A Family of Non-classical Pseudoknots in Influenza A and B Viruses

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.