Conformational analysis of arabinonucleosides and nucleotides A comparison with the ribonucleosides and nucleotides

Abstract

Conformations of arabino nucleosides and nucleotides have been analyzed by semiempirical energy calculations. It is found that the change in the configuration of the O(2′)-hydroxyl group in arabinoses compared to riboses exerts significant influence on the conformational priorities of the glycosyl and the exocyclic C(4′)-C(5′) bond torsions. While the anti conformations for the bases are preferred, the anti ⇌ syn interconversion is considerably hampered compared to ribosides due to large energy barrier. Further the preferred anti glycosyl torsions are shifted to higher values for C(3′)-endo puckers and to lower values for C(2′)-endo puckers, a trend which is reverse to those found in ribosides. While the gauche + conformation around the C(4′)-C(5′) bond is favored for C(3′)-endo arabinosides, it is strongly stabilized for C(2′)-endo arabinosides only in the presence of the intrasugar hydrogen bond O(2′)-H … O(5′). The net attractive electrostatic interactions between the phosphate and the base stabilizes the preferred conformations of 5′-arabinonucleotides also.