Influence of terminal 3' phosphates or 2',3'-cyclic phosphates on the conformations of oligoriboadenylates, oligoribocytidylates, and the corresponding monomers.

The circular dichroism spectra of chemically synthesized adenylate and cytidylate dinucleotides and trinucleotides bearing terminal 3' phosphates have been compared under a variety of conditions with the spectra obtained from the corresponding oligomers with 2',3'-terminal cyclic phosphate groups. Similar comparisons for the mononucleotides are also presented. Although the base stacking of an oligomer with a terminal cyclic phosphate might be expected to be greater than that of the corresponding oligomer with a 3' phosphate from charge repulsion considerations, the magnitudes of the Cotton effects in the former class are always considerably smaller than those in the latter class. This suggests a decreased stacking. The implications of these observations are discussed in light of the compelling crystallographic evidence that cytidine 2',3'-cyclic phosphate adopts an unusual sugar puckering and the syn conformation.