Structure and function of 5S ribosomal ribonucleic acid from Torulopsis utilis. III. Detection of single-stranded regions by digestion with nuclease S1.
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 degrees C and that regions around positions 12 and 40 are most exposed at 20 degrees 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.
D001483:Base Sequence; D002175:Candida; D004720:Endonucleases / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000032:analysis; D012335:RNA, Ribosomal / Q000032:analysis / Q000378:metabolism*; D012260:Ribonucleases / Q000378:metabolism*; D013696:Temperature
D009843:Oligoribonucleotides; D012335:RNA, Ribosomal; D004720:Endonucleases; D012260:Ribonucleases