Table 7.
Relative average number of hydrating water oxygens within a 3.5 Å cutoff for the 4 central base positions in strand 1. Values are averaged over the last 15 ns of simulation and are shown as differences from the values corresponding to the DD oligomer.
| Full Nucleotide |
Base | C8 or C6 |
Minor Groove |
Major Groove |
Sugar O or C* |
Ester O3′ |
Ester O5′ |
O− | |
|---|---|---|---|---|---|---|---|---|---|
| 6 | |||||||||
| DD | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| T7* | −0.3 | 0.0 | 0.1 | −0.4 | 0.3 | −0.1 | 0.0 | 0.1 | −0.1 |
| T8* | −0.6 | −0.7 | 0.0 | 0.0 | 0.0 | 0.1 | 0.1 | 0.0 | −0.2 |
| T7T8* | −0.4 | −0.2 | 0.1 | −0.3 | 0.2 | −0.2 | 0.0 | 0.2 | 0.0 |
| 7 | |||||||||
| DD | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| T7* | −0.3 | −0.9 | −0.3 | −0.2 | 0.2 | −0.9 | 0.1 | −0.1 | −0.3 |
| T8* | 0 | 0.0 | 0.0 | −0.2 | −0.1 | 0.0 | 0.0 | 0.0 | 0.1 |
| T7T8* | −0.6 | −1.1 | −0.3 | −0.2 | 0.1 | −0.9 | 0.2 | −0.1 | −0.2 |
| 8 | |||||||||
| DD | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| T7* | −0.7 | −0.5 | −0.1 | 0.1 | 0.1 | −0.1 | 0.2 | −0.2 | −0.1 |
| T8* | 0.3 | −0.7 | −0.3 | −0.2 | 0.0 | −1.2 | 0.1 | 0.2 | 0.0 |
| T7T8* | −0.4 | −1.1 | −0.3 | 0.2 | 0.1 | −1.0 | 0.1 | 0.0 | 0.2 |
| 9 | |||||||||
| DD | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| T7* | 1.9 | 0.4 | 0.0 | 0.1 | 0.0 | −0.1 | 0.1 | 0.0 | 0.7 |
| T8* | −0.5 | −0.3 | −0.1 | 0.0 | −0.1 | 0.0 | 0.1 | −0.1 | 0.1 |
| T7T8* | 1.1 | 0.2 | −0.2 | 0.1 | −0.1 | −0.1 | 0.3 | 0.0 | 0.5 |
O− indicates the anionic phosphate oxygens.