Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics.

ABSTRACT: The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representatio

SUBMITTER: Ben Imeddourene A 

PROVIDER: S-EPMC4689557 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature