Structure of influenza virus panhandle RNA studied by NMR spectroscopy andmolecular modeling

The structure of a 34 nucleotide RNA molecule in solution, which contains t he conserved panhandle sequences, was determined by NMR spectroscopy and mo lecular modeling. The partially double-stranded panhandle structure of the influenza virus RNA serves to regulate initiation and termination of viral transcription as well as polyadenylation. The panhandle RNA consists of int ernal loop flanked by short helices. The nucleotides at or near the interna l loop are crucial for polymerase binding and transcriptional activity. The y show more flexible conformational character than the Watson-Crick base-pa ired region, especially for the backbone torsion angles of alpha, gamma and delta. Although residues A10 and A12 are stacked in the helix, the phospho diester backbones are distorted. Residues A12, A13 and G25 show dynamic sug ar conformations and the backbone conformations of these nucleotides are fl exible. This backbone conformation and its associated flexibility may be im portant for protein-RNA interactions as well as base-specific interactions.