Molecular Modelling and Investigation of Bioactive Stable DNA G-Quadruplex d(G4T4G4) under Different Physiological Conditions using Molecular Dynamics Simulation

We are reporting a molecular dynamics study on the structure and conformation of the DNA quadruplex. The single molecule quadruplex's coordinates were obtained and modeled using PDB ID 1d59. The simulation's sequence is d(GGGGTTTTGGGG). In the beginning, two hairpin structures were constructed with loops holding thymine residues at either end, forming a four-stranded helical structure. The cyclic hydrogen bonds created by the structure kept the guanine residues of all four strands in one plane. The molecule was subjected to molecular dynamics simulation for 100ns and at periodic intervals of 10ns, the dynamical pathway's trajectory was examined. The deviations and fluctuations viz. RMSD, RMSF and Rg plots were analyzed, the structure and shape of the time-evolved trajectory were examined. The outcome was compared with the crystal structure. Our findings reveal a few peculiar properties which we have discussed in this paper. The helix axis and torsion angle parameters were calculated. The results of this interpretation give the idea about quadruplex interaction with external agents and inspire to do further research on DNA quadruplex structures in telomeric regions of living chromosomes.