Master equation approach to DNA-breathing in heteropolymer DNA
arXiv:cond-mat/0610547 · doi:10.1103/PhysRevE.75.021908
Abstract
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent single-stranded bubbles. Their unzipping and zipping dynamics can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.
12 pages, 8 figures
References in corpus (3)
Cited by in corpus (12)
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- Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities
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- LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA
- Polymer dynamics in the depinned phase: metastability with logarithmic barriers
- Looking into DNA breathing dynamics via quantum physics
- Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
- Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
- Self-organised criticality in base-pair breathing in DNA with a defect