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A new way to see RNA

Published online by Cambridge University Press:  18 May 2011

Kevin S. Keating
Affiliation:
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
Elisabeth L. Humphris
Affiliation:
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
Anna Marie Pyle*
Affiliation:
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA Howard Hughes Medical Institute and Department of Chemistry, Yale University, New Haven, CT 06511, USA
*
*Author for correspondence: A. M. Pyle, Tel.: 203-436-4047; Fax: 203-432-5316; Email: anna.pyle@yale.edu

Abstract

Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.

Type
Review Article
Copyright
Copyright © Cambridge University Press 2011

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