Effects of magnesium ions on two EMCV IRES key activity fragments

Julien A. Dupont, Karim Snoussi

Research output: Contribution to journalArticle

Abstract

Using NMR magnetization transfer from water and ammonia-catalyzed exchange of the imino protons, changes have been monitored in base-pair kinetics induced by Mg2+ in two key activity fragments r(CACCUGGCGACAGGUG) and r(GGCCAAAAGCC) of the encephalomyocarditis virus internal ribosome entry site. For r(CACCUGGCGACAGGUG), the addition of Mg2+ reveals two types of base-pairs: r(U545•A) and r(G546•C), in the first category, have lifetimes only slightly higher in the presence of Mg 2+, whereas their dissociation constants are substantially reduced. This behavior has been termed proximal. The base-pairs r(G553•C) and r(G554•C), in the second category, have lifetimes substantially higher in the presence of Mg2+, whereas their dissociation constants remain almost constant. This behavior has been termed distal. Mg2+ has a specific effect on r(CACCUGGCGACAGGUG), the magnitude of which is progressively modulated from the proximal region of the 16-mer towards its distal region. For r(GGCCAAAAGCC), an intermediate behavior is found for base-pairs r(G565•C) and r(G572•C). Their lifetimes are slightly higher in the presence of Mg2+ and their dissociation constants are significantly lower, a behavior resembling that of the 16-mer proximal region. These results indicate that Mg2+ diffusively moves around r(GGCCAAAAGCC).

Original languageEnglish (US)
Pages (from-to)61-68
Number of pages8
JournalJournal of Biological Physics
Volume37
Issue number1
DOIs
StatePublished - Jan 1 2011

Keywords

  • Base-pair kinetics
  • EMCV IRES
  • GNRA tetraloop
  • Imino proton exchange
  • Mg
  • NMR
  • RAAA hairpin motif

ASJC Scopus subject areas

  • Biophysics
  • Atomic and Molecular Physics, and Optics
  • Molecular Biology
  • Cell Biology

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