Structural Motifs in Ribosomal RNAs: Implications for RNA Design and Genomics

Julie Zorn, Hin Hark Gan, Nahum Shiffeldrim, Tamar Schlick

Research output: Contribution to journalArticlepeer-review


The various motifs of RNA molecules are closely related to their structural and functional properties. To better understand the nature and distributions of such structural motifs (i.e., paired and unpaired bases in stems, junctions, hairpin loops, bulges, and internal loops) and uncover characteristic features, we analyze the large 16S and 23S ribosomal RNAs of Escherichia coli. We find that the paired and unpaired bases in structural motifs have characteristic distribution shapes and ranges; for example, the frequency distribution of paired bases in stems declines linearly with the number of bases, whereas that for unpaired bases in junctions has a pronounced peak. Significantly, our survey reveals that the ratio of total (over the entire molecule) unpaired to paired bases (0.75) and the fraction of bases in stems (0.6), junctions (0.16), hairpin loops (0.12), and bulges/internal loops (0.12) are shared by 16S and 23S ribosomal RNAs, suggesting that natural RNAs may maintain certain proportions of bases in various motifs to ensure structural integrity. These findings may help in the design of novel RNAs and in the search (via constraints) for RNA-coding motifs in genomes, problems of intense current focus.

Original languageEnglish (US)
Pages (from-to)340-347
Number of pages8
Issue number3
StatePublished - Feb 15 2004


  • Paired and unpaired bases
  • RNA design
  • RNA motif search
  • RNA structural motif
  • Ribosomal RNA

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry


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