1
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Dantu SC, Khalil M, Bria M, Saint-Pierre C, Orio M, Gasparutto D, Sicoli G. Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions. Adv Sci (Weinh) 2024; 11:e2306710. [PMID: 38419268 DOI: 10.1002/advs.202306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/15/2024] [Indexed: 03/02/2024]
Abstract
A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.
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Affiliation(s)
- Sarath Chandra Dantu
- Department of Computer Science, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Mahdi Khalil
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Marc Bria
- Michle-Eugène Chevreul Institute, FR 2638, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Maylis Orio
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, UMR CNRS 7313, Marseille, 13397, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Giuseppe Sicoli
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
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2
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Zerbetto M, Saint-Pierre C, Piserchia A, Torrengo S, Gambarelli S, Abergel D, Polimeno A, Gasparutto D, Sicoli G. Intrinsic Flexibility beyond the Highly Ordered DNA Tetrahedron: An Integrative Spectroscopic and Molecular Dynamics Approach. J Phys Chem Lett 2023; 14:10032-10038. [PMID: 37906734 DOI: 10.1021/acs.jpclett.3c02383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process. To address such an issue, spin-labeled DNA sequences are chemically synthesized, self-assembled, and then analyzed by Continuous-Wave (CW) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopy. Interspin distance measurements based on PELDOR/DEER techniques combined with molecular dynamics (MD) thus revealed unexpected dynamic heterogeneity and flexibility of the assembled structures. The observation of flexibility in these ordered 3D structures demonstrates the sensitivity of this approach and its effectiveness in accessing the main dynamic and structural features with unprecedented resolution.
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Affiliation(s)
- Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Andrea Piserchia
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Simona Torrengo
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Daniel Abergel
- Laboratoire des biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Antonino Polimeno
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Giuseppe Sicoli
- CNRS UMRS 8516, LASIRE, University of Lille, Avenue Paul Langevin - C4 building, F-59655 Villeneuve d'Ascq Cedex, France
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3
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Yadav R, Kwon Y, Rivaux C, Saint-Pierre C, Ling WL, Reiss P. Narrow Near-Infrared Emission from InP QDs Synthesized with Indium(I) Halides and Aminophosphine. J Am Chem Soc 2023; 145:5970-5981. [PMID: 36866828 DOI: 10.1021/jacs.2c13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Nonpyrophoric aminophosphines reacted with indium(III) halides in the presence of zinc chloride have emerged as promising phosphorus precursors in the synthesis of colloidal indium phosphide (InP) quantum dots (QDs). Nonetheless, due to the required P/In ratio of 4:1, it remains challenging to prepare large-sized (>5 nm), near-infrared absorbing/emitting InP QDs using this synthetic scheme. Furthermore, the addition of zinc chloride leads to structural disorder and the formation of shallow trap states inducing spectral broadening. To overcome these limitations, we introduce a synthetic approach relying on the use of indium(I) halide, which acts as both the indium source and reducing agent for aminophosphine. The developed zinc-free, single-injection method gives access to tetrahedral InP QDs with an edge length > 10 nm and narrow size distribution. The first excitonic peak is tunable from 450 to 700 nm by changing the indium halide (InI, InBr, InCl). Kinetic studies using phosphorus NMR reveal the coexistence of two reaction pathways, the reduction of transaminated aminophosphine by In(I) and via redox disproportionation. Etching the surface of the obtained InP QDs at room temperature with in situ-generated hydrofluoric acid (HF) leads to strong photoluminescence (PL) emission with a quantum yield approaching 80%. Alternatively, surface passivation of the InP core QDs was achieved by low-temperature (140 °C) ZnS shelling using the monomolecular precursor zinc diethyldithiocarbamate. The obtained InP/ZnS core/shell QDs that emit in a range of 507-728 nm exhibit a small Stokes shift (110-120 meV) and a narrow PL line width (112 meV at 728 nm).
