TABLE 2.

Estimated free energies for the various d(GGGG)₄ models calculated using the MM-PBSA methodology (Srinivasan et al., 1998)

Model	G (no ions) (kcal/mol)	G (3 ions) (kcal/mol)	Gbinding ion d(GGGG)4	ΔGnative (kcal/mol)	−TΔS, 300 K (kcal/mol)
G-DNA native	−3171.2	−3722.4	−265.9	0.0	0.0
	(23.3)	(15.0)	(19.2)
G-DNA vacant	−3369.5	−3696.6	∼0.8*	+25.8	−5.4
	(15.8)	(16.1)	(4.5)
Slipped_D_2ions	−3265.8	−3710.4	−152.7	+12.0	−2.2
	(23.2)	(16.3)	(16.6)
Slipped_D_3ions	−3172.4	−3710.3	−252.6	+12.1	–
	(27.5)	(16.6)	(24.2)
Shift_AB	−3264.9	−3710.9	−154.0	+11.3	−4.8
	(24.5)	(16.6)	(20.7)
Spiral stem (2–4 ns)	−3353.7	−3659.5	∼−9.1*	+62.9	∼−4.2
	(20.4)	(19.9)	(5.0)
Spiral stem (7–9 ns)	−3372.9	−3672.8	∼−3.3*	+49.6	∼−2.8
	(21.4)	(21.3)	(5.4)

Total free energies do not include the solute entropic components. These are shown in the last column and represent the difference in total (rotational, translational, and vibrational) entropy, thermally weighted at 300 K, to the native G-DNA model with three explicitly bound ions. As discussed in Methods, translational entropic components of the “free” ions (representing 2–3 kcal/mol per free ion) are not included. Column 2 displays free energies neglecting any explicitly bound ions. Column 3 represents the absolute free energy of the d(GGGG)₄ model including three ions. Column 4 presents the interaction free energies for the three bound ions. The difference in the free energies (relative) of the G (3 ions) to the native G-DNA quadruplex are shown in column 5. Standard deviations are shown in parentheses. Standard deviations for the −TΔS term are on the order of 1–4 kcal/mol with higher values obtained when ions are included.

^*Numbers are approximate in that, due to ion motion, the solvent-accessible surface area calculation failed and therefore approximate values for this (small) energy component were used.