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. Author manuscript; available in PMC: 2011 Mar 4.
Published in final edited form as: J Phys Chem B. 2010 Mar 4;114(8):2876–2885. doi: 10.1021/jp9064246

Figure 3.

Figure 3

Representative structures of the model systems used to calculate DNA melting free energy for T·G (mispair) vs C·G. Explicit water and Na+ counterions are not shown. During the production MD trajectories, the 5’-dangling guanosine was observed to sample both the stacked and unstacked configurations while the DNA remained in the B-DNA form.