A Monte Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z form

Monte Carlo computer simulation is described for the hexamer d(CGCGCG) in the Z form together with 910 water molecules at an environmental density of 1 gm/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the non-bonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordination numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove, the minor groove, and the sugar-phosphate backbone were examined, and the probabilities of occurrence for one- and two-water bridges in the simulation were enumerated. The results are compared with observations of crystallographic ordered water sites from the X-ray diffraction studies.