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