On the structure of yeast tRNA Phe . Complementary-oligonucleotide binding studies.

Abstract

The availability of (yeast)tRNAPhe for helix formation with complementary oligoribonucleotides has been explored by equilibrium dialysis studies. Oligoribonucleotides complementary to sequences which are double‐stranded, according to the cloverleaf model of tRNAPhe, did not bind. Two regions of tRNAPhe were fully acessible to oligonucleotide binding: (a) the 3′‐terminus; (b) the sequence (3′‐5′)U‐G‐A‐A‐Y (33–37) of the anticodon loop. Two other regions were accessible to oligonucleotide binding: (a) part of the extra arm; (b) the (3′‐5′)T‐Ψ‐C sequence of the ribosylthymine loop. However, the binding constants of trimers and tetramers complementary to these parts of tRNAPhe are very low.The data indicate that the anticodon loop of tRNAPhe has an asymmetric structure, which is not compatible with the Fuller‐Hodgson model. The low binding constants for oligonucleotides complementary to the extra arm or to the TpΨpC sequence are discussed. They seem to be due either to sterical hindrance or to different conformations of tRNA. In the latter case, one conformation would be accessible to complementary oligonucleotides for helix formation, the other would not. Present available oligonucleotide binding data of four tRNAs suggest that each tRNA has an individual pairing scheme, according to which the loops of the cloverleaf contribute to the three‐dimensional structure.