Different solid-state nanopore translocation dynamics and times of dsDNA and ssDNA

By performing all-atomic molecular dynamics simulations of 22-nucleotides-long double stranded (ds) and single stranded (ss) DNA molecules near an aluminum oxide nanopore, we observe that the electrophoretic translocation of dsDNA molecules is significantly faster than their melted ssDNA counterparts. We attribute this phenomenon to vdW attraction between the high-permittivity surface and the nucleic acid aromatic rings, which are more exposed and freer to rotate for ssDNAs. With a scaling theory that captures the larger enthalpy of adsorption due to these vdW contacts at the rings, we are able to develop a transition state theory for the stick-slip translocation dynamics of both molecules. The difference in the translocation time is further enhanced by a normal electric field component, which enhances the vdW attractive interaction by electro-statically attracting the molecules to the surface. We also capture this field-effect on the translocation time by appropriately reducing the barrier to produce a scaling theory that collapses the experimental translocation time data at different voltage for tailor-designed sharp-tip nanopores with a large normal field leakage. This peculiar chromatograph separation between ssDNA and dsDNA is being exploited for biosensing applications.