title: 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.
authors.affiliation: IBM T. J. Watson Research Center, PO Box 218, Yorktown Heights, New York 10598, USA.
authors.forename: Binquan
authors.initials: B
authors.lastname: Luan
authors.forename: Hongbo
authors.initials: H
authors.lastname: Peng
authors.forename: Stas
authors.initials: S
authors.lastname: Polonsky
authors.forename: Steve
authors.initials: S
authors.lastname: Rossnagel
authors.forename: Gustavo
authors.initials: G
authors.lastname: Stolovitzky
authors.forename: Glenn
authors.initials: G
authors.lastname: Martyna
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009068:Movement; D058608:Nanopores; D055672:Static Electricity; D013696:Temperature
chemical_list: D004277:DNA, Single-Stranded