Comparative conformations of uridine and pseudouridine and their derivatives

Stimulated by the suggestion that pseudouridine psi-39 in yeast tRNAPhe could be in a syn conformation [R. E. Hurd and B. R. Reid (1977) Nucleic Acid Research 4, 2747-2755], we have made a comparative study of the solution conformations of psi and U derivatives, using the proton-proton Overhauser effect. Rotation around the glycosidic bond is observed for pseudouridine and 3 psi MP as well as for uridine and 3'UMP. However pseudouridine an 3 psi MP are mostly syn, whereas uridine, 3'-UMP and 5'UMP are mostly anti. There is no evidence for a correlation between sugar conformation and orientation around the glycosidic bond. The results are confirmed by relaxation measurements. They are discussed in the light of earlier studies. They tend to support the suggestion of Hurd and Reid. They raise the question of the orientation of the pseudouridine found elsewhere in tRNA (e.g. in the T psi C loop).