Conformational studies on guanosine nucleotides and polynucleotides. The effect of the base on the glycosyl and backbone conformations

Abstract

Potential energy calculations have been carried out on guanosine 5'-monophosphate and guanosine 3',5'-diphosphate by simultaneous variation of the rotation angles X and Ψ to assess the influence of the base on the glycosyl and the sugar-phosphate backbone conformations and their possible interdependence. The results obtained predict that guanine containing nucleotides tend to favor the syn glycosyl conformation in sharp contrast to the anti conformation found for adenine and the common pyrimidine nucleotides. This characteristic behavior of guanine nucleotides is largely a result of increased non-bonded van der Waals' and electrostatic attractive interactions between the 5'-phosphate and the amino group of the base. As seen previously [N. Yathindra and M. Sundaralingam, Biopolymers, 12, 297 (1973)] changes in the glycosyl conformation mainly affects the C(4')-C(5') bond rotations of the backbone. The most favored (χ ,ψ ) conformer corresponding to the global minimum both in 5'-GMP and 3',5'-GDP is syn-gg, (190°,80°) for C(2')-endo rings and (180°,50°) for C(3')-endo rings. It is noteworthy that the syn angle is different from the usually observed range of 210-260°. The next significant minimum in the (χ ,ψ ) energy surface corresponds to the syn-gt conformational combination (the syn angle now in the normal range), indicating that the occurrence of the normal syn conformer induces a distortion in the backbone c(4')-c(5') bond conformation from the preferred gg. These studies reveal the significant influence of the base not only on the glycosyl conformation but also on the backbone conformations of polynucleotides.