Translocation of ssDNA through Charged Graphene Nanopores: Effect of the Charge Density

Yuan-Shuo Zhang; Zhi-Ya Qi; Ming-Ming Ding; Ming-Lun Li; Tong-Fei Shi

doi:10.1007/s10118-024-3215-4

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Translocation of ssDNA through Charged Graphene Nanopores: Effect of the Charge Density

RESEARCH ARTICLE | Updated：2024-12-03

- Translocation of ssDNA through Charged Graphene Nanopores: Effect of the Charge Density
- Translocation of ssDNA through Charged Graphene Nanopores: Effect of the Charge Density
- 高分子科学（英文版） 2024年42卷第12期页码：2048-2058
- Affiliations：
  
  a.School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
  b.Jieyang Branch of Chemistry and Chemical Engineering Guangdong Laboratory, Jieyang 515200, China
  c.Department of Polymer Science and Engineering, University of Massachusetts Amherst, 120 Governors Drive, Amherst 01003, Massachusetts, United States
- Author bio：
  
  mmding@gdut.edu.cn (M.M.D.)
  minglunli@umass.edu (M.L.L.)
- Funds：
  
  This work was financially supported by the National Natural Science Foundation of China (Nos. 22373025 and 22227804).;Electronic supplementary information (ESI) is available free of charge in the online version of this article at http://doi.org/10.1007/s10118-024-3215-4.
- DOI：10.1007/s10118-024-3215-4
  中图分类号：
- 收稿：2024-07-04，
  
  修回：2024-07-23，
  
  录用：2024-08-03，
  
  网络首发：2024-11-07，
  
  纸质出版：2024-12-01
- Accepted：
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Zhang, Y. S.; Qi, Z. Y.; Ding, M. M.; Li, M. L.; Shi, T. F. Translocation of ssDNA through charged graphene nanopores: effect of the charge density. Chinese J. Polym. Sci. 2024, 42, 2048–2058

Yuan-Shuo Zhang, Zhi-Ya Qi, Ming-Ming Ding, et al. Translocation of ssDNA through Charged Graphene Nanopores: Effect of the Charge Density[J]. Chinese Journal of Polymer Science, 2024, 42(12): 2048-2058.
Zhang, Y. S.; Qi, Z. Y.; Ding, M. M.; Li, M. L.; Shi, T. F. Translocation of ssDNA through charged graphene nanopores: effect of the charge density. Chinese J. Polym. Sci. 2024, 42, 2048–2058 DOI： 10.1007/s10118-024-3215-4.

Yuan-Shuo Zhang, Zhi-Ya Qi, Ming-Ming Ding, et al. Translocation of ssDNA through Charged Graphene Nanopores: Effect of the Charge Density[J]. Chinese Journal of Polymer Science, 2024, 42(12): 2048-2058. DOI： 10.1007/s10118-024-3215-4.

摘要

The study utilizes molecular dynamics simulations to explore how graphene nanopore charge densities affect ssDNA translocation. Results show that higher negative charges on graphene significantly slow ssDNA movement

thereby enhancing DNA sequencing accuracy by improving ionic current blockades. This highlights the potential of negatively charged graphene nanopores in sequencing optimization.

Abstract

Nanopore sequencing harnesses changes in ionic current as nucleotides traverse a nanopore

enabling real-time decoding of DNA/RNA sequences. The instruments for the dynamic behavior of substances in the nanopore on the molecular scale are still very limited experimentally. This study employs all-atom molecular dynamics (MD) simulations to explore the impact of charge densities on graphene nanopore in the translocation of single-stranded DNA (ssDNA). We find that the magnitude of graphene’s charge

rather than the charge disparity between ssDNA and graphene

significantly influences ssDNA adsorption and translocation speed. Specifically

high negative charge densities on graphene nanopores are shown to substantially slow down ssDNA translocation

highlighting the importance of hydrodynamic effects and electrostatic repulsions. This indicates translocation is crucial for achieving distinct ionic current blockades

which plays a central role for DNA sequencing accuracy. Our findings suggest that negatively charged graphene nanopores hold considerable potential for optimizing DNA sequencing

marking a critical advancement in this field.

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Keywords

references

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