A simple low-cost simulation protocol for approximate localization of structural water molecules in DNA oligonucleotides

Using a computational low-cost protocol by combining molecular mechanics energy minimization and molecular dynamics employing the OPLS-AA force field, we were able to reproduce the main structural features of the first hydration shell of double-helix DNA hetero-oligonucleotides in the A (1DPL) and B-conformations (1DPN and 1ENN), whose coordinates are available with atomic resolution from crystallographic data. Our simple protocol also reproduced the main hydration patterns of DNA homo-oligonucleotides in the B-conformation [(AT)12 and (CG)12], obtained before by computer simulation using a longer and more sophisticated molecular dynamics protocol. A preliminary model of the first hydration shell of oligonucleotides may be very useful to those interested in performing quantum-mechanical calculations of systems where hydration features are unknown at the molecular level; the model may also be used by crystallographers during refinement steps.