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Nucleic Acids Research Advance Access first published online on November 26, 2008
This version published online on November 28, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn911
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

The UA_handle: a versatile submotif in stable RNA architectures{dagger}

Luc Jaeger*, Erik J. Verzemnieks and Cody Geary

Chemistry and Biochemistry Department, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA

*To whom correspondence should be addressed. Tel: +1 805 893 3628; Fax: +1 805 893 4120; Email: jaeger{at}chem.ucsb.edu Present address: Erik J. Verzemnieks, School of Medicine, University of Washington, Seattle, WA 98125, USA

Received July 30, 2008. Revised October 6, 2008. Accepted October 29, 2008.

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5'XU/ANnX3'). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.

{dagger}This article is dedicated to Prof. Jérôme Lejeune.


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