Structure of influenza virus panhandle RNA studied by NMR spectroscopy and molecular modeling

Hae Kap Cheong, Chaejoon Cheong, Yeon Sook Lee, Baik L. Seong, Byong Seok Choi

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

The structure of a 34 nucleotide RNA molecule in solution, which contains the conserved panhandle sequences, was determined by NMR spectroscopy and molecular 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 internal loop flanked by short helices. The nucleotides at or near the internal loop are crucial for polymerase binding and transcriptional activity. They show more flexible conformational character than the Watson-Crick base-paired region, especially for the backbone torsion angles of α, γ and δ. Although residues A10 and A12 are stacked in the helix, the phosphodiester backbones are distorted. Residues A12, A13 and G25 show dynamic sugar conformations and the backbone conformations of these nucleotides are flexible. This backbone conformation and its associated flexibility may be important for protein-RNA interactions as well as base-specific interactions.

Original languageEnglish
Pages (from-to)1392-1397
Number of pages6
JournalNucleic acids research
Volume27
Issue number5
DOIs
Publication statusPublished - 1999 Mar 1

All Science Journal Classification (ASJC) codes

  • Genetics

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