Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2006 34(22):6587-6604; doi:10.1093/nar/gkl963
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Nucleic Acids Research, 2006, Vol. 34, No. 22 6587-6604
© 2006 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.
Survey and Summary |
The interaction networks of structured RNAs
Architecture et Réactivité de l'ARN, Université Louis Pasteur IBMC, CNRS, 15 rue R.Descartes, F-67084 Strasbourg, France
*To whom correspondence should be addressed. Tel/Fax: +33 388 41 70 46; Email : E.Westhof{at}ibmc.u-strasbg.fr
Received August 25, 2006. Revised October 21, 2006. Accepted October 25, 2006.
All pairwise interactions occurring between bases which could be detected in three-dimensional structures of crystallized RNA molecules are annotated on new planar diagrams. The diagrams attempt to map the underlying complex networks of base–base interactions and, especially, they aim at conveying key relationships between helical domains: co-axial stacking, bending and all Watson–Crick as well as non-Watson–Crick base pairs. Although such wiring diagrams cannot replace full stereographic images for correct spatial understanding and representation, they reveal structural similarities as well as the conserved patterns and distances between motifs which are present within the interaction networks of folded RNAs of similar or unrelated functions. Finally, the diagrams could help devising methods for meaningfully transforming RNA structures into graphs amenable to network analysis.
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