Discrimination Of Single Base Pair Differences Among Individual Dna Molecules Using A Nanopore

Veronica DeGuzman, Nanopore Laboratory, University of California, Santa Cruz

Stevenson Hall 1300
12:00 PM - 12:50 PM

The protein toxin alpha-hemolysin form nanometer scale channels across lipidmembranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, basepair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, incurrent. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.