Fluorescence polarization studies on the local conformation of yeast tRNA

The effects of temperature and guanidine hydrochloride (GuHC1) on the fluorescence polarization of Y base in partially purified yeast phenylalanine tRNA (p.p.tRNAPhe) and in acriflavine conjugates of crude yeast tRNA were investigated to elucidate the stability of the conformation at the 3'-CpCpA terminus and the anticodon loop of tRNA. The results can be summarized as follows: (1) The kinetic unit of the internal rotational motion near Y base in the anticodon loop of p.p.tRNAPhe seems to be independent of the temperature over the range 5--60degrees. Accelerated depolarization is observed in the 3'-CpCpA terminus at temperatures over 30degrees. This suggests that a change occurs in the native conformation of the 3'-CpCpA-acriflavine terminus at temperatures over 30degrees. (2) The fluorescence polarization of Y base in p.p.t-RNAPhe is not affected by the addition of GuHC1 up to 6 M, while that of acriflavine conjugated to the 3'-CpCpA terminus decreases markedly in the presence of 0.8 M GuHC1 reflecting the disruption of the native conformation. These results indicate that the local conformation near Y base is stable, but that of the amino acid acceptor terminus is not.