SEQUENCE-SPECIFIC BINDING OF THE INFLUENZA-VIRUS RNA-POLYMERASE TO SEQUENCES LOCATED AT THE 5' ENDS OF THE VIRAL RNAS

The enzymatic activity of recombinant influenza virus RNA polymerase i s strictly dependent on the addition of a template RNA containing 5' a nd 3' viral sequences. Here we report the analysis of the binding spec ificity and physical characterization of the complex by using gel shif t, modification interference, and density gradient techniques. The 13S complex binds specifically to short synthetic RNAs that mimic the par tially double stranded panhandle structures found at the termini of bo th viral RNA and cRNA. The polymerase will also bind independently to the single-stranded 5' or 3' ends of viral RNA. It binds most strongly to specific sequences within the 5' end but is unable to bind these s equences in the context of a completely double stranded structure. Mod ification interference analysis identified the short sequence motifs a t the 5' ends of the viral RNA and cRNA templates that are critical fo r binding.