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. 2015 Jun 18;43(13):6473–6485. doi: 10.1093/nar/gkv610

Figure 3.

Figure 3.

Molecular Dynamics simulation for poly dA-dT and poly dG-dT dsDNA in site I. (A) Schematic of the molecular dynamics simulation system. The solvation water is shown as the transparent box and the sodium and chloride ions are shown as pink and purple sphere, respectively. The molecule in surface representation is the RecA-DNA complex. (B) Structure of the matched and mismatched DNA in site I at the end of the 15 ns conventional MD simulation. The initiating, and matched and mismatched complementary strands are shown in yellow, cyan and green, respectively. The overlapping structures are obtained from the last 10 ns of the simulation with 1 ns gap. (C and D). Detail illustrations of the stable nucleotide triplet at the end of the simulation for matched and mismatched strands.