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

BMC Bioinformatics

Proceedings

Peter Willett¹  Peter J Artymiuk²  Anne-Marie Harrison³  Mohd Firdaus-Raih⁴ 

[1] Department of Information Studies, University of Sheffield, S10 2TN, Sheffield, UK;Department of Molecular Biology and Biotechnology, University of Sheffield, S10 2TN, Sheffield, UK;Department of Molecular Biology and Biotechnology, University of Sheffield, S10 2TN, Sheffield, UK;Biomedical Research Centre, Sheffield Hallam University, S1 1WB, Sheffield, UK;Department of Molecular Biology and Biotechnology, University of Sheffield, S10 2TN, Sheffield, UK;School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Malaysia;

关键词: Protein Data Bank;    Hepatitis Delta Virus;    Hairpin Loop;    Large Ribosomal Subunit;    Peptidyl Transferase;   

DOI  :  10.1186/1471-2105-12-S13-S2

来源: Springer

【 摘 要 】

BackgroundHighly 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.ResultsWe 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.ConclusionsComparative 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.

【 授权许可】

Unknown   
© Firdaus-Raih et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.