Partial digestion of tRNA--aminoacyl-tRNA synthetase complexes with cobra venom ribonuclease.

Transfer RNA molecules have been labeled with 32P at the 5' or 3' end and digested with cobra venom ribonuclease, which preferentially cuts double-stranded regions. The products of yeast tRNAPhe and tRNAVal were analyzed by high-resolution gel electrohporesis. In the free state, these tRNAs were cut predominantly in the acceptor and anticodon stems. Minor cuts occurred in the T psi stem in tRNAVal. The topography of zones interacting with their cognate synthetases was studied by determining the tRNA regions shielded by protein. Nearly 100% protection was found in the anticodon and acceptor stem of tRNAVal, while in tRNAPhe only the stem of the anticodon was protected. Noncognate interactions between tRNAPhe and tryptophanyl-tRNA synthetase from beef pancreas were examined. The beef enzyme did not protect tRNAPhe despite the fact that efficient misaminoacylation occurred. The pattern of shielding obtained for each tRNA-synthetase complex was compared with the results of direct ultraviolet cross-linking experiments with these complexes.