Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 05-019

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Thermodynamics of RNA-RNA Binding

Ulrike M¨ckstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler, Ivo L. Hofacker

GCB 2005

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 signicant 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 eciency correlates well with the binding probabilities of the siRNAs to their respective mRNA target.

Keywords: RNA secondary structure, RNA hybridization, dynamic programming

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