Table 2.
Estimated relative binding free energy of damaged and undamaged DNA duplexes from MM/GBSA approach. (In each case, F is base paired to C in the anti-conformation (figure 2).)
| sequence | ΔΔEvdW (kcal mol−1) | ΔΔEes (kcal mol−1) | ΔΔEin (kcal mol−1) | ΔΔGpol (kcal mol−1) | ΔΔGnonpol (kcal mol−1) | ΔΔGbinding (kcal mol−1) |
|---|---|---|---|---|---|---|
| AFA-AGA | 0.4±3.0 | 5.5±5.8 | −2.4±1.7 | 3.1±9.4 | −0.3±0.1 | 6.4±8.7 |
| AFC-AGC | 1.2±3.3 | −0.1±5.2 | −2.9±1.6 | 7.0±9.9 | −0.2±0.1 | 5.1±9.4 |
| AFG-AGG | 0.5±3.0 | 7.3±6.4 | −3.1±1.5 | 4.6±9.2 | −0.2±0.1 | 9.1±7.8 |
| TFA-TGA | −0.6±3.2 | 8.5±5.8 | −3.0±1.9 | −1.4±10.2 | −0.3±0.1 | 5.1±10.0 |
| TFC-TGC | 0.3±3.3 | 4.4±5.6 | −2.4±1.8 | 5.1±9.3 | −0.4±0.1 | 7.0±8.2 |
| TFT-TGT | −0.3±3.0 | 8.8±5.6 | −2.7±1.6 | 4.5±10.5 | −0.3±0.1 | 10.0±8.9 |