Rapid nanopore discrimination between single polynucleotide molecules

A variety of different DNA polymers were electrophoretically driven through the nanopore of an alpha-hemolysin channel in a lipid bilayer, Single-chan nel recording of the translocation duration and current flow during travers al of individual polynucleotides yielded a unique pattern of events for eac h of the several polymers tested. Statistical data derived from this patter n of events demonstrate that in several cases a nanopore can distinguish be tween polynucleotides of similar length and composition that differ only in sequence. Studies of temperature effects on the translocation process show that translocation duration scales as similar to T-2. A strong correlation exists between the temperature dependence of the event characteristics and the tendency of some polymers to form secondary structure. Because nanopor es can rapidly discriminate and characterize unlabeled DNA molecules at low copy number, refinements of the experimental approach demonstrated here co uld eventually provide a low-cost high-throughput method of analyzing DNA p olynucleotides.