| Abstract: | Molecular mechanical simulations on base-paired deoxyhexanucleoside phosphates, (dAdT)3 · (dAdT)3, (dTdA)3 · (dTdA)3, (dGdC)3 · (dGdC)3, and (dCdG)3 · (dCdG)3, have been carried out to assess their energetic stabilities in left- and right-handed forms. These hexamers have also been simulated with alternating sugar-puckering profiles with the combinations (purine : C2′-endo–pyrimidine : C3′-endo) and (purine : C3′-endo–pyrimidine C2′-endo). The right-handed models have been found to be the energetically most stable structures and the left-handed structures are significantly destabilized. This instability has been rationalized in terms of competition between stabilizing stacking interactions on one hand, and distortions in the bond angles and torsion angles in the sugar-phosphate backbone on the other. |
