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Bubble merging in breathing DNA as a vicious walker problem in opposite potentials.
Jonas Nyvold Pedersen1, Mikael Sonne Hansen, Tomás Novotný
1Department of Mathematical Physics, Lund University, Box 118, 22100 Lund, Sweden.
The Journal of Chemical Physics
|May 2, 2009
Summary
This study models DNA bubble coalescence, revealing distinct behaviors below and above melting temperatures. The findings offer insights into DNA stability and dynamics for single-molecule experiments.
Area of Science:
- Biophysics
- Molecular Biology
- Computational Biology
Background:
- DNA bubbles form at weak domains and can coalesce.
- Understanding DNA bubble dynamics is crucial for molecular biology.
- Thermodynamic stability and unzipping/zipping rates are key DNA properties.
Purpose of the Study:
- To investigate the coalescence of two DNA bubbles separated by a stable barrier.
- To derive characteristic times and distributions for bubble coalescence.
- To explore the utility of DNA bubble dynamics for quantitative stability analysis.
Main Methods:
- Continuum Fokker-Planck approach to model bubble dynamics.
- Mapping bubble dynamics to vicious walkers in opposing potentials.
- Discrete master equation approach and stochastic simulations.
Main Results:
- Derived characteristic coalescence time and position distributions.
- Identified Kramers-type barrier crossing below melting temperature.
- Observed drift diffusion of bubble corners at high temperatures.
- Demonstrated excellent agreement between continuum and discrete methods.
Conclusions:
- Coalesced DNA bubble states are thermodynamically stabilized.
- The model system facilitates quantitative investigation of DNA thermodynamic stability.
- The study provides insights into DNA unzipping and zipping rate constants.
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