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. Author manuscript; available in PMC: 2012 Oct 4.
Published in final edited form as: Biochemistry. 2011 Sep 8;50(39):8463–8477. doi: 10.1021/bi201007t

Figure 10. Reaction coordinate diagram illustrating exchange from the G-C and 8oxoG-C base pairs.

Figure 10

The free energy difference between the closed state (GCcl and oxoGCcl) and the “open” state available for imino proton exchange (GCex and oxoGCex) is 6–7 kcal/mol, due to the cost of breaking three hydrogen bonds and unstacking one or both bases from the hydrophobic core of the helix. The two base pairs are shown with similar stabilities in both closed and exchangeable states because every method used in this study has found the oxoG-C base pair to be almost indistinguishable from G-C. Critically, many other open forms are likely to exist along the reaction coordinate pathway with similar or higher energies to GCex and oxoGCex, but these are not shown because they are not directly probed by this experiment. Dashed lines illustrate the effect of increasing or decreasing kop on the activation energy of base pair opening; the latter would extend the lifetime of the open state, and the former would decrease the activation energy of opening.