5S RNA structure and interaction with transcription factor A. 1. Ribonuclease probe of the structure of 5S RNA from Xenopus laevis oocytes

Abstract

The structure of Xenopus laevis oocyte (X1o) 5S ribosomal RNA has been probed with single-strand-specific RNases T1, T2 and A with double-strand-specific RNase V1 from cobra venom. The digestion of 5''- or 3''-labeled renatured 5S RNA samples followed by gel purification of the digested samples allowed the determination of primary cleavage sites. Results of these RNase digestions provide support for the generalized 5S RNA secondary structural model derived from comparative sequence analysis. However, 3 putative single-stranded regions of the molecule exhibited unexpected V1 cuts, found at C36, U73, U76 and U102. These V1 cuts reflect additional secondary structural features of the RNA including A .cntdot. G base pairs and support the extended base pairing in the stem containing helices IV and V which was proposed by Stahl et al. A conserved structure for helix V having a common unpaired uracil residue at X1o position 84 is proposed for all eukaryotic 5S RNAs. The results are compared with nuclease probes of other 5S RNAs.