All-atom crystal simulations of DNA and RNA duplexes.

ABSTRACT:

Background

Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data.

Methods

We report simulations of DNA and RNA duplexes in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64μs of duplex sampling for DNA and 16μs for RNA.

Results

The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequenc

SUBMITTER: Liu C 

PROVIDER: S-EPMC4339523 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature