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Nucleic Acids Research, 2000, Vol. 28, No. 14 2679-2689
© 2000 Oxford University Press

Structural analysis of new local features in SECIS RNA hairpins

Delphine Fagegaltier, Alain Lescure, Robert Walczak, Philippe Carbon and Alain Krol*

UPR CNRS Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire, 15, Rue René Descartes, 67084 Strasbourg Cedex, France

Decoding of the UGA selenocysteine codon for selenoprotein translation requires the SECIS element, a stem–loop motif in the 3'-UTR of the mRNA carrying short or large apical loops. In previous structural studies, we derived a secondary structure model for SECIS RNAs with short apical loops. Work from others proposed that intra-apical loop base pairing can occur in those SECIS that possess large apical loops, yielding form 2 SECIS versus the form 1 with short loops. In this work, SECIS elements arising from eight different selenoprotein mRNAs were assayed by enzymatic and/or chemical probing showing that seven can adopt form 2. Further, database searches led to the discovery in drosophila and zebrafish of SECIS elements in the selenophosphate synthetase 2, type 1 deiodinase and SelW mRNAs. Alignment of SECIS sequences not only highlighted the predominance of form 2 but also made it possible to classify the SECIS elements according to the type of selenoprotein mRNA they belong to. Interestingly, the alignment revealed that an unpaired adenine, previously thought to be invari­ant, is replaced by a guanine in four SECIS elements. Tested in vivo, neither the A to G nor the A to U changes at this position greatly affected the activity while the most detrimental effect was provided by a C. The putative contribution of the various SECIS motifs to function and ligand binding is discussed.

* To whom correspondence should be addressed. Tel: +33 3 88 41 70 50; Fax: +33 3 88 60 22 18; Email: A.Krol@ibmc.u-strasbg.fr Present address: Robert Walczak, Institut de Biologie Animale, Université de Lausanne, Lausanne, Switzerland


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