title: Secondary structure of a conserved domain in an intron of influenza A M1 mRNA.
abstract: Influenza A virus utilizes RNA throughout infection. Little is known, however, about the roles of RNA structures. A previous bioinformatics survey predicted multiple regions of influenza A virus that are likely to generate evolutionarily conserved and stable RNA structures. One predicted conserved structure is in the pre-mRNA coding for essential proteins, M1 and M2. This structure starts 79 nucleotides downstream of the M2 mRNA 5' splice site. Here, a combination of biochemical structural mapping, mutagenesis, and NMR confirms the predicted three-way multibranch structure of this RNA. Imino proton NMR spectra reveal no change in secondary structure when 80 mM KCl is supplemented with 4 mM MgCl2. Optical melting curves in 1 M NaCl and in 100 mM KCl with 10 mM MgCl2 are very similar, with melting temperatures ∼14 °C higher than that for 100 mM KCl alone. These results provide a firm basis for designing experiments and potential therapeutics to test for function in cell culture.
authors.affiliation: Department of Chemistry and Center for RNA Biology, University of Rochester , Rochester, New York 14627, United States.
authors.forename: Tian
authors.initials: T
authors.lastname: Jiang
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kennedy
authors.forename: Walter N
authors.initials: WN
authors.lastname: Moss
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D009980:Influenza A virus / Q000235:genetics / Q000378:metabolism*; D007438:Introns; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D012367:RNA, Viral