Secondary structure of a conserved domain in an intron of influenza A M1 mRNA

Biochemistry. 2014 Aug 19;53(32):5236-48. doi: 10.1021/bi500611j. Epub 2014 Aug 6.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computational Biology
  • Conserved Sequence
  • Influenza A virus / genetics
  • Influenza A virus / metabolism*
  • Introns*
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Oligonucleotide Array Sequence Analysis
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*

Substances

  • RNA, Messenger
  • RNA, Viral