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Affiliation(s)
- Ranjana Yadav
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Yongju Kwon
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Céline Rivaux
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | | | - Wai Li Ling
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Peter Reiss
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
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4
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Seck A, De Bonis S, Stelter M, Ökvist M, Senarisoy M, Hayek MR, Le Roy A, Martin L, Saint-Pierre C, Silveira CM, Gasparutto D, Todorovic S, Ravanat JL, Timmins J. Structural and functional insights into the activation of the dual incision activity of UvrC, a key player in bacterial NER. Nucleic Acids Res 2023; 51:2931-2949. [PMID: 36869664 PMCID: PMC10085695 DOI: 10.1093/nar/gkad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/10/2023] [Accepted: 02/06/2023] [Indexed: 03/05/2023] Open
Abstract
Bacterial nucleotide excision repair (NER), mediated by the UvrA, UvrB and UvrC proteins is a multistep, ATP-dependent process, that is responsible for the removal of a very wide range of chemically and structurally diverse DNA lesions. DNA damage removal is performed by UvrC, an enzyme possessing a dual endonuclease activity, capable of incising the DNA on either side of the damaged site to release a short single-stranded DNA fragment containing the lesion. Using biochemical and biophysical approaches, we have probed the oligomeric state, UvrB- and DNA-binding abilities and incision activities of wild-type and mutant constructs of UvrC from the radiation resistant bacterium, Deinococcus radiodurans. Moreover, by combining the power of new structure prediction algorithms and experimental crystallographic data, we have assembled the first model of a complete UvrC, revealing several unexpected structural motifs and in particular, a central inactive RNase H domain acting as a platform for the surrounding domains. In this configuration, UvrC is maintained in a 'closed' inactive state that needs to undergo a major rearrangement to adopt an 'open' active state capable of performing the dual incision reaction. Taken together, this study provides important insight into the mechanism of recruitment and activation of UvrC during NER.
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Affiliation(s)
- Anna Seck
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, SyMMES-UMR 5819, F-38000 Grenoble, France
| | | | - Meike Stelter
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France.,European Synchrotron Radiation Facility, F-38000 Grenoble, France
| | - Mats Ökvist
- European Synchrotron Radiation Facility, F-38000 Grenoble, France
| | - Müge Senarisoy
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Aline Le Roy
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Célia M Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS, SyMMES-UMR 5819, F-38000 Grenoble, France
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS, SyMMES-UMR 5819, F-38000 Grenoble, France
| | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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5
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Moinel A, Brochnow M, Aumaître C, Giannoudis E, Fize J, Saint-Pierre C, Pécaut J, Maldivi P, Artero V, Demadrille R, Chavarot-Kerlidou M. Push-pull organic dyes and dye-catalyst assembly featuring a benzothiadiazole unit for photoelectrochemical hydrogen production. Sustain Energy Fuels 2022; 6:3565-3572. [PMID: 35979141 PMCID: PMC9337615 DOI: 10.1039/d2se00292b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
In this work, we report the design and the preparation of two new dyes and a molecular dyad for the photoelectrochemical hydrogen production from water in a dye-sensitized photoelectrochemical cell (DSPEC). We designed dyes that include a benzothiadiazole (BTD) and an indacenodithiophene (IDT) units, and we obtained a new molecular dyad by covalent coupling with the cobalt diimine-dioxime catalyst. The introduction of the benzothiadiazole core in the structure improves the absorption properties and leads to an extension of the spectrum in the visible range up to 650 nm. The photoelectrochemical properties of the new dyad were evaluated on pristine and lithium-doped NiO electrodes. We demonstrate that increasing the light harvesting efficiency of the dyad by introducing a IDT-BTD chromophore is clearly beneficial for the photoelectrochemical activity. We also demonstrate that lithium doping of NiO, which improves the electronic conductivity of the mesoporous film, leads to a significant increase in performance, in terms of TON and F.E., more than doubled with our new dyad. This BTD-based molecular system outperforms the results of previously reported dyads using the same catalyst.
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Affiliation(s)
- A Moinel
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux 17 rue des Martyrs F-38000 Grenoble France
| | - M Brochnow
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
| | - C Aumaître
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
| | - E Giannoudis
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux 17 rue des Martyrs F-38000 Grenoble France
| | - J Fize
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux 17 rue des Martyrs F-38000 Grenoble France
| | - C Saint-Pierre
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
| | - J Pécaut
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
| | - P Maldivi
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
| | - V Artero
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux 17 rue des Martyrs F-38000 Grenoble France
| | - R Demadrille
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, SyMMES 17 rue des martyrs 38000 Grenoble France
| | - M Chavarot-Kerlidou
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux 17 rue des Martyrs F-38000 Grenoble France
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6
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Lena A, Benassi A, Stasi M, Saint-Pierre C, Freccero M, Gasparutto D, Bombard S, Doria F, Verga D. Photoactivatable V-Shaped Bifunctional Quinone Methide Precursors as a New Class of Selective G-quadruplex Alkylating Agents. Chemistry 2022; 28:e202200734. [PMID: 35441438 PMCID: PMC9322314 DOI: 10.1002/chem.202200734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 12/22/2022]
Abstract
Combining the selectivity of G‐quadruplex (G4) ligands with the spatial and temporal control of photochemistry is an emerging strategy to elucidate the biological relevance of these structures. In this work, we developed six novel V‐shaped G4 ligands that can, upon irradiation, form stable covalent adducts with G4 structures via the reactive intermediate, quinone methide (QM). We thoroughly investigated the photochemical properties of the ligands and their ability to generate QMs. Subsequently, we analyzed their specificity for various topologies of G4 and discovered a preferential binding towards the human telomeric sequence. Finally, we tested the ligand ability to act as photochemical alkylating agents, identifying the covalent adducts with G4 structures. This work introduces a novel molecular tool in the chemical biology toolkit for G4s.
