TBI-Preprint: Thermodynamics of RNA-RNA Binding

TBI-Preprint 05-07-002

Titel:
Thermodynamics of RNA-RNA Binding

Author(s):
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler, Ivo L. Hofacker

Appeared in:
Proceedings of the GCB 2005

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 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

Alternative Numbers:

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Last modified: 2005-10-31 01:42:18 ivo