Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT

Broyde, Suse B.; Wartell, Roger M.; Stellman, Steven D.; Hingerty, B.

Minimum energy conformations have been calculated for the deoxydinucleoside phosphates dGpdC, dApdA, dCpdC, dGpdG, and dTpdT. In these potential energy calculations the eight diheldral angles and the sugar pucker were flexible parameters. A substantial survey of conformation space was made in which all staggred combination of the dihedral angles ω′,ω, and ψ, in conjunction with C(2′)-endo pucker, were used as starting conformers for the energy minimization. The most important conformations in the C(3′)-endo-puckering domain have ψ = g+; ω′,ω = g−,g−(A-form),g+, g+, and g−,t. With C(2′)-endo-type pucker the most important conformations have ψ = g+; ω′,ω =g-,g-(B-form) and g+,t; and ψ =t; ω′,ω =g-,t(Watson-Crick from) and t,g+ (skewed). Stacked bases are a persistent feature of the low-energy conformations, the g+ conformer being an exception. Freeing the suger pucker allowed this conformation to become low energy, with C(3′)-exo pucker. It also caused other low-energy forms, such and the Waston-Crick conformation, to become more favourable. Conformation flexibility in the sugar pucker and in ψ, as well as the ω′,ω angle pair, is indicated for the dimeric subunits of DNA.


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May 9, 2014