Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore

By applying an electric field to an insulating membrane, movement of charged particles through a nanopore can be induced. The measured ionic current reports on biomolecules passing through the nanopore. In this paper, we explore the sequence-dependent dynamics of DNA unzipping using our recently developed coarse-grained model. We estimated three molecular profiles (the potential of mean force, position-dependent diffusion coefficient, and position-dependent effective charge) for the DNA unzipping of four hairpins with different sequences. We found that the molecular profiles are correlated with the ionic current and molecular events. We also explored the unzipping kinetics using Brownian dynamics. We found that the effect of hairpin structure on the unzipping/translocation times is not only energetic (weaker hairpins unzip more quickly) but also kinetic (different unzipping and translocation pathways play an important role).