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