Journal of Biological Physics

, Volume 37, Issue 1, pp 61–68 | Cite as

Effects of magnesium ions on two EMCV IRES key activity fragments

  • Julien A. Dupont
  • Karim Snoussi
Original Paper


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 Mg2 + , 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).


Base-pair kinetics EMCV IRES GNRA tetraloop Imino proton exchange Mg2 +  NMR RAAA hairpin motif 



Julien A. Dupont is a recipient of a studentship from the Fonds pour la formation à la Recherche dans l’Industrie et l’Agriculture. This work was supported by the Belgian National Foundation for Scientific Research and the Catholic University of Louvain (Fonds Spéciaux de Recherche).


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Free University of BrusselsBrusselsBelgium
  2. 2.Catholic University of LouvainLouvain-la-NeuveBelgium
  3. 3.Japan Science and Technology AgencySendaiJapan

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