title: A family of non-classical pseudoknots in influenza A and B viruses.
abstract: A very conserved pseudoknot structure has been shown to fold in influenza virus RNA. The pseudoknot encompasses the 3' splice site of segment 8 RNA in both influenza A and B viruses. By sequence comparison of influenza virus strains, we derive a consensus motif that defines a novel RNA pseudoknot family. The orientation of the coaxially stacked stems in the influenza pseudoknot differs from that in classical H-pseudoknots. Apart from the size of the loops, the topology of the influenza pseudoknot resembles that of some long-range pseudoknotted conformations. A seed alignment of the influenza pseudoknot family, containing representative strain sequences together with a consensus structure description, has been submitted to the RNA families (Rfam) database.
authors.affiliation: Department of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands. goultiaevap2@chem.leidenuniv.nl
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Gultyaev
authors.forename: René C L
authors.initials: RC
authors.lastname: Olsthoorn
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D005814:Genes, Viral / Q000235:genetics; D006801:Humans; D009980:Influenza A virus / Q000235:genetics*; D009981:Influenza B virus / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D012367:RNA, Viral