Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G·C) base-pair kinetics
Identifieur interne : 002875 ( Main/Exploration ); précédent : 002874; suivant : 002876Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G·C) base-pair kinetics
Auteurs : J. A. Dupont [Belgique] ; K. Snoussi [Belgique]Source :
- Journal of Biological Physics [ 0092-0606 ] ; 2009-08-01.
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Abstract
Abstract: 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·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·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·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.
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DOI: 10.1007/s10867-009-9151-2
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A." last="Dupont">J. A. Dupont</name><affiliation wicri:level="3"><country xml:lang="fr">Belgique</country><wicri:regionArea>Free University of Brussels, 1050, Brussels</wicri:regionArea><placeName><settlement type="city">Bruxelles</settlement><region nuts="2">Région de Bruxelles-Capitale</region></placeName></affiliation></author><author><name sortKey="Snoussi, K" sort="Snoussi, K" uniqKey="Snoussi K" first="K." last="Snoussi">K. Snoussi</name><affiliation wicri:level="1"><country xml:lang="fr">Belgique</country><wicri:regionArea>Catholic University of Louvain, 1348, Louvain-la-Neuve</wicri:regionArea><wicri:noRegion>Louvain-la-Neuve</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Belgique</country></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Biological Physics</title><title level="j" type="abbrev">J Biol Phys</title><idno type="ISSN">0092-0606</idno><idno type="eISSN">1573-0689</idno><imprint><publisher>Springer Netherlands</publisher><pubPlace>Dordrecht</pubPlace><date type="published" when="2009-08-01">2009-08-01</date><biblScope unit="volume">35</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="231">231</biblScope><biblScope unit="page" to="243">243</biblScope></imprint><idno type="ISSN">0092-0606</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0092-0606</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base-pair kinetics</term><term>EMCV IRES</term><term>GNRA tetraloop</term><term>Imino proton exchange</term><term>Mg2 + </term><term>NMR</term><term>RAAA hairpin motif</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: 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·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·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·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.</div></front></TEI><affiliations><list><country><li>Belgique</li></country><region><li>Région de Bruxelles-Capitale</li></region><settlement><li>Bruxelles</li></settlement></list><tree><country name="Belgique"><region name="Région de Bruxelles-Capitale"><name sortKey="Dupont, J A" sort="Dupont, J A" uniqKey="Dupont J" first="J. A." last="Dupont">J. A. Dupont</name></region><name sortKey="Snoussi, K" sort="Snoussi, K" uniqKey="Snoussi K" first="K." last="Snoussi">K. Snoussi</name><name sortKey="Snoussi, K" sort="Snoussi, K" uniqKey="Snoussi K" first="K." last="Snoussi">K. Snoussi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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