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Affiliation(s)
- Alberto Lena
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Alessandra Benassi
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Michele Stasi
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy.,Present Address: Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | | | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Didier Gasparutto
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES-UMR5819, 38054, Grenoble, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, 91405, Orsay, France
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, 91405, Orsay, France
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7
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Giannoudis E, Bold S, Müller C, Schwab A, Bruhnke J, Queyriaux N, Gablin C, Leonard D, Saint-Pierre C, Gasparutto D, Aldakov D, Kupfer S, Artero V, Dietzek B, Chavarot-Kerlidou M. Hydrogen Production at a NiO Photocathode Based on a Ruthenium Dye-Cobalt Diimine Dioxime Catalyst Assembly: Insights from Advanced Spectroscopy and Post-operando Characterization. ACS Appl Mater Interfaces 2021; 13:49802-49815. [PMID: 34637266 DOI: 10.1021/acsami.1c12138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The production of hydrogen by efficient, low-cost, and integrated photoelectrochemical water splitting processes represents an important target for the ecological transition. This challenge can be addressed thanks to bioinspired chemistry and artificial photosynthesis approaches by designing dye-sensitized photocathodes for hydrogen production, incorporating bioinspired first-row transition metal-based catalysts. The present work describes the preparation and photoelectrochemical characterization of a NiO photocathode sensitized with a phosphonate-derivatized ruthenium tris-diimine photosensitizer covalently linked to a cobalt diimine dioxime hydrogen-evolving catalyst. Under simulated AM 1.5G irradiation, hydrogen is produced with photocurrent densities reaching 84 ± 7 μA·cm-2, which is among the highest values reported so far for dye-sensitized photocathodes with surface-immobilized catalysts. Thanks to the unique combination of advanced spectroscopy and surface characterization techniques, the fast desorption of the dyad from the NiO electrode and the low yield of electron transfer to the catalyst, resulting in the Co demetallation from the diimine dioxime framework, were identified as the main barriers limiting the performances and the stability of the system. This work therefore paves the way for a more rational design of molecular photocathodes for solar fuel production and represents a further step toward the development of sustainable processes for the production of hydrogen from sunlight and water.
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Affiliation(s)
- Emmanouil Giannoudis
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Sebastian Bold
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 17 rue des Martyrs, F-38000 Grenoble, France
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Department Functional Interfaces, Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Philosophenweg 8, 07743 Jena, Germany
| | - Carolin Müller
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Department Functional Interfaces, Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Philosophenweg 8, 07743 Jena, Germany
| | - Alexander Schwab
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Jakob Bruhnke
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Nicolas Queyriaux
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Corinne Gablin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5, rue de la Doua, F-69100 Villeurbanne, France
| | - Didier Leonard
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5, rue de la Doua, F-69100 Villeurbanne, France
| | | | - Didier Gasparutto
- Univ. Grenoble Alpes, CNRS, CEA IRIG, SyMMES, F-38000 Grenoble, France
| | - Dmitry Aldakov
- Univ. Grenoble Alpes, CNRS, CEA IRIG, SyMMES, F-38000 Grenoble, France
| | - Stephan Kupfer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Vincent Artero
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Benjamin Dietzek
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Department Functional Interfaces, Leibniz Institute of Photonic Technology Jena (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Center for Energy and Environmental Chemistry Jena (CEEC Jena), Friedrich Schiller University Jena, Philosophenweg 8, 07743 Jena, Germany
| | - Murielle Chavarot-Kerlidou
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 17 rue des Martyrs, F-38000 Grenoble, France
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8
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Lu C, Saint-Pierre C, Gasparutto D, Roupioz Y, Ravelet C, Peyrin E, Buhot A. Melting Curve Analysis of Aptachains: Adenosine Detection with Internal Calibration. Biosensors (Basel) 2021; 11:112. [PMID: 33917864 PMCID: PMC8068264 DOI: 10.3390/bios11040112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022]
Abstract
Small molecules are ubiquitous in nature and their detection is relevant in various domains. However, due to their size, sensitive and selective probes are difficult to select and the detection methods are generally indirect. In this study, we introduced the use of melting curve analysis of aptachains based on split-aptamers for the detection of adenosine. Aptamers, short oligonucleotides, are known to be particularly efficient probes compared to antibodies thanks to their advantageous probe/target size ratio. Aptachains are formed from dimers with dangling ends followed by the split-aptamer binding triggered by the presence of the target. The high melting temperature of the dimers served as a calibration for the detection/quantification of the target based on the height and/or temperature shift of the aptachain melting peak.
