Table 1. Free energy rankings (kcal mol−1) of adducted DNA conformations with OTB-dG at the G1, G2 or G3 position in the NarI recognition sequencea.
| Lesion | Conformation | Rotamerb | Position | ||
|---|---|---|---|---|---|
| G1 | G2 | G3 | |||
| Major groove | α | 0.0 | 0.0 | 0.0 | |
| Neutral OTB-dGc | β | (8.3) | (0.9) | (2.3) | |
| Wedge | α | 1.6 | 5.1 | 1.7 | |
| β | (14.1) | (34.1) | (5.0) | ||
| Base-displaced (stacked) Intercalated | α | 1.8 | 2.1 | 1.7 | |
| β | (7.5) | (9.6) | (5.4) | ||
| Major groove | α | 0.0 | 0.0 | 7.0 | |
| Monoanionic OTB-dGc | β | (5.5) | (0.7) | (8.5) | |
| Wedge | α | 0.2 | 7.1 | 0.0 | |
| β | (9.5) | (16.5) | (16.3) | ||
| Base-displaced (stacked) | α | 6.3 | 0.7 | 2.9 | |
| Intercalated | β | (10.6) | (5.8) | (23.2) | |
| Major groove | α | 0.5 | 0.0 | 0.0 | |
| Dianionic OTB-dGc | β | (7.1) | (5.4) | (8.3) | |
| Wedge | α | 0.0 | 4.7 | 0.7 | |
| β | (12.7) | (18.3) | (30.2) | ||
| Base-displaced (stacked) | α | 7.5 | 4.4 | 8.3 | |
| Intercalated | β | (18.2) | (18.4) | (12.4) | |
aSee Supplementary Data for details of the free energy calculations.
bSee Supplementary Figure S1 for the definition of the α and β-rotamers.
cSee Figure 1 for the definition of OTA ionization states.