The electromechanics of DNA in a synthetic nanopore

J. B. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, G. Timp

Research output: Contribution to journalArticlepeer-review

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 ∼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.

Original languageEnglish (US)
Pages (from-to)1098-1106
Number of pages9
JournalBiophysical journal
Volume90
Issue number3
DOIs
StatePublished - Feb 2006

ASJC Scopus subject areas

  • Biophysics

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