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Nucleic Acids Research 2006 34(7):2015-2026; doi:10.1093/nar/gkl154
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Published online 13 April 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding

Ruud J. W. Schoemaker and Alexander P. Gultyaev*

Section Theoretical Biology, Leiden Institute of Biology, Leiden University Kaiserstraat 63, 2311 GP Leiden, The Netherlands

*To whom correspondence should be addressed. Tel: +31 71 5274814; Fax: +31 71 5274900; Email: gultyaev{at}rulsfb.leidenuniv.nl

Received December 4, 2005. Revised March 12, 2006. Accepted March 20, 2006.

Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2'-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNA–RNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using computer simulations of rRNA secondary structure formation by genetic algorithm. The effects of sRNA binding on rRNA structure are introduced as temporary structural constraints during co-transcriptional folding. Comparisons of the final predictions with simulations without sRNA binding and with phylogenetic structures show that sRNAs with two antisense elements may significantly facilitate the correct formation of long-range interactions in rRNAs, in particular at elevated temperatures. The simulations suggest that the main mechanism of this effect is a transient restriction of folding in rRNA domains where the termini are brought together by binding to double-guide sRNAs.


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