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

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.