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PLoS One. 2013 Sep 2;8(9):e70615. doi: 10.1371/journal.pone.0070615. eCollection 2013.

Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA.

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  • 1Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America.


Influenza A virus is a segmented single-stranded (-)RNA virus that causes substantial annual morbidity and mortality. The transcriptome of influenza A is predicted to have extensive RNA secondary structure. The smallest genome segment, segment 8, encodes two proteins, NS1 and NEP, via alternative splicing. A conserved RNA domain in the intron of segment 8 may be important for regulating production of NS1. Two different multi-branch loop structures have been proposed for this region. A combination of in vitro chemical mapping and isoenergetic microarray techniques demonstrate that the consensus sequence for this region folds into a hairpin conformation. These results provide an alternative folding for this region and a foundation for designing experiments to probe its functional role in the influenza life cycle.

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