Table 6.
Interaction energies (kcal/mol) between the sugar atoms of thymine 7 and 8 with backbone, base or neighboring sugar atoms
| T7 | T8 | |||||
|---|---|---|---|---|---|---|
| B-DNA | Average | S.E. | B-DNA | Average | S.E. | |
| Sugar-Backbone | ||||||
| DD | 43.4 | 39.4 | 5.9 | 43.5 | 40.6 | 5.9 |
| T7* | 27.1 | 14.8 | 2.0 | 43.5 | 36.5 | 2.9 |
| T8* | 43.4 | 43.3 | 4.8 | 27.4 | 17.4 | 1.5 |
| T7T8* | 27.1 | 16.3 | 2.4 | 27.4 | 13.0 | 1.3 |
| Sugar-Base | ||||||
| DD | −40.6 | −44.9 | 2.5 | −40.6 | −44.1 | 1.8 |
| T7* | 5.4 | −1.8 | 1.1 | −40.6 | −40.5 | 1.3 |
| T8* | −40.6 | −45.3 | 1.4 | 5.7 | −0.4 | 1.5 |
| T7T8* | 5.4 | −2.6 | 1.4 | 5.7 | −1.6 | 1.6 |
| Sugarn-Sugarn+1 | ||||||
| DD | −1.3 | −3.6 | 1.5 | −1.3 | −5.2 | 1.0 |
| T7* | −1.4 | 1.7 | 1.0 | −1.3 | −4.8 | 1.2 |
| T8* | −0.0 | 0.8 | 0.6 | −0.7 | 2.3 | 0.5 |
| T7T8* | 0.0 | −0.4 | 0.4 | −0.7 | 2.2 | 0.5 |
n refers to the base number, B-DNA energies are based on the canonical structures prior to dynamics