Structure of wye (Yt base) and wyosine (Yt) from Torulopsis utilis phenylalanine transfer ribonucleic acid

Abstract

A fluorescent base wye (Yt base) was isolated from Torulopsis utilis tRNAPhe. The structure was established as 4,9-dihydro-4,6-dimethyl-9-oxo-1H-imidazo[1,2-alpha]purine based on ultraviolet (uv), nuclear magnetic resonance (NMR), and mass spectra, and by direct comparison with synthetic material. The nucleoside, wyosine (Yt), was isolated from purified tRNAPhe by enzymatic degradations followed by column and thin-layer chromatographies. The structure of wyosine is proposed as 3-ribofuranosyl-4,9-dihydro-4,6-dimethyl-9-oxo-1H-imidazol[1,2-alpha]purine (the ribosyl group is attached to the N-9 position of guanine nucleus) on the basis of comparison with model compounds.

4-Demethylwyosine Synthase from Pyrococcus abyssi Is a Radical-S-adenosyl-l-methionine Enzyme with an Additional [4Fe-4S]+2 Cluster That Interacts with the Pyruvate Co-substrate

“…8B) and UV-visible spectroscopy (Fig. 8C) in agreement with previously published UV-visible spectrum (26). It is worth noticing that this new peak corresponding to ImG-14 co-elutes with a contaminant also present in the control experiment and m 1 G37-tRNA (asterisks on Figs.…”

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37th position in anticodon loop of tRNAPhe

“…The DFT optimized conformation retains similar hydrogen bonding interactions as found in most stable structure (Fig. 1b), additional interaction between O(6) and HN (18) may also provide extra stability to the this optimized structure. (15).…”

“…The structure of the fluorescent yW base was deduced by ultraviolet (UV), nuclear magnetic resonance (NMR), and mass spectroscopic methods [18]. Wybutosine maintains proper reading frame by stabilizing codon-anticodon interactions during decoding process on the ribosomes [19].…”

Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics

“…The base Y has been observed in slightly different forms: Y in yeast tRNA P he [9]; Yw in wheat germ tRNA P he [10] and Yt in Torulopsis utilis tRNA P he [11].…”