ssDNA Capture\nDynamics by Graphene Nanopores: The\nRole of Electrophoresis and Electro-osmotic Flow

Efficient capture of single-stranded DNA (ssDNA) is crucial\nfor\nhigh-throughput sequencing, which influences the speed and accuracy\nof genetic analysis. Electrophoresis (EP) and electro-osmotic flow\n(EOF) have a significant impact on the translocation behavior of ssDNA\nthrough the nanopore. Experimentally, dynamically tracking these two\neffects remains challenging, and conventional numerical methods also\nstruggle to capture their dynamic properties in the presence of DNA.\nWe use all-atom molecular dynamics (MD) simulations to study how do\nEP and EOF play a role in the capture of DNA under different surface\ncharge densities and graphene layer numbers. Our findings indicate\nthat positive surface charge densities work together with electrophoretic\nforces (<i>F</i><sub>EP</sub>) to enhance the EOF, resulting\nin rapid and efficient ssDNA capture with improved rates of up to\n88% and reduced capture times. Electro-osmotic force (<i>F</i><sub>EOF</sub>) substantially enhances capture efficiency by not\nonly lowering the energy barrier for ssDNA translocation through the\nnanopore but also increasing the probability of ssDNA locating and\naligning with the pore entrance. Negative charges create a repulsive\nelectrostatic environment. Along with the opposing EOF, this lowers\nthe chances of capture. Additionally, we found that an increased number\nof graphene layers can shield internal electric fields, affecting\nssDNA capture negatively by tempering the effects of EOF. This research\nhighlights the importance of precise control over nanopore surface\ncharge and layers to optimize the performance of graphene nanopore\nsequencing technologies, offering potential avenues for significant\nadvancements in genomic sequencing.