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Nucleic Acids Research, Vol 27, Issue 8 1859-1865, Copyright © 1999 by Oxford University Press

ARTICLES

A conserved motif in group IC3 introns is a new class of GNRA receptor

Y Ikawa, D Naito, N Aono, H Shiraishi and T Inoue
Department of Chemistry, Faculty of Science, Kyoto University, Kyoto 606-8502, Japan.

Terminal tetraloops consisting of GNRA sequences are often found in biologically active large RNAs. The loops appear to contribute towards the organization of higher order RNA structures by forming specific tertiary interactions with their receptors. Group IC3 introns which possess a GAAA loop in the L2 region often have a phylogenetically conserved motif in their P8 domains. In this report, we show that this conserved motif stands as a new class of receptor that distinguishes the sequences of GNRA loops less stringently than previously known receptors. The motif can functionally substitute an 11 nt motif receptor in the Tetrahymena ribozyme. Its structural and functional similarity to one class of synthetic receptors obtained from in vitro selection is observed.
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