Identification of base-triples in RNA using comparative sequence analysis

Journal of Molecular Biology
D GautheretR R Gutell

Abstract

Comparative sequence analysis has proven to be a very efficient tool for the determination of RNA secondary structure and certain tertiary interactions. However, base-triples, an important RNA structural element, cannot be predicted accurately from sequence data. We show here that the poor base correlations observed at base-triple positions are the result of two factors. (1) Base covariation is not as strictly required in triples as it is in Watson-Crick pairs. (2) Base-triple structures are less conserved among homologous molecules. A particularity of known triple-helical regions is the presence of multiple base correlations that do not reflect direct pairing. We suggest that natural mutations in base-triples create structural changes that require compensatory mutations in adjacent base-pairs and triples to maintain the triple-helix conformation. On the basis of these observations, we devised two new measures of association that significantly enhance the base-triple signal in correlation studies. We evaluated correlations between base-pairs and single stranded bases, and correlations between adjacent base-pairs. Positions that score well in both analyses are the best triple candidates. This procedure correctly identifies tripl...Continue Reading

Citations

Nov 7, 1995·Proceedings of the National Academy of Sciences of the United States of America·J S LodmellA E Dahlberg
Jan 11, 2000·Nucleic Acids Research·S T KelleyG D Stormo
May 23, 2001·Nucleic Acids Research·J GorodkinG D Stormo
Aug 15, 2002·Nucleic Acids Research·Neocles B LeontisEric Westhof
Jul 18, 2006·Nucleic Acids Research·Eckart BindewaldBruce A Shapiro
May 28, 2010·Cold Spring Harbor Perspectives in Biology·Eric WesthofFabrice Jossinet
Oct 6, 1998·Annual Review of Biochemistry·D N Frank, N R Pace
Jul 24, 2010·RNA·Samuel Coulbourn Flores, Russ B Altman
Feb 19, 2004·RNA·Hendrik HuthoffBen Berkhout
Oct 21, 2015·Nucleic Acids Research·Anthony M MustoeCharles L Brooks
Jan 28, 2015·RNA Biology·Michael P Guy, Eric M Phizicky
Jun 15, 1997·Nucleic Acids Research·T HermannH U Göringer
Sep 6, 2000·Journal of Molecular Biology·J K Strauss-Soukup, S A Strobel
Jan 6, 1999·Biophysical Journal·P AuffingerE Westhof
Nov 25, 2006·Journal of Computer-aided Molecular Design·Shayantani MukherjeeDhananjay Bhattacharyya
Nov 1, 1995·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·L Brakier-GingrasF Dragon
Jul 15, 2018·Nucleic Acids Research·Stephanie M ZimmermanEric M Phizicky
Jul 17, 2001·Journal of Molecular Biology·T ElgavishR R Gutell
Nov 25, 2000·Journal of Molecular Biology·R R GutellM J Serra
Apr 1, 1997·Current Opinion in Structural Biology·P SchusterA Renner
Sep 19, 2003·Molecular Phylogenetics and Evolution·Leslie R GoertzenRobert K Jansen
Mar 26, 1999·Biochemistry·D GuhaThakurta, D E Draper
Mar 9, 2010·New Biotechnology·Benoît MasquidaFabrice Jossinet

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