Table 4. Hydration contibutions^a and the total free energy changes (potentials of mean force) for the formation of base pair steps in the crystal (X-ray) and standard^b 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, ΔΔG_hydr (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. Δg_PMF (kcal/mol) values were obtained by combining the gas phase interaction energies ΔE (Table 1) with the ΔΔG_hydr terms according to equations 4 and 5.

^bIdeal B-DNA geometry (see Materials and Methods, Intrinsic base stacking energies).

^cΔΔg_PMF = Δg_PMF(X-ray) – Δg_PMF(standard).