TCBG Seminar

Translocation and Unzipping Kinetics of DNA Molecules using a Nanopore

Professor Amit Meller
Rowland Institute
Harvard University
Cambridge, MA

Friday, February 4, 2005
12:00 pm (CT)
3269 Beckman Institute


The discovery that a voltage gradient can be used to drive single-stranded DNA or RNA molecules through the ~1.5 nm ?-Hemolysin nanopore, has opened up the possibility of detecting and characterizing unlabelled individual polynucleotide molecules. Recently we have developed a method to dynamically set the voltage that drives the polynucleotides. This method makes it possible to study the unzipping kinetics of individual DNA molecules under fixed or time-varying forces. In particular, we have characterized the unzipping kinetics of DNA hairpin molecules under fixed voltage amplitudes (V) or steady voltage ramps (dV/dt). At high voltages (>30 mV) or at high voltage ramps (>5 V/s) the unzipping process can be described by a single step kinetics model with negligible re- zipping probability. But at the low voltage (or voltage ramp) regime re-zipping probability must be included to account for our data. A model that includes re-zipping is introduced and is used to fit our data at low and at high voltages. From the fits we estimate the effective DNA charge inside the nanopore and the unzipping rate of the hairpins at the limit of zero force.

Tea and coffee will be served in R3151 Beckman Institute at 2:30pm.

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