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Coupled nucleotide covariations reveal dynamic RNA interaction patterns

Published online by Cambridge University Press:  08 December 2000

ALEXANDER P. GULTYAEV ,
THOMAS FRANCH  and
KENN GERDES
ALEXANDER P. GULTYAEV
Affiliation:
Section Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences of Leiden University, 2311 GP Leiden, The Netherlands Leiden Institute of Chemistry, Leiden, The Netherlands
THOMAS FRANCH
Affiliation:
Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark
KENN GERDES
Affiliation:
Department of Molecular Biology, Odense University, DK-5230 Odense M, Denmark
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Abstract

Evolutionarily conserved structures in related RNA molecules contain coordinated variations (covariations) of paired nucleotides. Analysis of covariations is a very powerful approach to deduce phylogenetically conserved (i.e., functional) conformations, including tertiary interactions. Here we discuss conserved RNA folding pathways that are revealed by covariation patterns. In such pathways, structural requirements for alternative pairings cause some nucleotides to covary with two different partners. Such “coupled” covariations between three or more nucleotides were found in various types of RNAs. The analysis of coupled covariations can unravel important features of RNA folding dynamics and improve phylogeny reconstruction in some cases. Importantly, it is necessary to distinguish between multiple covariations determined by mutually exclusive structures and those determined by tertiary contacts.

Keywords

antisense RNAhokRNA evolutionRNA structure
Type
PERSPECTIVE
Information
RNA , Volume 6 , Issue 11 , November 2000 , pp. 1483 - 1491
Copyright
2000 RNA Society

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