Dynamics of a bubble formed in double-stranded DNA

Abstract

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