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Affiliation(s)
- Chenze Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China;
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Christine Saint-Pierre
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Didier Gasparutto
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Yoann Roupioz
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Corinne Ravelet
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Eric Peyrin
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Arnaud Buhot
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
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9
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Taipakova S, Kuanbay A, Saint-Pierre C, Gasparutto D, Baiken Y, Groisman R, Ishchenko AA, Saparbaev M, Bissenbaev AK. The Arabidopsis thaliana Poly(ADP-Ribose) Polymerases 1 and 2 Modify DNA by ADP-Ribosylating Terminal Phosphate Residues. Front Cell Dev Biol 2020; 8:606596. [PMID: 33324653 PMCID: PMC7726343 DOI: 10.3389/fcell.2020.606596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyze the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are viewed as DNA damage sensors that, upon binding to strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. The flowering plant Arabidopsis thaliana contains three genes encoding homologs of mammalian PARPs: atPARP1, atPARP2, and atPARP3. Both atPARP1 and atPARP2 contain poly(ADP-ribosyl)ating activity; however, it is unknown whether they could covalently modify DNA by ADP-ribosylating the strand break termini. Here, we report that similar to their mammalian counterparts, the plant atPARP1 and atPARP2 proteins ADP-ribosylate 5′-terminal phosphate residues in duplex DNA oligonucleotides and plasmid containing at least two closely spaced DNA strand breaks. AtPARP1 preferentially catalyzes covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 5′-phosphate, whereas atPARP2 preferentially ADP-ribosylates the nicked and gapped DNA duplexes containing the terminal 5′-phosphate. Similar to their mammalian counterparts, the plant PARP-catalyzed DNA ADP-ribosylation is particularly sensitive to the distance that separates two strand breaks in the same DNA molecule, 1.5 and 1 or 2 turns of helix for atPARP1 and atPARP2, respectively. PAR glycohydrolase (PARG) restored native DNA structure by hydrolyzing the PAR–DNA adducts generated by atPARPs. Biochemical and mass spectrometry analyses of the PAR–DNA adducts showed that atPARPs utilize phosphorylated DNA termini as an alternative to protein acceptor residues to catalyze PAR chain synthesis via phosphodiester bond formation between C1′ of ADP-ribose and a phosphate residue of the terminal nucleotide in DNA fragment. Taken together, these data establish the presence of a new type of DNA-modifying activity in Arabidopsis PARPs, suggesting a possible role of DNA ADP-ribosylation in DNA damage signaling and repair of terrestrial plants.
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Affiliation(s)
- Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigerim Kuanbay
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | | | - Didier Gasparutto
- CEA, CNRS, IRIG/SyMMES-UMR 5819/CREAB, Université Grenoble Alpes, Grenoble, France
| | - Yeldar Baiken
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Regina Groisman
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Alexander A Ishchenko
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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10
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Delices A, Moodelly D, Hurot C, Hou Y, Ling WL, Saint-Pierre C, Gasparutto D, Nogues G, Reiss P, Kheng K. Aqueous Synthesis of DNA-Functionalized Near-Infrared AgInS 2/ZnS Core/Shell Quantum Dots. ACS Appl Mater Interfaces 2020; 12:44026-44038. [PMID: 32840358 DOI: 10.1021/acsami.0c11337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Biocompatibility, biofunctionality, and chemical stability are essential criteria to be fulfilled by quantum dot (QD) emitters for bio-imaging and -sensing applications. In addition to these criteria, achieving efficient near-infrared (NIR) emission with nontoxic QDs remains very challenging. In this perspective, we developed water-soluble NIR-emitting AgInS2/ZnS core/shell (AIS/ZnS) QDs functionalized with DNA. The newly established aqueous route relying on a two-step hot-injection synthesis led to highly luminescent chalcopyrite-type AIS/ZnS core/shell QDs with an unprecedented photoluminescence quantum yield (PLQY) of 55% at 700 nm and a long photoluminescence (PL) decay time of 900 ns. Fast and slow hot injection of the precursors were compared for the AIS core QD synthesis, yielding a completely different behavior in terms of size, size distribution, stoichiometry, and crystal structure. The PL peak positions of both types of core QDs were 710 (fast) and 760 nm (slow injection) with PLQYs of 36 and 8%, respectively. The slow and successive incorporation of the Zn and S precursors during the subsequent shell growth step on the stronger emitting cores promoted the formation of a three-monolayer thick ZnS shell, evidenced by the increase of the average QD size from 3.0 to 4.8 nm. Bioconjugation of the AIS/ZnS QDs with hexylthiol-modified DNA was achieved during the ZnS shell growth, resulting in a grafting level of 5-6 DNA single strands per QD. The successful chemical conjugation of DNA was attested by UV-vis spectroscopy and agarose gel electrophoresis. Importantly, surface plasmon resonance imaging experiments using complementary DNA strands further corroborated the successful coupling and the stability of the AIS/ZnS-DNA QD conjugates as well as the preservation of the biological activity of the anchored DNA. The strong NIR emission and biocompatibility of these AIS/ZnS-DNA QDs provide a high potential for their use in biomedical applications.
