Table 3. Conformational Free Energies from MMPB/SA Analysis for the GC-Rich Dodecamera.
| Ab | Bc | canonical Ad | (B – A) | (B – Can.A) | |
|---|---|---|---|---|---|
| ⟨E(gas)⟩e | 2181.2 (4.1) | 2331.1 (4.1) | 2371.2 (4.2) | 149.9 | –40.1 |
| ⟨E(nonpolar)⟩f | 26.9 (0.0) | 26.9 (0.0) | 26.3 (0.0) | 0.0 | 0.6 |
| ⟨E(PB), ε = 80⟩g | –5837.5 (3.2) | –5965.5 (3.5) | –6069.4 (3.7) | –128.0 | 103.9 |
| ⟨E(total), ε = 80⟩ | –3629.4 (4.0) | –3607.5 (3.9) | –3672.0 (2.3) | 21.9 | 64.5 |
| ⟨ΔE(total), salt: 0.1 M⟩ | –40.6 (0.0) | –41.1 (0.0) | –42.9 (0.0) | –0.5 | 1.8 |
| ⟨ΔE(total), salt: 1.0 M⟩ | –53.4 (0.1) | –54.5 (0.1) | –58.5 (0.1) | –1.1 | 4.0 |
| ⟨ΔE(total), ε = 20⟩ | 242.6 (0.2) | 247.3 (0.2) | 261.1 (0.3) | 4.7 | –13.8 |
a
Standard errors are given in the parentheses.
b
100 snapshots selected from GC1 and GC2 clusters closest to cluster centers and with minimal distortions at terminal base pairs.
c
100 snapshots selected from GC5 cluster as in b.
d
Snapshots from 1 ns restrained implicit solvent simulation of canonical A-DNA structure taken at 5 ps intervals starting from 0.5 ns.
e
CHARMM force field energy in vacuum.
f
Solvent-accessible surface area term: γ*SASA+β with γ = 0.00542 kcal/mol/Å2 and β = 0.92 kcal/mol.63,64
g
Solution of Poisson–Boltzmann equation using PBEQ module65 in CHARMM program with a grid spacing of 0.25 Å.