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Nucleic Acids Research Advance Access originally published online on January 21, 2009
Nucleic Acids Research 2009 37(4):e29; doi:10.1093/nar/gkn1044
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Nucleic Acids Research, 2009, Vol. 37, No. 4 e29
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Finding 3D motifs in ribosomal RNA structures

Alberto Apostolico1,2, Giovanni Ciriello2,*, Concettina Guerra1,2, Christine E. Heitsch3, Chiaolong Hsiao4 and Loren Dean Williams4

1College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA, 2Department of Information Engineering, University of Padova, Via Gradenigo 6a, Padova, Italy, 3School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0160 and 4School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA

*To whom correspondence should be addressed. Tel: +39 049 827 7928; Fax: +39 049 827 7799; Email: ciriello{at}dei.unipd.it

Received August 21, 2008. Revised December 13, 2008. Accepted December 15, 2008.

The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.


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