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Affiliation(s)
- Annette Delices
- Université Grenoble Alpes, CEA, CNRS, IRIG, PHELIQS, Grenoble F-38000, France
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, Grenoble F-38000, France
| | - Davina Moodelly
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, Grenoble F-38000, France
| | - Charlotte Hurot
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, Grenoble F-38000, France
| | - Yanxia Hou
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, Grenoble F-38000, France
| | - Wai Li Ling
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
| | | | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, Grenoble F-38000, France
| | - Gilles Nogues
- University Grenoble Alpes, CNRS, Institut Néel, Grenoble F-38000, France
| | - Peter Reiss
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, Grenoble F-38000, France
| | - Kuntheak Kheng
- Université Grenoble Alpes, CEA, CNRS, IRIG, PHELIQS, Grenoble F-38000, France
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11
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Taverna Porro ML, Saint-Pierre C, Gasparutto D, Ravanat JL. Solid-phase synthesis of branched oligonucleotides containing a biologically relevant dCyd341 interstrand crosslink DNA lesion. Org Biomol Chem 2020; 18:1892-1899. [PMID: 31960874 DOI: 10.1039/c9ob01021a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Branched oligonucleotides containing a biologically relevant DNA lesion, dCyd341, which involves an interstrand crosslink between a cytosine base on one strand and a ribose moiety on the opposite strand, were prepared in a single automated solid-phase synthesis. For this, we first prepared the phosphoramidite analogue of dCyd341 bearing an orthogonal levulinyl protecting group. Then, following the synthesis of the first DNA strand containing dCyd341, the levulinic group was removed and the synthesis was then continued from the free base hydroxyl group at the branching point, using traditional phosphoramidites. The synthesized oligonucleotides were fully characterized by MALDI-TOF/MS and were enzymatically digested, and the presence of the lesion was confirmed by HPLC-MS/MS and the sequence was finally controlled upon exonuclease digestion followed by MALDI-TOF/MS analysis. The developed strategy was successfully employed for the preparation of several short linear and branched oligonucleotides containing the aforementioned lesion.
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Affiliation(s)
| | | | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS IRIG/SyMMES, F-38054 Grenoble Cedex 9, France.
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes, CEA, CNRS IRIG/SyMMES, F-38054 Grenoble Cedex 9, France.
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12
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Zarkovic G, Belousova EA, Talhaoui I, Saint-Pierre C, Kutuzov MM, Matkarimov BT, Biard D, Gasparutto D, Lavrik OI, Ishchenko AA. Characterization of DNA ADP-ribosyltransferase activities of PARP2 and PARP3: new insights into DNA ADP-ribosylation. Nucleic Acids Res 2019; 46:2417-2431. [PMID: 29361132 PMCID: PMC5861426 DOI: 10.1093/nar/gkx1318] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/28/2017] [Indexed: 12/22/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) act as DNA break sensors and catalyze the synthesis of polymers of ADP-ribose (PAR) covalently attached to acceptor proteins at DNA damage sites. It has been demonstrated that both mammalian PARP1 and PARP2 PARylate double-strand break termini in DNA oligonucleotide duplexes in vitro. Here, we show that mammalian PARP2 and PARP3 can PARylate and mono(ADP-ribosyl)ate (MARylate), respectively, 5′- and 3′-terminal phosphate residues at double- and single-strand break termini of a DNA molecule containing multiple strand breaks. PARP3-catalyzed DNA MARylation can be considered a new type of reversible post-replicative DNA modification. According to DNA substrate specificity of PARP3 and PARP2, we propose a putative mechanistic model of PARP-catalyzed strand break–oriented ADP-ribosylation of DNA termini. Notably, PARP-mediated DNA ADP-ribosylation can be more effective than PARPs’ auto-ADP-ribosylation depending on the DNA substrates and reaction conditions used. Finally, we show an effective PARP3- or PARP2-catalyzed ADP-ribosylation of high-molecular-weight (∼3-kb) DNA molecules, PARP-mediated DNA PARylation in cell-free extracts and a persisting signal of anti-PAR antibodies in a serially purified genomic DNA from bleomycin-treated poly(ADP-ribose) glycohydrolase-depleted HeLa cells. These results suggest that certain types of complex DNA breaks can be effectively ADP-ribosylated by PARPs in cellular response to DNA damage.
