Nucleic Acid Sciences Article

Structural motifs in ribosomal RNAs: Implications for RNA design and genomics

  1. Julie Zorn1,
  2. Hin Hark Gan1,3,
  3. Nahum Shiffeldrim1,3,
  4. Tamar Schlick1,2,3,*

Article first published online: 13 NOV 2003

DOI: 10.1002/bip.10525

Issue

Biopolymers

Biopolymers

Volume 73, Issue 3, pages 340–347, 15 February 2004

Additional Information

How to Cite

Zorn, J., Gan, H. H., Shiffeldrim, N. and Schlick, T. (2004), Structural motifs in ribosomal RNAs: Implications for RNA design and genomics. Biopolymers, 73: 340–347. doi: 10.1002/bip.10525

Author Information

  1. 1

    Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East New York, NY 10003

  2. 2

    Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012

  3. 3

    Howard Hughes Medical Institute

*Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East New York, NY 10003

Publication History

  1. Issue published online: 27 JAN 2004
  2. Article first published online: 13 NOV 2003
  3. Manuscript Accepted: 15 MAY 2003
  4. Manuscript Received: 29 APR 2003

Funded by

  • Joint NSF/NIGMS Initiative to Support Research Grants in the Area of Mathematical Biology. Grant Number: DMS-0201160

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article (HTML) Get PDF (517K)

Keywords:

  • ribosomal RNA;
  • RNA structural motif;
  • paired and unpaired bases;
  • RNA design;
  • RNA motif search

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. © 2003 Wiley Periodicals, Inc. Biopolymers 73: 340–347, 2004

View Full Article (HTML) Get PDF (517K)