Annotation of tertiary interactions in RNA structures reveals variations and correlations

Yurong Xin, Christian Laing, Neocles B. Leontis, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

RNA tertiary motifs play an important role in RNA folding and biochemical functions. To help interpret the complex organization of RNA tertiary interactions, we comprehensively analyze a data set of 54 high-resolution RNA crystal structures for motif occurrence and correlations. Specifically, we search seven recognized categories of RNA tertiary motifs (coaxial helix, A-minor, ribose zipper, pseudoknot, kissing hairpin, tRNA D-loop/T-loop, and tetraloop-tetraloop receptor) by various computer programs. For the nonredundant RNA data set, we find 613 RNA tertiary interactions, most of which occur in the 16S and 23S rRNAs. An analysis of these motifs reveals the diversity and variety of A-minor motif interactions and the various possible loop-loop receptor interactions that expand upon the tetraloop-tetraloop receptor. Correlations between motifs, such as pseudoknot or coaxial helix with A-minor, reveal higher-order patterns. These findings may ultimately help define tertiary structure restraints for RNA tertiary structure prediction. A complete annotation of the RNA diagrams for our data set is available at http://www.biomath.nyu.edu/motifs/. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)2465-2477
Number of pages13
JournalRNA
Volume14
Issue number12
DOIs
StatePublished - Dec 2008

Keywords

  • Annotation
  • RNA structure
  • RNA tertiary motif

ASJC Scopus subject areas

  • Molecular Biology

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