Novel base triples in RNA structures revealed by graph theoretical searching methods

Mohd Firdaus Mohd Raih, Anne Marie Harrison, Peter Willett, Peter J. Artymiuk

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background: Highly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs.Results: We describe the graph theoretical identification and searching of highly hydrogen bonded base triples, where each base is involved in at least two hydrogen bonds with the other bases. Our approach correlates theoretically predicted base triples with literature-based compilations and other actual occurrences in crystal structures. The use of 'fuzzy' search tolerances has enabled us to discover a number of triple interaction types that have not been previously recorded nor predicted theoretically.Conclusions: Comparative analyses of different ribosomal RNA structures reveal several conserved base triple motifs in 50S rRNA structures, indicating an important role in structural stabilization and ultimately RNA function.

Original languageEnglish
Article numberS2
JournalBMC Bioinformatics
Volume12
Issue numberSUPPL. 13
DOIs
Publication statusPublished - 30 Nov 2011

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Ribosomal RNA
RNA
Hydrogen
Catalytic RNA
Graph in graph theory
Transfer RNA
Hydrogen bonds
Hydrogen Bonds
Stabilization
Crystal structure
Crystal Structure
Compilation
Interaction
Correlate
Molecules
Tolerance

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

Novel base triples in RNA structures revealed by graph theoretical searching methods. / Mohd Raih, Mohd Firdaus; Harrison, Anne Marie; Willett, Peter; Artymiuk, Peter J.

In: BMC Bioinformatics, Vol. 12, No. SUPPL. 13, S2, 30.11.2011.

Research output: Contribution to journalArticle

Mohd Raih, Mohd Firdaus ; Harrison, Anne Marie ; Willett, Peter ; Artymiuk, Peter J. / Novel base triples in RNA structures revealed by graph theoretical searching methods. In: BMC Bioinformatics. 2011 ; Vol. 12, No. SUPPL. 13.
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