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

Dupont, Julien; Snoussi, Karim

doi:10.1007/s10867-009-9151-2

Cited by 8 publications

(11 citation statements)

References 22 publications

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“…In contrast, we have also shown that the EMCV IRES key activity RNA fragment r(GGCCAAAAGCC) containing the AAAA submotif adopts only a hairpin topology [1]. The present paper is an extension of our earlier article [1]. It completes the experimental study of Mg 2+ effects on the two RNA fragments r(CACCUGGCGACAGGUG) and r(GGCCAAAAGCC) (see Fig.…”

Section: Introductionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 52%

“…Imino proton exchange theory, oligonucleotide synthesis, and the NMR methods used have already been described [1].…”

Section: Methodsmentioning

confidence: 99%

“…To reach this situation, both samples were heated to 90 • C for 3 min, rapidly cooled in an ice-water bath, and subsequently kept at 4 • C. The hairpin/duplex interconversion rates are extremely low under such conditions [1]. The addition of Mg 2+ was carried out by adding microliter volumes from MgCl 2 stock solutions, such that the stoichiometries of Mg 2+ to RNA were in a ratio of 1, 2, or 3.…”

Section: Sample Preparationmentioning

confidence: 99%

“…We have recently established that the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) key activity RNA fragment r(CACCUGGCGACAGGUG), containing the GCGA tetraloop, adopts two topologies [1], a palindromic duplex with two conformations and a monomeric hairpin; the duplex form is destabilized by addition of Mg 2+ and by temperature increase, the hairpin lifetime is around 6 months. In contrast, we have also shown that the EMCV IRES key activity RNA fragment r(GGCCAAAAGCC) containing the AAAA submotif adopts only a hairpin topology [1].…”

Section: Introductionmentioning

confidence: 99%

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Effects of magnesium ions on two EMCV IRES key activity fragments

Dupont¹,

Snoussi

2010

J Biol Phys

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Using NMR magnetization transfer from water and ammonia-catalyzed exchange of the imino protons, changes have been monitored in base-pair kinetics induced by Mg 2+ in two key activity fragments r(CACCUGGCGACAGGUG) and r(GGCCAAAAGCC) of the encephalomyocarditis virus internal ribosome entry site. For r(CACCUGGCGACAGGUG), the addition of Mg 2+ reveals two types of base-pairs: r(U 545 ·A) and r(G 546 ·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(G 553 ·C) and r(G 554 ·C), in the second category, have lifetimes substantially higher in the presence of Mg 2+ , whereas their dissociation constants remain almost constant. This behavior has been termed distal. Mg 2+ 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(G 565 ·C) and r(G 572 ·C). Their lifetimes are slightly higher in the presence of Mg 2+ and their dissociation constants are significantly lower, a behavior resembling that of the 16-mer proximal region. These results indicate that Mg 2+ diffusively moves around r(GGCCAAAAGCC).Keywords Base-pair kinetics · EMCV IRES · GNRA tetraloop · Imino proton exchange · Mg 2+ · NMR · RAAA hairpin motif

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Section: Introductionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 52%

“…Imino proton exchange theory, oligonucleotide synthesis, and the NMR methods used have already been described [1].…”

Section: Methodsmentioning

confidence: 99%

Section: Sample Preparationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Effects of magnesium ions on two EMCV IRES key activity fragments

Dupont¹,

Snoussi

2010

J Biol Phys

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RNA Dynamics by NMR Spectroscopy

2019

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An ever‐increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so‐called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined—Lego like—than in proteins, hence the numerous revelations of RNA excited states.

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Viral internal ribosomal entry sites: four classes for one goal

2017

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To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. WIREs RNA 2018, 9:e1458. doi: 10.1002/wrna.1458 This article is categorized under: Translation > Ribosome Structure/Function Translation > Translation Mechanisms RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

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

Cited by 8 publications

References 22 publications

Effects of magnesium ions on two EMCV IRES key activity fragments

Effects of magnesium ions on two EMCV IRES key activity fragments

RNA Dynamics by NMR Spectroscopy

Viral internal ribosomal entry sites: four classes for one goal

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