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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
  • 70 Downloads

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 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).

Keywords

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

Notes

Acknowledgements

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).

References

  1. 1.
    Dupont, J.A., Snoussi, K.: Mg2 +  modulation of EMCV IRES key activity fragment equilibria and r(G·C) base-pair kinetics. J. Biol. Phys. 35, 231–243 (2009)CrossRefGoogle Scholar
  2. 2.
    Hermann, T., Westhof, E.: Exploration of metal binding sites in RNA folds by Brownian-dynamics simulations. Structure 6, 1303–1314 (1998)CrossRefGoogle Scholar
  3. 3.
    Searle, M.S., William, D.H.: On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res. 21, 2051–2056 (1993)CrossRefGoogle Scholar
  4. 4.
    Jucker, F.M., Heus, H.A., Yip, P.F., Moors, E.H.M., Pardi, A.: A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol. 264, 968–980 (1996)CrossRefGoogle Scholar
  5. 5.
    Uhlenbeck, O.C.: Nucleic-acid structure tetraloops and RNA folding. Nature 20, 613–614 (1990)CrossRefADSGoogle Scholar
  6. 6.
    Antao, V.P., Tinoco, I. Jr.: Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res. 20, 819–824 (1992)CrossRefGoogle Scholar

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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