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Nucleic Acids Research, 1986, Vol. 14, No. 3 1365-1378
© 1986

Articles

Secondary structure of Tetrahymena thermophilia 5S ribosomal RNA as revealed by enzymatic digestion and microdensitometric analysis

Barbara Sneath, Calvin Vary1, George Pavlakis2 and John Vournakis*,

1Allied Corporation, Corporate Technology Center P.O. Box 102112, Morristown, NJ 07960 2National Cancer Institute, Frederick Cancer Research Facility P.O. Box B, Frederick, MD 21701, USA Biological Research Laboratories, Department of Biology, Syracuse University 130 College Place, Syracuse, NY 13210

*To whom correspondence should be addressed

Received August 23, 1985. Revised January 3, 1986. Accepted January 3, 1986.

The secondary structure of [32p] end-labeled 5S rRNA from Tetrahymena thermophilia (strain B) has been investigated using the enzymes SI nuclease, cobra venom ribonuclease and T2 ribonuclease. The results, analyzed by scanning microdensitometry and illustrated by three-dimensional computer graphics, support the secondary structure model of Curtiss and Vournakis for 5S rRNA (1). Aberrent mobility of certain RNA fragments on sequencing gels was observed as regions of band compression. These regions are postulated to be caused by stable internal base-pairing. The molecule was probed with T2 RNase in neutral (pH 7.5) and acidic (pH 4.5) buffers and only minor structural differences were revealed. One of the helices was found to be susceptible to enzymatic attack by both the single-strand and double-strand specific enzymes. These observations are evidence for the existence of dynamic structural equilibria in 5S rRNA.


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