NANOSECOND DYNAMICS AND STRUCTURE OF A MODEL DNA TRIPLE-HELIX IN SALTWATER SOLUTION

The structure and stability of a DNA triple helix was examined by mole cular dynamics (MD) simulation using an all-atom force field. A 1.3 ns simulation was performed on a d(CG . G)(7) triple helix in a 1 M salt water solution. The Ewald method was used to calculate the electrostat ic interactions of the system. The behavior of the DNA in the saltwate r solution was determined by examining the structure, energetics, and mobility of water and ions in the system. The simulation results for t he helical parameters support the validity of a model-built triplex-DN A structure. A low root mean square deviation of the dynamic structure from the initial structure demonstrates the stability of the tripler in the salt solution. The sugar pseudorotation, the backbone conformat ions, and the average helical parameters suggest that the conformation of strands I and III is strictly neither A-form nor B-form, whereas t he conformation of strand II remains near the A-form. A higher mobilit y of both the cytosine strand and the triplex-forming guanine strand a nd also a longer residence time of water molecules in the spine of hyd ration were observed and are consistent with available NMR results.