RNAup


Thermodynamics of RNA-RNA Binding





Reliable predictions 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. We use an extension of the standard partition function approach to RNA secondary structures that computes the probabilities that a sequence interval is unpaired. Furthermore we compute the probability of a local interaction between a small RNA and its target site, given that an interaction is possible. As an additional information we provide the optimal free energy of binding at a given position along the target sequence.

We implemented a C program based on a modified version of the recursion for the equilibrium partition function introduced by McCaskill (McCaskill 90). 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 energies of siRNAs to their respective mRNA target. A preprint of the first RNAup paper is here.

RNAup is now a part of the regular distribution of the Vienna RNA package.

We have programmed a new version of RNAup that considers the secondary structure of both interacting RNA molecules (option -b). The new version is about 6 times faster than the previous one. Additionally we enhanced the output of the new version: The free engery necessary to open a sequence intervall is now added to the output file. In interaction mode we print the minimal free energy of interaction and all its contributions to stdout. Furthermore we print the coordinates of the region of minimal free energy of interaction. For more information about the new version look at the manpage of RNAup. A preprint of the paper describing the new features of RNAup is here.
Ulli Mückstein, <ulim@tbi.univie.ac.at>
Institut für theoretische Chemie, Währingerstr. 17,
A-1090 Wien, Austria

Last modified: 2007-12-13 10:49:26 ulim