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Affiliation(s)
- Gabriella Zarkovic
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Ekaterina A Belousova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Ibtissam Talhaoui
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, INAC/SyMMES-UMR5819/CREAB, F-38000 Grenoble, France
| | - Mikhail M Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Bakhyt T Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Denis Biard
- CEA, Institut de Biologie François Jacob, SEPIA, Team Cellular Engineering and Human Syndromes, Université Paris-Saclay, F-92265 Fontenay-aux-Roses, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, INAC/SyMMES-UMR5819/CREAB, F-38000 Grenoble, France
| | - Olga I Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
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13
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Labbe C, Martel S, Fournier B, Saint-Pierre C. P1.15-13 Wait Times for Diagnosis and Treatment of Lung Cancer Across the Province of Quebec, Canada. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Malfatti MC, Balachander S, Antoniali G, Koh KD, Saint-Pierre C, Gasparutto D, Chon H, Crouch RJ, Storici F, Tell G. Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Nucleic Acids Res 2017; 45:11193-11212. [PMID: 28977421 PMCID: PMC5737539 DOI: 10.1093/nar/gkx723] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoside 5′-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3′-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,University of California, San Francisco, UCSF, School of Medicine, San Francisco, CA, USA
| | - Christine Saint-Pierre
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Didier Gasparutto
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Hyongi Chon
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
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15
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Lu C, Saint-Pierre C, Gasparutto D, Roupioz Y, Peyrin E, Buhot A. Linear Chain Formation of Split-Aptamer Dimers on Surfaces Triggered by Adenosine. Langmuir 2017; 33:12785-12792. [PMID: 29035542 DOI: 10.1021/acs.langmuir.7b02104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The detection of small molecules impacts various fields; however, their small size and low concentration are usually the cause of limitations in their detection. Thus, the need for biosensors with appropriate probes and signal amplification strategies is required. Aptamers are appropriate probes selected specifically against small targets such as adenosine. The possibility to split aptamers in parts led to original amplification strategies based on sandwich assays. By combining the self-assembling of oligonucleotide dimers with split-aptamer dangling ends and a surface plasmon resonance imaging technique, we developed an original amplification approach based on linear chain formation in the presence of the adenosine target. In this article, on the basis of sequence engineering, we analyzed its performance and the effect of the probe grafting density on the length of the chains formed at the surface of the biosensor.
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Affiliation(s)
- Chenze Lu
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
- Univ. Grenoble Alpes, CNRS, DPM , F-38000 Grenoble, France
| | | | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
| | - Eric Peyrin
- Univ. Grenoble Alpes, CNRS, DPM , F-38000 Grenoble, France
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
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16
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Chatelain G, Clavé G, Saint-Pierre C, Gasparutto D, Campidelli S. Self-assembly of porphyrin–DNA hybrids into large flat nanostructures. Org Biomol Chem 2017; 15:6257-6263. [DOI: 10.1039/c7ob01267e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two complementary 21-mer oligonucleotide/porphyrin hybrids were synthesized and assembled into nanostructures.
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Affiliation(s)
| | - G. Clavé
- LICSEN
- NIMBE
- CEA
- CNRS
- Université Paris-Saclay
| | - C. Saint-Pierre
- Université Grenoble Alpes
- INAC-SyMMES/UMR 5819 CEA-CNRS-UGA
- CEA-Grenoble
- F-38000 Grenoble
- France
| | - D. Gasparutto
- Université Grenoble Alpes
- INAC-SyMMES/UMR 5819 CEA-CNRS-UGA
- CEA-Grenoble
- F-38000 Grenoble
- France
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17
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Raibaut L, Vasseur W, Shimberg GD, Saint-Pierre C, Ravanat JL, Michel SLJ, Sénèque O. Design of a synthetic luminescent probe from a biomolecule binding domain: selective detection of AU-rich mRNA sequences. Chem Sci 2016; 8:1658-1664. [PMID: 28451295 PMCID: PMC5364516 DOI: 10.1039/c6sc04086a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/02/2016] [Indexed: 12/12/2022] Open
Abstract
We report the design of a luminescent sensor based upon the zinc finger protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA.
