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Nucleic Acids Research Advance Access published online on May 6, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn206
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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

Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture

Shoji P. Ohuchi1, Yoshiya Ikawa2,3 and Yoshikazu Nakamura1,4,*

1Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, 2Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, 3PRESTO, Precursory Research for Embryonic Science and Technology, Japan Science and Technology Corporation, Saitama 332-0012 and 4CREST, Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Saitama 332-0012, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5307; Fax: +81 3 5449 5415; Email: nak{at}ims.u-tokyo.ac.jp

Received December 19, 2007. Revised March 5, 2008. Accepted April 7, 2008.

To develop molecular tools for the detection and control of RNA molecules whose functions rely on their 3D structures, we have devised a selection system to isolate novel RNA motifs that interact with a target RNA structure within a given structural context. In this system, a GAAA tetraloop and its specific receptor motif (11-ntR) from an artificial RNA ligase ribozyme with modular architecture (the DSL ribozyme) were replaced with a target structure and random sequence, respectively. Motifs recognizing the target structure can be identified by in vitro selection based on ribozyme activity. A model selection targeting GAAA-loop successfully identified motifs previously known as GAAA-loop receptors. In addition, a new selection targeting a C-loop motif also generated novel motifs that interact with this structure. Biochemical analysis of one of the C-loop receptor motifs revealed that it could also function as an independent structural unit.


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