Molecular dynamics simulation on DNA translocating through MoS<sub>2</sub> nanopores with various structures

doi:10.1007/s11705-020-2004-z

Front. Chem. Sci. Eng.

2021, Vol. 15

Issue (4) : 922-934 https://doi.org/10.1007/s11705-020-2004-z

RESEARCH ARTICLE

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

Daohui Zhao^1,², Huang Chen¹, Yuqing Wang², Bei Li², Chongxiong Duan³, Zhixian Li¹, Libo Li¹(

)

¹. School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
². School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, China
³. School of Materials Science and Hydrogen Energy, Foshan University, Foshan 528231, China

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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.

Keywords DNA sequencing MoS₂ molecular dynamics simulation nanopore ionic current

Corresponding Author(s): Libo Li

Just Accepted Date: 25 August 2020 Online First Date: 18 January 2021 Issue Date: 04 June 2021

Cite this article:

Daohui Zhao,Huang Chen,Yuqing Wang, et al. Molecular dynamics simulation on DNA translocating through MoS₂ nanopores with various structures[J]. Front. Chem. Sci. Eng., 2021, 15(4): 922-934.

URL:

https://academic.hep.com.cn/fcse/EN/10.1007/s11705-020-2004-z
https://academic.hep.com.cn/fcse/EN/Y2021/V15/I4/922

Fig.1 The schematic diagrams of (a) initial configuration of the simulation system and (b) a poly(A)₂₀ translocating through the MoS₂ nanopore. The Mo atoms are colored in cyan, and the sulfur atoms are in yellow. The bases of poly(A)₂₀ are assigned different colors, and the ions are omitted for the sake of clarity.

Fig.2 (a) I–V profiles of three MoS₂ nanopores: Mo only, S only and Mixed; (b) electrostatic potential map for three MoS₂ nanopores under an external bias of 1.2 V (All point charges were approximated by Gaussian spheres with an inverse width b = 0.25 Å^–1. The charge of Mo or S only nanopore rim may change the electrical potential in the nanopore; thus, the nanopore size in the electrostatic potential map may be different from the actual physical size); (c) the average electrostatic potential profile across the pore along the z axis for three MoS₂ nanopores at 1.2 V bias.

Fig.3 ssDNA interacts with MoS₂ surface. (a) The snapshot of poly(C)₂₀ adsorbed onto MoS₂ surface (The MoS₂ is represented by van der Waals spheres: yellow (S) and cyan (Mo). The bases are represented by the NewRibbons model); (b) the adhesion number between ssDNA and the MoS₂ surface; (c) the number of contacts between ssDNA and the MoS₂ surface; (d) time series for the interaction energies between ssDNA and MoS₂ surface.

Fig.4 The translocation traces of ssDNA driven through Mo only nanopore by different voltages of 0.5 V, 0.8 V and 1.2 V: (a) poly(A)₂₀, (b) poly(C)₂₀, (c) poly(G)₂₀ and (d) poly(T)₂₀.

Fig.5 The translocation speeds of ssDNA (poly(A)₂₀, poly(C)₂₀, poly(G)₂₀ and poly(T)₂₀) driven through Mo only nanopore by different voltages.

Fig.6 The changes in translocation base number and ionic current of ssDNA over time driven through Mo only nanopore at a 0.8 V bias: (a) poly(A)₂₀, (b) poly(C)₂₀, (c) poly(G)₂₀ and (d) poly(T)₂₀. The insets show the instantaneous conformation corresponding to the ionic current values.

Fig.7 The translocation traces of ssDNA driven through S only nanopore by different voltages: (a) poly(A)₂₀, (b) poly(C)₂₀, (c) poly(G)₂₀ and (d) poly(T)₂₀ .

Fig.8 The translocation speeds of ssDNA driven through S only nanopore by different voltages: poly(A)₂₀, poly(C)₂₀, poly(G)₂₀ and poly(T)₂₀.

Fig.9 The translocation traces and ionic current blockages of ssDNA driven through S only nanopore at a 2.4 V bias: (a) poly(A)₂₀, (b) poly(C)₂₀, (c) poly(G)₂₀ and (d) poly(T)₂₀.

Fig.10 The translocation traces of ssDNA driven through Mixed nanopore by different voltages: (a) poly(A)₂₀, (b) poly(C)₂₀, (c) poly(G)₂₀ and (d) poly(T)₂₀.

Fig.11 The translocation speeds of ssDNA driven through the Mixed nanopore by different voltages: poly(A)₂₀, poly(C)₂₀, poly(G)₂₀ and poly(T)₂₀.

Fig.12 The translocation traces and ionic current blockages of ssDNA driven through a Mixed nanopore at a 1.2 V bias: (a) poly(A)₂₀, (b) poly(C)₂₀, (c) poly(G)₂₀ (2.4 V) and (d) poly(T)₂₀.

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