The nanopore is an established tool for studying the kinetic and thermodynamic properties of polynucleotide and polynucleotide-protein molecules at the single molecule level, and continues to show great promise for inexpensive genomic sequencing. Our experiments are the first to combine the nanopore with control logic that enables control over the temporal availability of a single DNA molecule, trapped in the nanopore, to associating molecules in solution above the nanopore. Using this approach, I will present our results in studying the kinetics of DNA hybridization and of DNA-DNA polymerase assembly. The method is statistically rich: tens of thousands of molecular interactions can be measured during a 1 hour experiment. From the measured distributions, I will describe our efforts to uncover and model the kinetic states and state transition parameters (equilibrium and rate constants) for the molecular complex being studied. Using tools from systems and control theory, future work will aim toward online estimation and regulation of the state(s) of the molecule.
William B. Dunbar received the B.S. degree in engineering science and mechanics from the Virginia Polytechnic Institute and State University in 1997, the M.S. degree in applied mechanics and engineering science from the University of California, San Diego, in 1999, and the Ph.D. degree in control and dynamical systems from the California Institute of Technology, Pasadena, in 2004. He is currently an Associate Professor with the Department of Computer Engineering, University of California, Santa Cruz. Current research is focused primarily on the application of systems and control tools to single molecule biophysics and instrumentation. Dunbar is a recipient of a five-year retraining award from the National Institutes of Health (NHGRI, 2006) and an NSF CAREER award (ECCS, 2009).
