DNA测序的纳米孔。然而，电流变化的原因仍不明确。我们的工作通过全原子分子动力学模拟揭示了单链DNA通过MspA纳米孔时电流变化的微观机制。除了核苷酸的物理刚性和尺寸外，还观察到核苷酸的方向会引起不可忽视的电流变化。除了通常考虑的MspA纳米孔收缩区外，还发现当单链DNA以碱基-收缩-碱基啮合和棘轮方式穿过纳米孔收缩区时，与其他区域相比，收缩区下方的区域可用于检测和区分单个核苷酸。这项工作为推动低成本、高通量纳米孔DNA测序的发展提供了新的见解。
