Table 4. Hydration contibutionsa and the total free energy changes (potentials of mean force) for the formation of base pair steps in the crystal (X-ray) and standardb geometries.
| Base pairs involved | Step | ΔΔGhydr | ΔgPMF | ΔΔgPMFc | ||
|---|---|---|---|---|---|---|
| X-ray | Standard | X-ray | Standard | (kcal/mol) | ||
| C1G24/A2T23 | CA | 4.3 | 7.4 | –7.6 | –4.9 | –2.7 |
| A2T23/T3A22 | AT | 2.1 | –0.4 | –10.5 | –11.0 | 0.5 |
| T3A22/G4C21 | CA | 3.9 | 7.4 | –7.7 | –4.9 | –2.8 |
| G4C21/G5C20 | GG | –2.2 | –0.4 | –10.0 | –9.9 | –0.1 |
| G5C20/G6C19 | GG | –1.7 | –0.4 | –10.1 | –9.9 | –0.2 |
| G6C19/C7G18 | GC | 6.1 | 4.6 | –7.9 | –8.6 | 0.7 |
| C7G18/C8G17 | GG | –0.7 | –0.4 | –9.1 | –9.9 | 0.8 |
| C8G17/C9G16 | GG | –1.9 | –0.4 | –9.5 | –9.9 | 0.4 |
| C9G16/A10T15 | CA | 4.1 | 7.4 | –7.4 | –4.9 | –2.5 |
| A10T15/T11A14 | AT | 1.9 | –0.4 | –10.8 | –11.0 | 0.2 |
| T11A13/G12C13 | CA | 4.2 | 7.4 | –4.8 | –4.9 | 0.1 |
| GG steps | –6.5 | –1.6 | –38.7 | –39.6 | 0.9 | |
| Total 11 steps | 20.1 | 31.8 | –95.4 | –89.8 | –5.6 |
aHydration free energies, ΔΔGhydr (kcal/mol), correspond to the free energy for the transfer of 1 M solute from the gas phase to 1 M aqueous solution extrapolated to infinite dilution, under standard conditions. ΔgPMF (kcal/mol) values were obtained by combining the gas phase interaction energies ΔE (Table 1) with the ΔΔGhydr terms according to equations 4 and 5.
bIdeal B-DNA geometry (see Materials and Methods, Intrinsic base stacking energies).
cΔΔgPMF = ΔgPMF(X-ray) – ΔgPMF(standard).