American Institute of Physics, The Journal of Chemical Physics, 13(132), p. 135101, 2010
DOI: 10.1063/1.3328875
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We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus α-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the α-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based “molecular rulers” may prove useful in deducing the structures of nanometer-scale pores in general.