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Slow nucleic acid unzipping kinetics from sequence-defined barriers
S Cocco1, J F Marko, R Monasson
1CNRS-Laboratoire de Dynamique des Fluides Complexes, 3 rue de l'Université, 67000 Strasbourg, France. cocco@ldfc.u-strasbg.fr
The European Physical Journal. E, Soft Matter
|March 11, 2004
Summary
Force-induced unzipping of RNA helix-loop structures reveals slow transitions between open and closed states. A dynamical model explains these transitions via large free energy barriers, analyzing sequence and loop size effects.
Area of Science:
- Biophysics
- Molecular Biology
- Chemical Physics
Background:
- Force-induced unzipping experiments reveal kinetic transitions in RNA helix-loop structures.
- These transitions occur between distinct 'open' and 'closed' states on a timescale of approximately 1 second.
Purpose of the Study:
- To explain the observed kinetic transitions using a simple dynamical model.
- To analyze the dependence of free energy barriers on sequence and loop size.
- To propose DNA and RNA sequences exhibiting novel unzipping dynamics.
Main Methods:
- Development and application of a simple dynamical model.
- Analysis of free energy barriers separating conformational states.
- Simulation of long DNA molecule unzipping under constant force.
Main Results:
- The model demonstrates that slow kinetics of crossing large free energy barriers cause the observed open/closed state transitions.
- The dependence of these barriers on sequence and loop size was quantified.
- The model was successfully applied to predict dynamics of long DNA molecules.
Conclusions:
- The dynamical model provides a mechanistic explanation for force-induced RNA unzipping kinetics.
- Sequence and loop size are critical factors modulating unzipping dynamics.
- The model offers insights into the behavior of both short RNA and long DNA molecules under force.