Paper Citing NAMD - Abstract
Heng, J.B.; Aksimentiev, A.; Ho, C.; Marks, P.; Grinkova, Y.V.; Sligar, S.; Schulten, K.; Timp, G.
The electromechanics of DNA in a synthetic nanopore
BIOPHYSICAL JOURNAL, 90:1098-1106, FEB 2006
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 similar to 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.
DOI:10.1529/biophysj.105.070672
