Partial degradation of transfer RNAs by different preparations of snake venom exonuclease

The degradation of yeast tRNASer with eight different exonuclease preparations from four snake venoms was investigated. The reaction products were separated on polyacrylamide gels containing 7 M urea. Patterns of sharp bands were obtained which were more or less similar. Two tRNA fragments were characterized by oligonucleotide analyses, one of which was tRNA degraded by the exonuclease up to the beginning of the T-phi-C-stem. The other one was generated by the additional loss of several nucleotides from the 5'-terminus. The formation of the latter fragment was very probably caused by an endonuclease activity in the exonuclease. The endonuclease contaminant, which was found in all preparations, was further investigated by experiments with modified tRNAs whose 3'-terminus should be resistant to exonuclease (tRNASer-A, tRNASerOX-red). With 3'-AMP as substrate no phosphatase activity was found under the conditions of tRNA degradation. Not only in tRNASer, but also in yeast tRNATyr and tRNAAla as well as in fragments of tRNASer and tRNAPhe, the degradation by exonuclease was inhibited at the beginning of the T-phi-C-stem. The finding of such a retardation site in addition to the general retardation of exonuclease digestion after removal of the C-C-A sequence may indicate that retardation at certain elements of secondary structure is a more general feature of degradations by this enzyme.