We report the design of a luminescent sensor based upon the zinc finger (ZF) protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA. This sensor is composed of the tandem ZF RNA binding domain of TIS11d functionalized with a luminescent Tb3+ complex on one of the ZFs and a sensitizing antenna on the other. This work provides the proof of principle that an RNA binding protein can be re-engineered as an RNA sensor and, more generally, that tunable synthetic luminescent probes for biomolecules can be obtained by modifying biomolecule-binding domains.
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Affiliation(s)
- Laurent Raibaut
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
| | - William Vasseur
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
| | - Geoffrey D Shimberg
- Department of Pharmaceutical Sciences , School of Pharmacy , University of Maryland , Baltimore , Maryland 21201-1180 , USA .
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences , School of Pharmacy , University of Maryland , Baltimore , Maryland 21201-1180 , USA .
| | - Olivier Sénèque
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
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18
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Barbier E, Lagorce A, Hachemi A, Dutertre M, Gorlas A, Morand L, Saint-Pierre C, Ravanat JL, Douki T, Armengaud J, Gasparutto D, Confalonieri F, Breton J. Oxidative DNA Damage and Repair in the Radioresistant Archaeon Thermococcus gammatolerans. Chem Res Toxicol 2016; 29:1796-1809. [PMID: 27676238 DOI: 10.1021/acs.chemrestox.6b00128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The hyperthermophilic archaeon Thermococcus gammatolerans can resist huge doses of γ-irradiation, up to 5.0 kGy, without loss of viability. The potential to withstand such harsh conditions is probably due to complementary passive and active mechanisms, including repair of damaged chromosomes. In this work, we documented the formation and repair of oxidative DNA lesions in T. gammatolerans. The basal level of the oxidized nucleoside, 8-oxo-2'-deoxyguanosine (8-oxo-dGuo), was established at 9.2 (± 0.9) 8-oxo-dGuo per 106 nucleosides, a higher level than those usually measured in eukaryotic cells or bacteria. A significant increase in oxidative damage, i.e., up to 24.2 (± 8.0) 8-oxo-dGuo/106 nucleosides, was measured for T. gammatolerans exposed to a 5.0 kGy dose of γ-rays. Surprisingly, the yield of radiation-induced modifications was lower than those previously observed for human cells exposed to doses corresponding to a few grays. One hour after irradiation, 8-oxo-dGuo levels were significantly reduced, indicating an efficient repair. Two putative base excision repair (BER) enzymes, TGAM_1277 and TGAM_1653, were demonstrated both by proteomics and transcriptomics to be present in the cells without exposure to ionizing radiation. Their transcripts were moderately upregulated after gamma irradiation. After heterologous production and purification of these enzymes, biochemical assays based on electrophoresis and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry indicated that both have a β-elimination cleavage activity. TGAM_1653 repairs 8-oxo-dGuo, whereas TGAM_1277 is also able to remove lesions affecting pyrimidines (1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxyhydantoin (5-OH-dHyd) and 1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd)). This work showed that in normal growth conditions or in the presence of a strong oxidative stress, T. gammatolerans has the potential to rapidly reduce the extent of DNA oxidation, with at least these two BER enzymes as bodyguards with distinct substrate ranges.
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Affiliation(s)
- Ewa Barbier
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Arnaud Lagorce
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France.,University of Perpignan, IHPE - UMR 5244 CNRS/IFREMER/Univ. Montpellier, Montpellier, F-34095, France
| | - Amine Hachemi
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Aurore Gorlas
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Lucie Morand
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Christine Saint-Pierre
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Thierry Douki
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean Armengaud
- CEA, DSV-Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, Bagnols-sur-Cèze, F-30207, France
| | - Didier Gasparutto
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Fabrice Confalonieri
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Jean Breton
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
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Talhaoui I, Lebedeva NA, Zarkovic G, Saint-Pierre C, Kutuzov MM, Sukhanova MV, Matkarimov BT, Gasparutto D, Saparbaev MK, Lavrik OI, Ishchenko AA. Poly(ADP-ribose) polymerases covalently modify strand break termini in DNA fragments in vitro. Nucleic Acids Res 2016; 44:9279-9295. [PMID: 27471034 PMCID: PMC5100588 DOI: 10.1093/nar/gkw675] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 07/14/2016] [Indexed: 11/22/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs/ARTDs) use nicotinamide adenine dinucleotide (NAD+) to catalyse the synthesis of a long branched poly(ADP-ribose) polymer (PAR) attached to the acceptor amino acid residues of nuclear proteins. PARPs act on single- and double-stranded DNA breaks by recruiting DNA repair factors. Here, in in vitro biochemical experiments, we found that the mammalian PARP1 and PARP2 proteins can directly ADP-ribosylate the termini of DNA oligonucleotides. PARP1 preferentially catalysed covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 3′-cordycepin, 5′- and 3′-phosphate and also to 5′-phosphate of a single-stranded oligonucleotide. PARP2 preferentially ADP-ribosylated the nicked/gapped DNA duplexes containing 5′-phosphate at the double-stranded termini. PAR glycohydrolase (PARG) restored native DNA structure by hydrolysing PAR-DNA adducts generated by PARP1 and PARP2. Biochemical and mass spectrometry analyses of the adducts suggested that PARPs utilise DNA termini as an alternative to 2′-hydroxyl of ADP-ribose and protein acceptor residues to catalyse PAR chain initiation either via the 2′,1″-O-glycosidic ribose-ribose bond or via phosphodiester bond formation between C1′ of ADP-ribose and the phosphate of a terminal deoxyribonucleotide. This new type of post-replicative modification of DNA provides novel insights into the molecular mechanisms underlying biological phenomena of ADP-ribosylation mediated by PARPs.
