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Nucleic Acids Research 2005 33(18):5924-5935; doi:10.1093/nar/gki886
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Published online 19 October 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids

Rob Knight1,*, Hans De Sterck2, Rob Markel3, Sandra Smit, Alexander Oshmyansky4 and Michael Yarus2

1Department of Chemistry and Biochemistry, University of Colorado Boulder, CO 80309-0215, USA 2Department of Molecular, Cellular and Development Biology, University of Colorado Boulder, CO 80309-0215, USA 3Scientific Computing Division, National Center for Atmospheric Research Boulder, CO 80309, USA 4School of Medicine, Duke University Durham, NC 27710, USA

*To whom correspondence should be addressed. Tel: +1 303 492 1984; Fax: 303 492 7744; Email: rob{at}spot.colorado.edu

Received September 16, 2005. Accepted September 20, 2005.

Although functional RNA molecules are known to be biased in overall composition, the effects of background composition on the probability of finding a particular active site by chance has received little attention. The probability of finding a particular motif has important implications both for understanding the distribution of functional RNAs in ancient and modern organisms with varying genome compositions and for tuning SELEX pools to optimize the chance of finding specific functions. Here we develop a new method for calculating the probability of finding a modular motif containing base-paired regions, and use a computational grid to fold several hundred million random RNA sequences containing the core elements of the isoleucine aptamer and the hammerhead ribozyme to estimate the probability that a sequence containing these structural elements will fold correctly when isolated from background sequences of different compositions. We find that the two motifs are most likely to be found in distinct regions of compositional space, and that the regions of greatest abundance are influenced by the probability of finding the conserved bases, finding the flanking helices, and folding, in that order of importance. Additionally, we can refine our estimates of the number of random sequences required for a 50% probability of finding an example of each site in unbiased random pools of length 100 to 4.1 x 109 for the isoleucine aptamer and 1.6 x 1010 for the hammerhead ribozyme. These figures are consistent with the facile recovery of these motifs from SELEX experiments.


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