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La Penna, G ; Perico, A ; Genest, D

Dynamics of a double stranded DNA oligomer : Mode-coupling diffusion approach and reduced rigid fragment models

Journal of Biomolecular Structure & Dynamics 17 (4) 673-685

par Administrateur - publié le

Abstract :

The local dynamics of a double stranded DNA fragment [d(CpGpCpApApApTpTpTpGpCpG)](2) of twelve base pairs is ;obtained to second order in the mode-coupling expansion of the Smoluchowski diffusion theory. The DNA is considered a fluctuating three-dimensional (3D) structure undergoing rotational diffusion. The starting structure for the calculations is the B canonical structure of the fragment, while the fluctuations are evaluated using molecular dynamics simulations, with the ensemble averages approximated by time averages along a trajectory of length 1.5 ns.