Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics 2005 (GCB 2005), 5.-7. October 2005, Hamburg, Germany P-71, 3-13 (2005).



Andrew Torda, Stefan Kurtz, Matthias Rarey (eds.)


Thermodynamics of RNA-RNA binding

Ulrike Mückstein , Hakim Tafer , Jörg Hackermüller , Stephan H. Bernhart , Peter F. Stadler and Ivo L. Hofacker


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. 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 to a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding probabilities of siRNAs to their respective mRNA target.

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ISBN 3-88579-400-4

Last changed 24.01.2012 21:51:52