Sequence-dependent gating of an ion channel by DNA hairpin molecules

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Abstract
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 differ- ences of a single base pair or even a single nucleotide (Vercoutere,W.A. et al .( 2003)Nucleic Acids Res. ,3 1, 1311-1318). Here we investigate the mechanism(s) that may account for the ionic current gating sig- natures. The ionic current resistance profile of con- ductance 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 signa- tures 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 30 and 50 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 detec- tors. In addition, this well-defined molecular system may prove useful for investigating models of ligand-gated channels in biological membranes.