Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study.

ABSTRACT: Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of DNA, to Z-DNA is accomplished. Due to the complexity of the B-Z-DNA transition, experimental and computational studies have resulted in several different, apparently contradictory models. Here, we use molecular dynamics simulations coupled with state-of-the-art enhanced sampling techniques operating through non-conventional reaction coordinates, to investigate the B-Z-DNA transition at the atomic level. Our results show a complex free energy landscape, where several phenomena

SUBMITTER: Moradi M 

PROVIDER: S-EPMC3592462 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature