BIOPHYSICAL THEORY AND MODELING |
Extracting kinetics from single-molecule force spectroscopy:
Nanopore unzipping of DNA hairpins
Olga K Dudko 1, Jerome Mathe 2, Atilla Szabo 3, Amit Meller 4 and Gerhard Hummer 3*
1 National Institutes of Health
2 Universite d'Evry, Evry, France
3 NIH
4 Boston University
* To whom correspondence should be addressed. E-mail: gerhard.hummer{at}nih.gov.
Submitted on December 8, 2006
Revised on January 10, 2007
Accepted on 31 January 2007
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Abstract |
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Single-molecule force experiments provide powerful new tools to explore biomolecular interactions. Here, we describe a systematic procedure for extracting kinetic information from force-spectroscopy experiments, and apply it to nanopore unzipping of individual DNA hairpins. Two types of measurements are considered: unzipping at constant voltage, and unzipping at constant voltage-ramp speed. We perform a global maximum-likelihood analysis of the experimental data at low-to-intermediate ramp speeds. To validate the theoretical models, we compare their predictions with two independent sets of data, collected at high ramp speeds and at constant voltage, by using a quantitative relation between the two types of measurements. Microscopic approaches based on Kramers theory of diffusive barrier crossing allow us to estimate not only intrinsic rates and transition state locations, as in the widely used phenomenological approach based on Bell's formula, but also free energies of activation. The problem of extracting unique and accurate kinetic parameters of a molecular transition is discussed in light of the apparent success of the microscopic theories in reproducing the experimental data.
Key Words:
DNA unfolding, Kramers theory, alpha-hemolysin, single-molecule pulling
