Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.

ABSTRACT: In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+) ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take corre

SUBMITTER: Bian Y 

PROVIDER: S-EPMC3983051 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature