A molecular simulation picture of DNA hydration around A- and B-DNA.
Recent results from molecular dynamics (MD) simulations on hydration of DNA with respect to conformation are reviewed and compared with experimental data. MD simulations of explicit solvent around DNA can now give a detailed model of DNA that not only matches well with the experimental data but provides additional insight beyond current experimental limitations. Such simulation results are analyzed with a focus on differential hydration properties between A- and B-DNA and between C/G and A/T base pairs. The extent of hydration is determined from the number of waters in the primary shell and compared to experimental numbers from different measurements. High-resolution hydration patterns around the whole DNA are shown and correlated with the conformations. The role of ions associating with DNA is discussed with respect to changes in the hydration structure correlating with DNA conformation.
Feig
M
M
Department of Chemistry Institute for Molecular Design, University of Houston, 4800 Calhoun, Houston, TX 77204-5641, USA.
Pettitt
B M
BM
D000818:Animals; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012997:Solvents / Q000378:metabolism; D014867:Water / Q000737:chemistry / Q000378:metabolism*
D012997:Solvents; D014867:Water; D004247:DNA