The Electromechanics of DNA in a Synthetic Nanopore

Abstract

We have explored the electromechanical properties of DNA on a nanometer-length scale using an electric field to force single molecules through synthetic nanopores in ultrathin silicon nitride membranes. At low electric fields, E<200mV/10nm, we observed that single-stranded DNA can permeate pores with a diameter ≥1.0nm, whereas double-stranded DNA only permeates pores with a diameter ≥3nm. For pores <3.0nm diameter, we find a threshold for permeation of double-stranded DNA that depends on the electric field and pH. For a 2nm diameter pore, the electric field threshold is ∼3.1V/10nm at pH=8.5; the threshold decreases as pH becomes more acidic or the diameter increases. Molecular dynamics indicates that the field threshold originates from a stretching transition in DNA that occurs under the force gradient in a nanopore. Lowering pH destabilizes the double helix, facilitating DNA translocation at lower fields.