Solution Conformation of tRNAs: Correlation with Crystal Structures

A comparative study of the solution conformation of yeast tRNAAsp and tRNAPhe was undertaken with chemical reagents as structural probes. The accessibility of phosphates was assayed with ethylnitrosourea, that of N7 positions in guanines and adenines with dimethylsulfate and diethylpyrocarbonate and that of the N3 position in cytosines with dimethylsulfate. Statistical modifications were done on end-labelled tRNAs subsequently split at the modified positions and analyzed using sequencing gel methodologies. The results were correlated with the crystal conformations of both tRNAs which were analyzed with a graphic modelling program. Three particular positions are xiscussed. In all tRNAs so far studied, including tRNAAsp and tRNAPhe, phosphate 60 is protected against alkylation, even in the isolated 3’half-molecule of tRNAAsp. This indicates a common T-loop conformation in tRNA which is correlated with the constant presence of residue C61. A similar conformation is found in turnip yellow mosaic virus tRNA-like structure. Adenosine 21 and guanosine 45, two common residues in tRNAAsp and tRNAPhe, exhibit different reactivities against diethylpyrocarbonate and dimethylsulfate. A21 is reactive in tRNAAsp and protected in tRNAPhe; for G45 the situation is inversed. As to A21, the different reactivity is correlated with the extra-loop structures in the two tRNAs; in the case of G45 the results are explained by a different stacking of A9 between G45 and residue 46.