title: Structural motifs in ribosomal RNAs: implications for RNA design and genomics.
abstract: 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.
authors.affiliation: Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY 10003, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Zorn
authors.forename: Hin Hark
authors.initials: HH
authors.lastname: Gan
authors.forename: Nahum
authors.initials: N
authors.lastname: Shiffeldrim
authors.forename: Tamar
authors.initials: T
authors.lastname: Schlick
mesh_terms: D001483:Base Sequence; D015195:Drug Design; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D023281:Genomics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry
chemical_list: D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; D012343:RNA, Transfer