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RNA. 2006 Jan;12(1):83-93.

Topology of three-way junctions in folded RNAs.

Author information

  • 1Institut de Biologie Moléculaire et Cellulaire du CNRS, Bioinformatique, modélisation et simulations des acides nucléiques, UPR 9002 Architecture et Réactivité de l'ARN, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg Cedex, France.

Abstract

The three-way junctions contained in X-ray structures of folded RNAs have been compiled and analyzed. Three-way junctions with two helices approximately coaxially stacked can be divided into three main families depending on the relative lengths of the segments linking the three Watson-Crick helices. Each family has topological characteristics with some conservation in the non-Watson-Crick pairs within the linking segments as well as in the types of contacts between the segments and the helices. The most populated family presents tertiary interactions between two helices as well as extensive shallow/minor groove contacts between a linking segment and the third helix. On the basis of the lengths of the linking segments, some guidelines could be deduced for choosing a topology for a three-way junction on the basis of a secondary structure. Examples and prediction bas'ed on those rules are discussed.

PMID:
16373494
[PubMed - indexed for MEDLINE]
PMCID:
PMC1370888
Free PMC Article

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