Free energy analysis and mechanism of base pair stacking in nicked DNA.

ABSTRACT: The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparis

SUBMITTER: Hase F 

PROVIDER: S-EPMC5009751 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature