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The Electromechanics of DNA in a Synthetic Nanopore

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

^* Department of Electrical and Computer Engineering, and Department of Physics, Beckman Institute, University of Illinois, Urbana, Illinois 61801; and Department of Biochemistry, University of Illinois, Urbana, Illinois 61801

Correspondence: Address reprint requests to Gregory Timp, 3311 Beckman Institute, 405 North Mathews Ave., Urbana, IL 61801. Tel.: 217-244-9629; Fax: 217-244-6622; E-mail: gtimp{at}uiuc.edu.

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.

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