Studies on transfer ribonucleic acids and related compounds. 24. Influence of terminal 3' phosphates or 2',3'-cyclic phosphates on the conformations of oligoriboadenylates, oligoribocytidylates, and the corresponding monomers

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Abstract
The circular dichroism spectra of chemically synthesized adenylate and cytidylate dinucleotides and trinucleotides bearing terminal 3'' phosphates were 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.