Hairpin loop structure in the 3 ' arm of the influenza A virus virion RNA promoter is required for endonuclease activity

Previous studies have shown that the 5' arm of the influenza A virus virion RNA promoter requires a hairpin loop structure for efficient endonuclease activity of influenza virus RNA polymerase, an activity that is required fo r the cap-snatching activity of primers from host pre-mRNA, Here we examine whether a hairpin loop is also required in the 3' arm of the viral RNA pro moter. We study point mutations at each nucleotide position (1 to 12) withi n the 3' arm of the promoter as well as complementary "rescue" mutations wh ich restored base pairing in the stem of a potential hairpin loop. Our resu lts suggest that endonuclease activity is absolutely dependent on the prese nce of a 3' hairpin loop structure. This is the first direct evidence for R NA secondary structure within the 3' arm being required for a specific stag e, i.e., endonuclease cleavage, in the influenza virus replicative cycle.