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Nucleic Acids Research, 2001, Vol. 29, No. 24 5079-5089
© 2001 Oxford University Press

Conserved RNA secondary structures in Picornaviridae genomes

Christina Witwer1, Susanne Rauscher1, Ivo L. Hofacker1 and Peter F. Stadler1,2,*

1Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria and 2The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA

The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200–8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards the 5'-end. This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family Picornaviridae. Compared with previous studies we find: (i) that only smaller sections of the IRES region than previously reported are conserved at single base-pair resolution and (ii) that there is a number of significant structural elements in the coding region. Furthermore, we identify potential cis-acting replication elements in four genera where this feature has not been reported so far.

* To whom correspondence should be addressed at: Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria. Tel: +43 1 4277 52737; Fax: +43 1 4277 52793; Email: studla{at}tbi.univie.ac.at


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