Effect of ribose O(2')-methylation on the conformation of nucleosides and nucleotides

Abstract

Semi-empirical conformational energy calculations using partitioned functions have been carried out on 2'-O-methyladenosine, the corresponding 5'-nucleotide and the 3',5'-diphosphate to assess the influence of the 2'-methoxy group on their favored conformations. Calculations have been performed for the two modes of sugar puckerings observed in the crystal structure of 2'-O-methyladenosine, C(3')-endo-C(2')-exo, ³T₂, and C(2')-exo-C(3')-endo, ²T³. It is found that the anti conformation is favored for both puckers and the conformation about the C(4')-C(5') bond shows a very slight preference for gauche-gauche in C(3')-endo-C(2')-exo and gauche-trans in C(2')-exo-C(3')-endo. In the corresponding 5'-nucleotide, the anti-gg combination is strongly favored for the C(3')-endo pucker while it constitutes less than 50% for the C(2')-exo pucker. Further the C(2')-exo rings favor lower values (< 0°) of glycosyl torsions than the C(3')-endo rings. While O(2')-methylation apparently has little effect on the preferred conformations of either the nucleosides or 5'-nucleotides, the range of favored conformations of the 3'-phosphate group is considerably restricted. The conformation of the methyl group (defined by the torsion C(1')-C(2')-O(2')-methyl itself is restricted to values of 80-160° in nucleosides and 5'-nucleotides and is further constrained to values 90-130° in the presence of the 3'-phosphate. It is anticipated that this may be important in restricting the backbone conformations in 2'-O-methylated polynucleotides.