Physics of DNA Threading through a Nanometer Pore and Applications to Simultaneous Multianalyte Sensing

Polymer transport is central to many biological processes, including protein translocation, bacterial gene transduction and some modes of viral infection. To better understand the mechanisms of macromolecular transport, we are studying the ability of polymers to partition into and thread through single protein ion channels. It was recently shown in our laboratory that individual molecules of single-stranded DNA and RNA can be detected and characterized as they are driven electrophoretically through a single channel formed by Staphylococcus aureus α-hemolysin. We demonstrate that polynucleotides partition more readily into one entrance of this channel than the other and that the rate at which the polymer enters the pore increases exponentially with the magnitude of the applied electrostatic potential. A simple model provides an estimate for both the height of the energy barrier that limits polynucleotide entry into the channel and the number of charges on polyanionic ssDNA that initiate voltage-driven transport through the pore. We show that polynucleotides can be used to probe the geometric properties of an ion channel, and that the interaction between the polynucleotides and a nanopore can be used to estimate the concentration of analytes in solution. A statistical analysis of the current blockades provides information about the structures of both the polymer and the nanopore.