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 for 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 promoter. We study point mutations at each nucleotide position (1 to 12) within the 3 arm of the promoter as well as complementary "rescue" mutations which restored base pairing in the stem of a potential hairpin loop. Our results suggest that endonuclease activity is absolutely dependent on the presence of a 3 hairpin loop structure. This is the first direct evidence for RNA secondary structure within the 3 arm being required for a specific stage, i.e., endonuclease cleavage, in the influenza virus replicative cycle.Influenza A virus is a segmented, negative-sense RNA virus. The virion RNA of influenza virus serves several functions. During transcription it acts as the template and as a cofactor in endonuclease cleavage of host pre-mRNA (17, 31), leading to the synthesis of viral mRNA which is capped at its 5Ј end and polyadenylated at its 3Ј end (18). Virion RNA (vRNA) also acts as the template for full-length cRNA, which in turn serves as a template for the synthesis of new vRNA molecules. Influenza virus RNA synthesis takes place within the nucleus of infected cells, consistent with the requirement for host cell pre-mRNAs and for splicing (26), suggesting that influenza virus transcription may be coupled to host cell RNA polymerase II transcription (14). Inhibitors selective for either influenza virus endonuclease or RNA polymerase activities suggest that the active site for endonuclease cleavage is separate from the transcription active site (50, 51).The influenza virus RNA polymerase is a heterotrimer formed by the PB1, PB2, and PA subunits (25, 26). All three subunits are required for transcription and replication, although the role of PA is poorly understood (37,44,45). In the virion the polymerase proteins are associated with vRNA and the nucleoprotein to form ribonucleoprotein complexes. It is likely that base pairing between the conserved 3Ј and 5Ј termini of the influenza virus vRNA leads to the formation of an RNA panhandle structure; however, it is probable that the polymerase itself helps to stabilize the interactions between the 5Ј and 3Ј termini (7,19,20,23,31,33,35).PB1 interacts with both PB2 and PA (20,22,52) and is also involved in binding vRNA (11,12,15,31). PB1 also binds cRNA, although the binding sites are different from those for vRNA (16). PB1 contains amino acid motifs present in other RNA-dependent RNA polymerases (38) and is the subunit responsible for polymerization (24). Although it has been reported that the endonuclease site residues in PB2 (32), recent evidence favors its location being in PB1 (31a).PB2 is the cap-binding protein. Cap-binding regions have been mapped, and capped RNA can be cross-linked to PB2 (3, ...