Binding of the influenza virus NS1 protein to model genome RNAs

We have previously shown that the influenza virus NS1 protein exhibits stable binding to a model mini vRNA which is stronger than its binding to dsRNA. In this study, we confirmed that the binding depended on a higher-order structure of the model RNA, probably the panhandle structure formed by pairing between the 5'- and 3'-terminal common sequences. The formation of the structure was enhanced by the NS1 protein itself. We propose that an A bulge in a stretch of double helix results in a binding site with greater affinity for the NS1 protein.