Highly conserved modified nucleosides influence Mg2+‐dependent tRNA folding

Transfer RNA structure involves complex folding interactions of the TΨC domain with the D domain. However, the role of the highly conserved nucleoside modifications in the TΨC domain, rT54, Ψ55 and m5C49, in tertiary folding is not understood. To determine whether these modified nucleosides have a role in tRNA folding, the association of variously modified yeast tRNAPhe T‐half molecules (nucleosides 40–72) with the corresponding unmodified D‐half molecule (nucleosides 1–30) was detected and quantified using a native polyacrylamide gel mobility shift assay. Mg2+ was required for formation and maintenance of all complexes. The modified T‐half folding interactions with the D‐half resulted in Kds (rT54 = 6 ± 2, m5C49 = 11 ± 2, Ψ55 = 14 ± 5, and rT54,Ψ55 = 11 ± 3 µM) significantly lower than that of the unmodified T‐half (40 ± 10 µM). However, the global folds of the unmodified and modified complexes were comparable to each other and to that of an unmodified yeast tRNAPhe and native yeast tRNAPhe, as determined by lead cleavage patterns at U17 and nucleoside substitutions disrupting the Levitt base pair. Thus, conserved modifications of tRNA’s TΨC domain enhanced the affinity between the two half‐molecules without altering the global conformation indicating an enhanced stability to the complex and/or an altered folding pathway.