Nucleic Acids Research Advance Access originally published online on November 27, 2006
Nucleic Acids Research 2006 34(22):6425-6437; doi:10.1093/nar/gkl754
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Nucleic Acids Research, 2006, Vol. 34, No. 22 6425-6437
Published by Oxford University Press 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Sequence-dependent gating of an ion channel by DNA hairpin molecules
1 Ames Associate, Life Sciences Division, NASA Ames Research Center Moffett Field, CA, USA 2 MAP Pharmaceuticals Palo Alto, CA, USA 3 US Genomics, Woburn MA, USA 4 Center for Biomolecular Science and Engineering, University of California Santa Cruz, CA 95064 5 Life Sciences Division, NASA Ames Research Center Moffett Field, CA, USA
*To whom correspondence should be addresssed at NASA Ames Research Center, Mail Stop 236-7 Moffett Field, CA, USA. Tel: +1 650 604 6014; Fax: +1 650 604 3159; Email: wvercoutere{at}mail.arc.nasa.gov
Received July 22, 2006. Revised September 18, 2006. Accepted September 27, 2006.
DNA hairpins produce ionic current signatures when captured by the alpha-hemolysin nano-scale pore under conditions of single molecule electrophoresis. Gating patterns produced by individual DNA hairpins when captured can be used to distinguish differences of a single base pair or even a single nucleotide [Vercoutere,W.A. et al. (2003) Nucleic Acids Res., 31, 1311–1318]. Here we investigate the mechanism(s) that may account for the ionic current gating signatures. The ionic current resistance profile of conductance states produced by DNA hairpin molecules with 3–12 bp stems showed a plateau in resistance between 10 and 12 bp, suggesting that hairpins with 10–12 bp stems span the pore vestibule. DNA hairpins with 9–12 bp stems produced gating signatures with the same relative conductance states. Systematic comparison of the conductance state dwell times and apparent activation energies for a series of 9–10 bp DNA hairpins suggest that the 3' and 5' ends interact at or near the limiting aperture within the vestibule of the alpha-hemolysin pore. The model presented may be useful in predicting and interpreting DNA detection using nanopore detectors. In addition, this well-defined molecular system may prove useful for investigating models of ligand-gated channels in biological membranes.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors