The kinetics of codon-anticodon interaction in yeast phenylalanine transfer RNA

Abstract

Temperature-jump kinetic studies have been done on the binding of U-U-C and U-U-C-A to yeast tRNA Phe . The fluorescence of the Y base was used to follow the kinetics. The data show that the rate of formation of the U-U-C complex ( k r =2×10 5 m −1 s −1 ) is about ten times slower than that found for complementary oligonucleotides. The rate of formation of the U-U-C-A complex ( k r =2×10 7 m −1 s −1 ) is about 100 times faster than the U-U-C complex. This can be explained by a difference in kinetic mechanisms. The rate of dissociation of both complexes ( k d ∼100 s −1 at 0°C) is about three ordors of magnitude smaller than expected. The differences in kinetics from model oligonucleotides are all in the entropies of activation; the enthalpies of activation are the same. Fluorescence-detected circular dichroism measurements of yeast tRNA Phe show that the circular dichroism of the Y nucleotide decreases on binding U-U-C and U-U-C-A. The data suggest that the anticodon loop is flexible and changes conformation on binding the codon.