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Structural motifs in ribosomal RNAs: Implications for RNA design and genomics
Author(s) -
Zorn Julie,
Gan Hin Hark,
Shiffeldrim Nahum,
Schlick Tamar
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10525
Subject(s) - rna , ribosomal rna , structural motif , computational biology , small nucleolar rna , genome , structural genomics , biology , chemistry , non coding rna , gene , genetics , protein structure , biochemistry
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. © 2003 Wiley Periodicals, Inc. Biopolymers 73: 340–347, 2004