Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy

摘要: A-tracts in DNA are generally associated with reduced nucleosome occupancy relative to other sequences, such that the longer A-tract, less likely nucleosomes found. In this paper, we use molecular dynamics methods study structural properties of A-tracts, and particular role spine hydration plays allowing distort highly bent structure needed form nucleosomes. This includes a careful assessment ability Amber (parmbsc0), CHARMM27, BMS force fields describe these waters for AAATTT sequence (here capped CGC GCG), including comparisons X-ray results. All three show hydration, but better correlation measured properties, as narrowing minor groove width A-tract. We have used several 6 14 base-pair (all GCG). These calculations tightly bound "pure" allow A-water-T links, AT steps T-water-T link, sequences disfavor water, especially those lead A-water-A, G-water-G, C-water-A structures. addition, pure favor roll values close Watson-Crick value linear DNA, while A-tract containing embedded T's, C's, or G's favorable water more flexible. implies essential disfavoring formation.