The electromechanics of DNA in a synthetic nanopore

Biophys J. 2006 Feb 1;90(3):1098-106. doi: 10.1529/biophysj.105.070672. Epub 2005 Nov 11.

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 < 200 mV/10 nm, we observed that single-stranded DNA can permeate pores with a diameter >/=1.0 nm, whereas double-stranded DNA only permeates pores with a diameter >/=3 nm. For pores <3.0 nm diameter, we find a threshold for permeation of double-stranded DNA that depends on the electric field and pH. For a 2 nm diameter pore, the electric field threshold is approximately 3.1 V/10 nm 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biophysics / methods*
  • Computer Simulation
  • DNA / chemistry*
  • Electrochemistry / methods
  • Electromagnetic Fields
  • Electrophoresis
  • Electrophoresis, Agar Gel
  • Hydrogen-Ion Concentration
  • Ions
  • Membrane Potentials
  • Microscopy, Electron, Transmission
  • Models, Molecular
  • Nanostructures
  • Nanotechnology / methods*
  • Nucleic Acid Conformation*
  • Polymerase Chain Reaction
  • Porosity
  • Silicon Compounds
  • Time Factors

Substances

  • Ions
  • Silicon Compounds
  • DNA
  • silicon nitride