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Nucleic Acids Research Advance Access published online on December 23, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm1048
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© 2007 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

Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors

Cody Geary, Stéphanie Baudrey and Luc Jaeger*

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

*To whom correspondence should be addressed. Tel: +1 8058933628; Fax: +1 8058934120; Email: Jaeger{at}chem.ucsb.edu

Received September 14, 2007. Revised October 24, 2007. Accepted November 5, 2007.

Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. However, in contrast to GYRA and GAAA tetraloops, very few GNRA/receptor interactions have yet been identified to involve GGAA tetraloops in nature. A novel in vitro selection scheme based on a rigid self-assembling tectoRNA scaffold designed for isolation of intermolecular interactions with A-minor motifs has yielded new GGAA tetraloop-binding receptors with affinity in the nanomolar range. One of the selected receptors is a novel 12 nt RNA motif, (CCUGUG ... AUCUGG), that recognizes GGAA tetraloop hairpin with a remarkable specificity and affinity. Its physical and chemical characteristics are comparable to those of the well-studied ‘11nt’ GAAA tetraloop receptor motif. A second less specific motif (CCCAGCCC ... GAUAGGG) binds GGRA tetraloops and appears to be related to group IC3 tetraloop receptors. Mutational, thermodynamic and comparative structural analysis suggests that natural and in vitro selected GNRA receptors can essentially be grouped in two major classes of GNRA binders. New insights about the evolution, recognition and structural modularity of GNRA and A-minor RNA–RNA interactions are proposed.

Present address: Stéphanie Baudrey, Architecture et Réactivité de l’ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France.


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