Molecular dynamics simulation on DNA translocating through MoS₂ nanopores with various structures

Abstract

The emergence of MoS₂ nanopores has provided a new avenue for high performance DNA sequencing, which is critical for modern chemical/biological research and applications. Herein, molecular dynamics simulations were performed to design a conceptual device to sequence DNA with MoS₂ nanopores of different structures (e.g., pore rim contained Mo atoms only, S atoms only, or both Mo and S atoms), where various unfolded single-stranded DNAs (ssDNAs) translocated through the nanopores driven by transmembrane bias; the sequence content was identified by the associating ionic current. All ssDNAs adsorbed onto the MoS₂ surface and translocated through the nanopores by transmembrane electric field in a stepwise manner, where the pause between two permeation events was long enough for the DNA fragments in the nanopore to produce well-defined ionic blockage current to deduce the DNA’s base sequence. The transmembrane bias and DNA-MoS₂ interaction could regulate the speed of the translocation process. Furthermore, the structure (atom constitution of the nanopore rim) of the nanopore considerably regulated both the translocate process and the ionic current. Thus, MoS₂ nanopores could be employed to sequence DNA with the flexibility to regulate the translocation process and ionic current to yield the optimal sequencing performance.

Graphical abstract

Keywords

DNA sequencing / MoS₂ / molecular dynamics simulation / nanopore / ionic current

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Acknowledgements

The financial support from the Science and Technology Key Project of Guangdong Province (No. 2020B010188002), Guangdong Natural Science Foundation (No. 2019A1515011121), Guangzhou Technology Project (No. 201804010219), the National Natural Science Foundation of China (Grant Nos. 21908046 and 22078104), Hubei Natural Science Foundation (No. 2019CFB293), Guangdong Basic and Applied Basic Research Foundation (No. 2019A1515110706), State Key Laboratory of Pulp and Paper Engineering (No. SCUT201828) and the Fundamental Research Funds for the Central Universities were gratefully acknowledged.

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