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 molecular 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 saltwater solution. The Ewald method was used to calculate the electrostatic interactions of the system. The behavior of the DNA in the saltwater solution was determined by examining the structure, energetics, and mobility of water and ions in the system. The simulation results for the helical parameters support the validity of a model-built triplex-DNA structure. A low root mean square deviation of the dynamic structure from the initial structure demonstrates the stability of the triplex in the salt solution. The sugar pseudorotation, the backbone conformations, and the average helical parameters suggest that the conformation of strands I and III is strictly neither A-form nor B-form, whereas the conformation of strand II remains near the A-form. A higher mobility of both the cytosine strand and the triplex-forming guanine strand and also a longer residence time of water molecules in the spine of hydration were observed and are consistent with available NMR results.