Table 3.
The base specific cross-stacking parameters, . Cross-stacking interactions are only considered if one of the dimer base pairs is a Watson-Crick base pair. The 5′-(top) base pair is listed in the left column and the 3′-(bottom) base pair is listed along the top of the table. The table is read so that =15.9.
| ↑AA↓ | ↑AC↓ | ↑AG↓ | ↑AT↓ | ↑CA↓ | ↑CC↓ | ↑CG↓ | ↑CT↓ | ↑GA↓ | ↑GC↓ | ↑GG↓ | ↑GT↓ | ↑TA↓ | ↑TC↓ | ↑TG↓ | ↑TT↓ | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ↑AA↓ | – | – | – | 8.8 | – | – | 16.5 | – | – | 12.1 | – | – | 11.0 | – | – | – |
| ↑AC↓ | – | – | – | 11.0 | – | – | 16.5 | – | – | 16.5 | – | – | 8.8 | – | – | – |
| ↑AG↓ | – | – | – | 8.8 | – | – | 15.4 | – | – | 14.3 | – | – | 12.1 | – | – | – |
| ↑AT↓ | 11.0 | 7.7 | 12.1 | 11.0 | 8.8 | 6.6 | 15.9 | 6.6 | 12.1 | 14.3 | 13.2 | – | 6.4 | 5.5 | – | 5.5 |
| ↑CA↓ | – | – | – | 6.6 | – | – | 11.0 | – | – | 12.1 | – | – | 7.7 | – | – | – |
| ↑CC↓ | – | – | – | 7.7 | – | – | 12.1 | – | – | 7.7 | – | – | 6.6 | – | – | – |
| ↑CG↓ | 12.1 | 12.1 | 17.6 | 15.8 | 16.5 | 7.7 | 20.2 | 11.0 | 14.3 | 24.6 | 15.4 | – | 14.3 | 5.5 | – | 7.7 |
| ↑CT↓ | – | – | – | 7.7 | – | – | 8.8 | – | – | 5.5 | – | – | 5.5 | – | – | – |
| ↑GA↓ | – | – | – | 8.8 | – | – | 15.4 | – | – | 17.6 | – | – | 12.1 | – | – | – |
| ↑GC↓ | 16.5 | 11.0 | 15.4 | 14.1 | 16.5 | 12.1 | 23.9 | 15.4 | 15.4 | 20.2 | 17.6 | – | 15.9 | 8.8 | – | 13.2 |
| ↑GG↓ | – | – | – | 8.8 | – | – | 17.6 | – | – | 15.4 | – | – | 13.2 | – | – | – |
| ↑GT↓ | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| ↑TA↓ | 8.8 | 6.6 | 8.8 | 9.7 | 11.0 | 7.7 | 14.1 | 8.8 | 8.8 | 15.8 | 8.8 | – | 11.0 | 7.7 | – | 8.8 |
| ↑TC↓ | – | – | – | 8.8 | – | – | 15.4 | – | – | 11.0 | – | – | 6.6 | – | – | – |
| ↑TG↓ | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| ↑TT↓ | – | – | – | 8.8 | – | – | 13.2 | – | – | 7.7 | – | – | 5.5 | – | – | – |