A comparative proton magnetic resonance conformational study of the tRNA "wobble" nucleosides 5-carboxymethyl-, 5-methoxycarbonylmethyl-, and 5-carbamoylmethyl-uridine.

The 270-MHz proton magnetic resonance spectra of 5-carboxymethyluridine, 5-methoxycarbonylmethyluridine, and 5-carbamoylmethyluridine have been obtained, and analyzed iteratively using LAOCOON 3. A standard treatment of the obtained data reveals that in each the 5-substituent produces no significant alteration in the furanose puckers, their equilibrium state, and the relative populations of the gg, tg, and gt exocyclic hydroxymethyl rotamers relative to uridine. The analogous similarity in furanose chemical shifts suggests that these derivatives favor the anti glycosyl state. The 5-substituent may act at the polynucleotide level in modulating the conformation and interaction(s) of the anticodon loop.