Escape Dynamics of DNA from a Nanopore under the Influence of an AC Bias

Monitoring the escape of ssDNA from a protein nanopore provides new insight into the dynamics of DNA translocation and a direct means of measuring progress of the escape. New instrumentation has been developed that allows for simultaneous application of an AC and DC bias across a protein nanopore. Initial measurements with the system have focused on the capture and release of ssDNA tails attached to DNA hairpins. Polynucleotide tails attached to 24 nucleotide DNA hairpins are threaded into the beta-barrel of an alpha-hemolysin channel under the influence of a strong DC driving voltage. After the capture of the hairpin, the DC voltage is turned off and the subsequent escape of the hairpin is directly monitored via an AC bias. Escape times were measured as a function of AC amplitude (20 to 250 mV), AC frequency (60-200 kHz), DC drive voltage (0 to 100 mV), and temperature (-10°C to 20°C). The applied AC voltage has been shown to play a significant role in the DNA/nanopore interaction. The results are well described by a one-dimensional diffusion model across an asymmetric, periodic potential.