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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2007 35(20):6820-6831; doi:10.1093/nar/gkm674
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Nucleic Acids Research, 2007, Vol. 35, No. 20 6820-6831
© 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

A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme

Atef Nehdi, Jonathan Perreault, Jean-Denis Beaudoin and Jean-Pierre Perreault*

RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada

* To whom correspondence should be addressed. Tel: +1 819 564 5310; Fax: +1 819 564 5340; Email: jean-pierre.perreault{at}usherbrooke.ca

Received May 7, 2007. Revised August 17, 2007. Accepted August 18, 2007.

A bioinformatic covariation analysis of a collection of 119 novel variants of the antigenomic, self-cleaving hepatitis delta virus (HDV) RNA motif supported the formation of all of the Watson–Crick base pairs (bp) of the catalytic centre except the C19–G81 pair located at the bottom of the P2 stem. In fact, a novel Watson–Crick bp between C19 and G80 is suggested by the data. Both chemical and enzymatic probing demonstrated that initially the C19–G81 pair is formed in the ribozyme (Rz), but upon substrate (S) binding and the formation of the P1.1 pseudoknot C19 switches its base-pairing partner from G81 to G80. As a result of this finding, the secondary structure of this ribozyme has been redrawn. The formation of the C19–G80 bp results in a J4/2 junction composed of four nucleotides, similar to that seen in the genomic counterpart, thereby increasing the similarities between these two catalytic RNAs. Additional mutagenesis, cleavage activity and probing experiments yield an original characterization of the structural features involving the residues of the J4/2 junction.


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