Base-by-base ratcheting of single stranded DNA through a solid-state nanopore

Abstract

We investigate the base-by-base translocation dynamics of single-stranded DNA (ssDNA) confined in a solid-state nanopore dressed with an electrostatic trap, using all-atom molecular dynamics (MD) simulation. We observe on the simulation time scale of tens of nanoseconds that ssDNA can be driven through the nanopore in a ratchetlike fashion, with a step size equal to the spacing between neighboring phosphate groups in the ssDNA backbone. A 1D-Langevin-like model is derived from atomistic dynamics which can quantitatively describe simulation results and can be used to study dynamics on longer time scales. The controlled ratcheting motion of DNA could potentially enhance the signal-to-noise ratio for nanoelectronic DNA sensing technologies. © 2010 The American Physical Society.