Structural analysis of O2'-methyl-5-carbamoylmethyluridine, a newly discovered constituent of yeast transfer RNA

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Abstract
A compound tentatively identified as O2''-methyl-5-carboxymethyluridine (cm5Um) was recently isolated from bulk yeast transfer RNA. Alkaline hydrolysis of yeast tRNA releases this nucleoside as part of an alkali-stable dinucleotide, cm5Um-Ap, from which sufficient cm5Um was prepared in the present investigation for a detailed examination of its properties. The UV absorption spectra and chromatographic and electrophoretic properties of cm5Um were consistent with the proposed structure, which was confirmed by characterization of the base and sugar moieties as 5-carboxymethyluracil and 2-O-methylribose, respectively. Snake venom hydrolysis of yeast tRNA releases cm5Um in the form of a carboxyl-blocked 5''-nucleotide, designated pU-2. Identification of the alkali-labile blocking group in pU-2 as an amide was based on quantitative assay for ammonia released upon acid hydrolysis of the corresponding nucleoside, U-2, and by chromatographic comparison of U-2 with the semisynthetic methyl ester and amide derivatives of cm5Um (mcm5Um and ncm5Um, respectively). Quantitative analysis indicated that ncm5Um may be confined to a single species of yeast tRNA. In view of the unique localization (the "Wobble" position of the anticodon sequence) and coding properties (pairing with A but not with G) of other cm5U derivatives in transfer RNA, the dinucleotide cm5Um-Ap may be derived from the first 2 positions of the anticodon sequence of a yeast tRNA species recognizing an NUA codon. This predicts that O2''-methyl-5-carbamoylmethyluridine will be found in an isoleucine, leucine, or valine isoacceptor.