Polyacrylic Acid as a Molecular Brake Modulating the Dynamics of ssDNA Translocation through Graphene Nanopores

Solid-state nanopores have been widely used in the detection of biomolecules, but improving DNA sequencing resolution remains a significant challenge. Polyacrylic acid (PAA), known for its abundant carboxyl groups and excellent hydrophilicity, emerges as an ideal material for nanopore sensors. This study, based on molecular dynamics simulations, demonstrates that nanopore sensors incorporating PAA exhibit a "braking" effect. This effect slows down the translocation speed of single-stranded DNA (ssDNA) while enhancing its recognition capability. Findings reveal that a 15% mass fraction of PAA with a polymerization degree of 60 increases the dwell time of ssDNA by approximately 21-fold. In contrast, a 30% mass fraction of PAA with a polymerization degree of 15 extends the ssDNA dwell time by about 30-fold. The addition of a 20% mass fraction PAA with a polymerization degree of 15 significantly increased the dwell times of all ssDNA sequences, with poly(dG)₂₀ showing a notable 20-fold increase. Moreover, the relative current blockage surpassed 0.5 for all ssDNA sequences, with significant variations observed among different sequences. As the polymerization degree or mass fraction of PAA increases, enhanced electrostatic and van der Waals interactions with ssDNA, along with increased hydrogen bond formation, prolong the ssDNA dwell time. Our research demonstrates that PAA effectively enhances the resolution of nanopore DNA sequencing, providing novel insights for developing high-performance nanopore sensors.