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J. Biochem, 1977, Vol. 81, No. 4 995-1003
© 1977 Japanese Biochemical Society

research-article

Structure and Function of 5S Ribosomal Ribonucleic Acid from Torulopsis utilis

III. Detection of Single-Stranded Regions by Digestion with Nuclease S11

Kazuya NISHIKAWA and Shosuke TAKEMURA

Institute of Molecular Biology, Faculty of Science, Nagoya University Chikusa-ku, Nagoya 464

Identification of single-stranded regions in Torulopsis utilis 5S RNA was attempted by the use of Nuclease S1, a single-strand specific endonuclease. When T. utilis 5S RNA was subjected to prolonged incubation with Nuclease S1, about 50% of the substrate 5S RNA remained as large oligonucleotide "cores." Such Nuclease S1-resistant fragments were purified and sequenced by column chromatographic procedures. These analyses revealed that regions around positions 12, 40, 57, and 110 are in exposed single-stranded loops at 37°C and that regions around positions 12 and 40 are most exposed at 20°C. These results are compatible with our secondary structure model for T. utilis 5S RNA (Nishikawa & Takemura (1974) J. Biochem. 76, 935–947) except that the 5' part of the molecule (from the region around position 22 to that around position 57) might have a somewhat looser conformation than our secondary structure model suggests. The implications of such results are also discussed in relation to the presumed function of the sequence C-G-A-U-C (around position 40) as one of the recognition sites for initiator tRNA binding on ribosomes

1This work was supported in part by a grant-in-aid for scientific research (No. 147129) from the Ministry of Education, Science and Culture of Japan.


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