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Nucleic Acids Research, 1981, Vol. 9, No. 20 5331-5344
© 1981

MOLECULAR BIOLOGY

Location of single-stranded and double-stranded regions in rat liver ribosomal 5S RNA and 5.8S RNA

Indrek Toots, Andres Metspalu*, Richard Villems and Mart Saarma

Laboratory of Molecular Genetics, Institute of Chemical Physics and Biophysics, Estonian Academy of Sciences 14/16 Kingissepa Street, 202400 Tartu, Estonian SSR, USSR *Laboratory of Molecular Biology, Institute of General and Molecular Pathology, Tartu University 14/16 Kingissepa Street, 202400 Tartu, Estonian SSR, USSR

Received July 1, 1981. Rat liver 5S rRNA and 5.8S rRNA were end-labelled with 32P at 5'-end or 3'-end of the polynucleotide chain and partially digested with single-strand specific S1 nuclease and double-strand specific endonuclease from the cobra Naja naja oxiana venom. The parallel use of these two structure-specific enzymes in combination with rapid sequencing technique allowed the exact localization of single-stranded and double-stranded regions in 5S RNA and 5.8 S RNA. The most accessible regions to S1 nuclease in 5S RNA are regions 33–42, 74–78, 102–103 and in 5.8S RNA 16–20, 26–29, 34–36, 74–80 and a region around 125–130. The cobra venom endonuclease cleaves the following areas in 5S RNA: 7–8, 17–20, 28–30, 49–51, 56–57, 60–64, 69–70, 81–82, 95–97, 106–112. In 5.8S RNA the venom endonuclease cleavage sites are 4–7, 10–13, 21–22, 33–35, 43–45, 51–55, 72–74, 85–87, 98–99, 105–106, 114–115, 132–135. According to these results the tRNA binding sequences proposed by Nishikawa and Takemura [ (1974) FEBS Lett. 40, 106–109], in 5S RNA are located in partly single-stranded region, but in 5.8S RNA in double-stranded region.


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