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Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G center dot C) base-pair kinetics

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Dupont, J. A. [Université Libre de Bruxelles (ULB)] Snoussi, Karim [UCL - SC/CHIM - Département de Chimie]

NMR magnetization transfer from water and ammonia-catalyzed exchange of the imino proton have been used to probe enhanced thermostability and conformational rearrangements induced by Mg2 + in two key activity fragments r(CACCUGGCGACAGGUG) and r(GGCCAAAAGCC) of the encephalomyocarditis virus (EMCV) picornavirus internal ribosome entry site (IRES). We have measured some of their r(G center dot C) base-pair lifetimes and dissociation constants under different MgCl2 conditions, and we compare them with those of other short RNA duplexes. The RNA fragment r(CACCUGGCGACAGGUG) adopts two topologies, a palindromic duplex with two conformations and a hairpin, whose equilibrium can be monitored: the duplex form is destabilized by Mg2 + and temperature, a delicate balance wherein the entropic contribution of the free energy helps populate the hairpin state. For both fragments, the opening rates of the r(G center dot C) pairs are lower in the presence of Mg2 + and their dissociation constants are smaller or comparable. Analysis of the results suggests that Mg2 + has a preferential and specific effect on the r(CACCUGGCGACAGGUG) hairpin in the region close to the r(G center dot C) closing pair of the GCGA tetraloop, and the ion moves diffusively around r(GGCCAAAAGCC), thereby differentiating the GNRA and RAAA hairpin motifs that are both involved in the biological regulation functions of the EMCV IRES.

Document type Article de périodique (Journal article) – Article de recherche
Access type Accès restreint
Publication date 2009
Language Anglais
Journal information "Journal of Biological Physics : an international journal for the formulation and application of physical and mathematical models in the biological sciences" - Vol. 35, no. 3, p. 231-243 (2009)
Peer reviewed yes
Publisher Springer (Dordrecht)
issn 0092-0606
e-issn 1573-0689
Publication status Publié
Affiliation UCL
Keywords Base-pair kinetics ; EMCV IRES ; GNRA tetraloop ; Imino proton exchange ; Mg2+ ; NMR ; RAAA hairpin motif
Links
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Bibliographic reference Dupont, J. A. ; Snoussi, Karim. Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G center dot C) base-pair kinetics. In: Journal of Biological Physics : an international journal for the formulation and application of physical and mathematical models in the biological sciences, Vol. 35, no. 3, p. 231-243 (2009)
Permanent URL http://hdl.handle.net/2078.1/35456