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Bioinformatics Advance Access originally published online on January 29, 2006
Bioinformatics 2006 22(10):1177-1182; doi:10.1093/bioinformatics/btl024
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Thermodynamics of RNA–RNA binding

Ulrike Mückstein 1, Hakim Tafer 1, Jörg Hackermüller 2, Stephan H. Bernhart 1, Peter F. Stadler 1,3,4 and Ivo L. Hofacker 1,*

1 Institute for Theoretical Chemistry, University of Vienna Währingerstrasse 17, A-1090 Vienna, Austria
2 Fraunhofer Institut für Zelltherapie und Immunologie, IZI Deutscher Platz 5e, D-04103 Leipzig, Germany
3 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig Härtelstrasse 16-18, D-04107 Leipzig, Germany
4 The Santa Fe Institute 1399 Hyde Park Rd., Santa Fe, New Mexico

*To whom correspondence should be addressed.

Background: Reliable prediction of RNA–RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA–mRNA binding and antisense interactions. The thermodynamics of such RNA–RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to ‘open’ the binding site and (2) the energy gained from hybridization.

Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired.

Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.

Availability: RNAup will be distributed as part of the Vienna RNA Package, www.tbi.univie.ac.at/~ivo/RNA/

Contact: ivo{at}tbi.univie.ac.at

Received on November 18, 2005; revised on December 22, 2005; accepted on January 23, 2006

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