### Thermodynamics of RNA-RNA binding

*Ulrike MÃ¼ckstein*

*, Hakim Tafer*

*, JÃ¶rg HackermÃ¼ller*

*, Stephan H. Bernhart*

*, Peter F. Stadler*

*and Ivo L. Hofacker*

#### Abstract

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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