TCB Publications - Abstract

J. B. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. The electromechanics of DNA in a synthetic nanopore. Biophysical Journal, 90:1098-1106, 2006. (PMC: 1367096)

HENG2006 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 ultra-thin silicon nitride membranes. At low electric fields E <200mV/10nm, we observed that single stranded DNA can permeate pores with a diameter $\ge$ 1.0nm, while double stranded DNA only permeates pores with a diameter $\ge$ 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 about 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.

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