Table 1. Base pair step stacking energies ΔE(AB,CD) (kcal/mol) evaluated at the MP2/6-31G*(0.25) level along the d(CATGGGCCCATG)2 crystal structure, standard base pair step geometries and some other high resolution crystal geometries.
| Base pair step | Present crystal | Standard geometry | Another B-DNA crystal |
|---|---|---|---|
| C1G24/A2T23 | –11.9 (+8.0) | –12.1 (+4.2) | –11.7 (+1.1)a,b |
| A2T23/T3A22 | –12.6 (+8.0) | –10.7 (+11.6) | |
| T3A22/G4C21 | –11.6 (+9.9) | –12.1 (+4.2) | |
| G4C21/G5C20 | –7.8 (+13.4) | –9.5 (+12.2) | –8.9 (+12.9)c |
| G5C20/G6C19 | –8.4 (+13.8) | –9.5 (+12.2) | |
| G6C19/C7G18 | –14.0 (+5.2) | –13.2 (+8.5) | –11.5 (+8.5)d |
| C7G18/C8G17 | –8.4 (+11.6) | –9.5 (+12.2) | |
| C8G17/C9G16 | –7.6 (+12.2) | –9.5 (+12.2) | |
| C9G16/A10T15 | –11.5 (+10.1) | –12.1 (+4.2) | |
| A10T15/T11A14 | –12.7 (+9.5) | –10.7 (+11.6) | |
| T11A14/G12C13 | –9.0 (+7.8) | –12.1 (+4.2) | |
| Total 11 steps | –115.5 | –121.0 | |
| Total GG steps | –32.2 | –38.0 |
The values in parentheses show the HF component of the interaction energies.
aC2A3 step of the d(CCAAGATTGG)2 decamer 1.5 Å crystal structure (52).
bHigh twist, high slide, low roll geometry.
cG4G5 step of the d(CCAGGCCTGG)2 decamer 1.6 Å resolution crystal structure (53).
dG5C6 step of the d(CCAGGCCTGG)2 (53).