Double Electron–Electron Resonance (DEER): A Convenient Method To Probe DNA Conformational Changes

Département de Recherche Fondamentale sur la Matière, Condensée, Laboratoire de Chimie Inorganique et Biologique, UMR-E no 3 CEA-UJF, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France.
Angewandte Chemie International Edition (Impact Factor: 11.26). 01/2008; 47(4):735-7. DOI: 10.1002/anie.200704133
Source: PubMed

ABSTRACT Die DEER-Technik offenbart selbst kleine Konformationsänderungen in gezielt spinmarkierten DNA-Strukturen und ist herkömmlichen Methoden hierin überlegen. Der B-A-Übergang (siehe Bild) in DNA-Doppelsträngen wird durch Trifluorethanol induziert. DEER kann eingesetzt werden, um die DNA-Modifizierung durch verschiedene Agentien zu untersuchen.

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Available from: Yves Boulard, Apr 17, 2015
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    • "EPR spectroscopy in combination with SDSL has been shown to be ideally suited to elucidate the conformations and conformational dynamics of biological systems such as proteins, protein complexes, DNA, and RNA under physiological conditions (Hubbell et al. 2000; Cai et al. 2006; Bordignon and Steinhoff 2007). By means of spin labeled folded DNA or RNA a nanometer distance ruler was developed (Schiemann et al. 2003, 2004; Piton et al. 2005), B/A conformational transitions of DNA (Sicoli et al. 2008), and DNA damages (Sicoli et al. 2009) were studied by double electron-electron resonance (DEER) spectroscopy (Jeschke and Polyhach 2007) showing its high sensitivity toward small structural changes. In the present study, we apply this technique to examine the dynamics and conformational transition of the spin labeled Tc aptamer upon ligand binding. "
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    ABSTRACT: RNA aptamers are in vitro-selected binding domains that recognize their respective ligand with high affinity and specificity. They are characterized by complex three-dimensional conformations providing preformed binding pockets that undergo conformational changes upon ligand binding. Small molecule-binding aptamers have been exploited as synthetic riboswitches for conditional gene expression in various organisms. In the present study, double electron-electron resonance (DEER) spectroscopy combined with site-directed spin labeling was used to elucidate the conformational transition of a tetracycline aptamer upon ligand binding. Different sites were selected for post-synthetic introduction of either the (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate by reaction with a 4-thiouridine modified RNA or of 4-isocyanato-2,6-tetramethylpiperidyl-N-oxid spin label by reaction with 2'-aminouridine modified RNA. The results of the DEER experiments indicate the presence of a thermodynamic equilibrium between two aptamer conformations in the free state and capture of one conformation upon tetracycline binding.
    RNA 01/2011; 17(1):182-8. DOI:10.1261/rna.2222811 · 4.94 Impact Factor
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    • "Recently, we have shown that using DEER experiments combined with molecular dynamics simulations, we were able to follow B-form to A-form conformational changes [4]. We observed an excellent agreement between the experimental distances and the predicted ones. "
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    ABSTRACT: we use Double Electron-Electron Resonance (DEER) combined to molecular dynamics simulations to study conformational changes induced in DNA duplexes by selective damages. This study confirms the good agreement obtained between measured and calculated spin-spin distances and provides information on the structural changes undergoned by DNA.
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