Dynamics of a bubble formed in double stranded DNA

Abstract

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.

11 pages, 4 figures. submitted to Phys. Rev. Lett

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Cited by in corpus (7)

• Physics of base-pairing dynamics in DNA
• The probability analysis of opening of DNA
• DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals
• Base pair fluctuations in helical models for nucleic acids
• Strand diffusion-limited closure of denaturation bubbles in DNA
• First-passage probability: a test for DNA Hamiltonian parameters
• Bubble dynamics in double stranded DNA : A Rouse chain based approach