Structural analysis of d G 7 parallel quadruplex structures

Energy component analysis was earried out for the two simulations and it was observed that the quadruplex, as well as the counter ions and water appeared to reach a stable configuration after the first 100 ps of dynamics run. Average energies and their standard deviation are calculated over 100-1100 ps and are shown in Table 4. The d(G)7 quadruplex molecule, alongwith the 6 intercalated Na ions, when present, was treated as solute, while the water molecules and 24 Na ions in the surrounding medium constitute the solvent in both cases. 

Interaction energj between the 7-mer G-quadruplex structures and the solvent molecules during the MD simulation with and without intercalated ions. Energies are averaged over the 100-1100 ps of the dynamics run and the values are in kcal/mol. Standard deviations are listed within parentheses. 

06-06 distances in middie three G-tetrads with intercalated Na ion 

06-06 distances in middle three G-tetrads without intercalated ion 

The intra as well as inter-basepair structural parameters were calculated for the middle three tetrads taking all four strands pairwise and using the NUPARM software [63], For both simulations, local dinucleotide step, intra base-pair and global helical parameters were calculated for the GG base pairs in the middle three tetrads and averaged between 100 to 1100 ps. Only the global helical and 

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