Structural Motifs in Ribosomal RNAs

Implications for RNA Design and Genomics

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)340-347
Number of pages8
JournalBiopolymers - Peptide Science Section
Volume73
Issue number3
DOIs
StatePublished - Feb 15 2004

Fingerprint

23S Ribosomal RNA
16S Ribosomal RNA
Nucleotide Motifs
Ribosomal RNA
Genomics
RNA
Genome
Escherichia coli
Molecules
Structural integrity
Genes

Keywords

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

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Structural Motifs in Ribosomal RNAs : Implications for RNA Design and Genomics. / Zorn, Julie; Gan, Hin Hark; Shiffeldrim, Nahum; Schlick, Tamar.

In: Biopolymers - Peptide Science Section, Vol. 73, No. 3, 15.02.2004, p. 340-347.

Research output: Contribution to journalArticle

Zorn, Julie ; Gan, Hin Hark ; Shiffeldrim, Nahum ; Schlick, Tamar. / Structural Motifs in Ribosomal RNAs : Implications for RNA Design and Genomics. In: Biopolymers - Peptide Science Section. 2004 ; Vol. 73, No. 3. pp. 340-347.
@article{c3934e77a3e4496b84b6857566ff2a13,
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.",
keywords = "Paired and unpaired bases, Ribosomal RNA, RNA design, RNA motif search, RNA structural motif",
author = "Julie Zorn and Gan, {Hin Hark} and Nahum Shiffeldrim and Tamar Schlick",
year = "2004",
month = "2",
day = "15",
doi = "10.1002/bip.10525",
language = "English (US)",
volume = "73",
pages = "340--347",
journal = "Biopolymers",
issn = "0006-3525",
publisher = "John Wiley and Sons Inc.",
number = "3",

}

TY - JOUR

T1 - Structural Motifs in Ribosomal RNAs

T2 - Implications for RNA Design and Genomics

AU - Zorn, Julie

AU - Gan, Hin Hark

AU - Shiffeldrim, Nahum

AU - Schlick, Tamar

PY - 2004/2/15

Y1 - 2004/2/15

N2 - 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.

AB - 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.

KW - Paired and unpaired bases

KW - Ribosomal RNA

KW - RNA design

KW - RNA motif search

KW - RNA structural motif

UR - http://www.scopus.com/inward/record.url?scp=1242269423&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=1242269423&partnerID=8YFLogxK

U2 - 10.1002/bip.10525

DO - 10.1002/bip.10525

M3 - Article

VL - 73

SP - 340

EP - 347

JO - Biopolymers

JF - Biopolymers

SN - 0006-3525

IS - 3

ER -