MOLECULAR-DYNAMICS SIMULATION OF IONS AND WATER AROUND TRIPLEX DNA

We report the results of a 100-ps molecular dynamics simulation study of triple helical DNA with explicit water, counterions, and salt using periodic boundary conditions at 300 K. The simulation involved an antiparallel reverse-Hoogsteen-like homopolymeric CGG 7-mer triple helix, 837 water molecules, 21 Na+ ions, and 1 M NaCl. We have used the Ewald method to compute the electrostatic interactions. Specific ion and water associations as well as relative solvent and ion mobilities are reported. Specific patterns of ion and water molecule associations are found which are novel and may have implications for stability and recognition of triplex-forming oligonucleotides by duplex DNA. Exchanges of ions around neighboring phosphate were found to correspond to a concerted mechanism of displacement. Comparisons are made with available data from related systems.