Self-consistent calculation of localized DNA vibrational properties at a double-helix–single-strand junction with anharmonic potential

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Abstract
We study the dynamics of H-bond motion for a model of a replicating DNA fork. The model contains effects both from the creation of the fork and from self-consistent changes in the H bonds due to the creation of the fork. We use a Morse potential to describe the H-bond interactions. The anharmonic behavior does alter the final H-bond dynamics. The anharmonic aspect increases the H-bond fluctuations by more than a factor of 2 over the harmonic fork results in some frequency regions. We also display the frequency dependence of the H-bond motion and suggest spectral features that can be a signature for the existence of forks in DNA samples.