Stochastic approach to DNA breathing dynamics

Abstract

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.

7 pages, 6 figures, epl.cls

References in corpus (4)

• Force and kinetic barriers in unzipping of DNA
• Bubble dynamics in DNA
• Poland-Scheraga models and the DNA denaturation transition
• Comment on "Why is the DNA denaturation transition first order?"

Cited by in corpus (16)

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• DNA bubble dynamics as a quantum Coulomb problem
• Sequence sensitivity of breathing dynamics in heteropolymer DNA
• Breathing dynamics in heteropolymer DNA
• Physics of base-pairing dynamics in DNA
• Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins
• Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
• Master equation approach to DNA-breathing in heteropolymer DNA
• Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization
• Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
• DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals
• Diffusion of two particles with a finite interaction potential in one dimension
• Diffusion of Macromolecules across the Nuclear Pore Complex
• Blinking statistics of a molecular beacon triggered by end-denaturation of DNA
• Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
• Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach