Thermodynamics of local DNA openings.

A mechanism connecting the local untwisting and opening of DNA double helix is proposed. The presented thermodynamical approach is based on two models: the Peyrard-Bishop model that describes the denaturation of DNA due to thermal fluctuations and the model developed by the author describing solitary torsional waves, which propagate along the DNA molecule forced by advancing RNA polymerase. The torsional wave implies that the DNA untwists locally causing a local decrease in the stacking interaction between adjacent base pairs. Molecular dynamics simulations have shown that thermal fluctuations (which are too small at physiological temperatures to denaturate the twisted DNA) may lead to the formation of a denaturation bubble placed in the untwisted region.