Conformational studies on pyrimidine 5'-monophosphates and 3',5'-diphosphates. Effect of the phosphate groups on the backbone conformation of polynucleotides

Abstract

In continuation of our studies on the effect of the base and the phosphate groups on the glycosyl and the sugar-phosphate backbone conformation, we have carried out semi-empirical potential energy calculations on the common 5'- and 3'5'-ribopyrimidine mono- and diphosphates by considering simultaneous rotations about the glycosyl (χ ) and the C(4')-C(5') (ψ ) bonds. This calculation provides an assessment of the nature and orientation of the base on the sugar-phosphate backbone conformation of nucleotides and polynucleotides. It is found that the attractive inetractions between the 5'-phosphate group and the base mutually stabilize the antiand the gauche-gauche (gg) conformations about χ and ψ , respectively, in 5'-ribopyrimidine nucleotides. The introduction of the 3'-phosphate group as in 3',5'-ribopyrimidine diphosphates, still leaves the anti-gg as the most favored conformation with the important difference that the probability of occurrence of the anti, gauche-trans (gt) is how substantially increased. This is dependent to a large extent on the sugar conformation and to a lesser extent on the base. Uracil and thymine show a greater probability for the anti-gt than cytosine. The syn conformation is considerably less likely and its occurrence is also dependent on the base type, cytosine showing a lesser tendency than uracil and thymine. For the syn base, the most favourec conformation for ψ is gt, since gg is sterically disallowed and tg is destabilized by electrostatic repulsive interactions between the 3' and 5'-phosphate groups. Thus, there is a striking correlation between the glycoysl and the backbone C(4')-C(5') bond conformations. The rest of the bonds of the backbone are considerable less dependent on the glycosyl conformation. These studies reveal that in poly-ribopyrimidine nucletides the majority of the nucleotide residues are expected to occur in the anti-gg conformation.