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Updated: Aug 11, 2026
RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Primary and secondary structure in a precursor of 5 S rRNA
Abstract:
In order to shed some light on the mechanism of action of RNAase E, we studied primary and secondary structure in 9 S (a precursor of 5 S rRNA), p5 and 5 S rRNAs. These molecules were digested with RNAases A and T1 in the presence of a high salt concentration; conditions under which single-stranded RNA is differentially digested. The double-stranded RNA fragments were isolated and analyzed. The analyses suggested that p5 and 5 S rRNA contain a stem of ten basepairs which consists of sequences from the 5' and 3' regions of the molecule, while 9 S contains a similar stem which is three basepairs longer and includes also a bulge of three unpaired bases. The stem in the 9 S RNA contains four sites where RNA processing cleavages occur. One of the cleavage sites which leads to the formation of p5 is in a junction between single-stranded and double-stranded RNA. The 9 S RNA molecule contains another large stem of at least 15 basepairs which is derived from the 3' end of the 9 S precursor molecular; it is apparently the transcription termination stem.
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