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Affiliation(s)
- Ibtissam Talhaoui
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Natalia A Lebedeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Gabriella Zarkovic
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, INAC/SPrAM UMR5819 CEA CNRS UGA, F-38000 Grenoble, France
| | - Mikhail M Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Maria V Sukhanova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Bakhyt T Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, INAC/SPrAM UMR5819 CEA CNRS UGA, F-38000 Grenoble, France
| | - Murat K Saparbaev
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Olga I Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia .,Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France .,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
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20
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Flaender M, Costa G, Nonglaton G, Saint-Pierre C, Gasparutto D. A DNA array based on clickable lesion-containing hairpin probes for multiplexed detection of base excision repair activities. Analyst 2016; 141:6208-6216. [DOI: 10.1039/c6an01165a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An electrophoresis-free fluorescent functional assay has been developed to measure DNA repair activities in a miniaturized and parallelized manner.
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Affiliation(s)
- Mélanie Flaender
- Université Grenoble Alpes
- INAC – SyMMES/CEA
- F-38000 Grenoble
- France
| | - Guillaume Costa
- Université Grenoble Alpes
- LETI/DTBS-SBSC/CEA
- F-38000 Grenoble
- France
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21
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Talhaoui I, Shafirovich V, Liu Z, Saint-Pierre C, Akishev Z, Matkarimov BT, Gasparutto D, Geacintov NE, Saparbaev M. Oxidatively Generated Guanine(C8)-Thymine(N3) Intrastrand Cross-links in Double-stranded DNA Are Repaired by Base Excision Repair Pathways. J Biol Chem 2015; 290:14610-7. [PMID: 25903131 DOI: 10.1074/jbc.m115.647487] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 11/06/2022] Open
Abstract
Oxidatively generated guanine radical cations in DNA can undergo various nucleophilic reactions including the formation of C8-guanine cross-links with adjacent or nearby N3-thymines in DNA in the presence of O2. The G*[C8-N3]T* lesions have been identified in the DNA of human cells exposed to oxidative stress, and are most likely genotoxic if not removed by cellular defense mechanisms. It has been shown that the G*[C8-N3]T* lesions are substrates of nucleotide excision repair in human cell extracts. Cleavage at the sites of the lesions was also observed but not further investigated (Ding et al. (2012) Nucleic Acids Res. 40, 2506-2517). Using a panel of eukaryotic and prokaryotic bifunctional DNA glycosylases/lyases (NEIL1, Nei, Fpg, Nth, and NTH1) and apurinic/apyrimidinic (AP) endonucleases (Apn1, APE1, and Nfo), the analysis of cleavage fragments by PAGE and MALDI-TOF/MS show that the G*[C8-N3]T* lesions in 17-mer duplexes are incised on either side of G*, that none of the recovered cleavage fragments contain G*, and that T* is converted to a normal T in the 3'-fragment cleavage products. The abilities of the DNA glycosylases to incise the DNA strand adjacent to G*, while this base is initially cross-linked with T*, is a surprising observation and an indication of the versatility of these base excision repair proteins.
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Affiliation(s)
- Ibtissam Talhaoui
- From the Groupe "Réparation de l'ADN," CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, F-94805 Villejuif Cedex, France
| | | | - Zhi Liu
- the Chemistry Department, New York University, New York, New York 10003-5180
| | | | - Zhiger Akishev
- Department of Molecular Biology and Genetics, Faculty of Biology, al-Farabi Kazakh National University, 530038, Almaty, Kazakhstan
| | - Bakhyt T Matkarimov
- Nazarbayev University Research and Innovation System, Astana 010000, Kazakhstan, and
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, INAC/SCIB-UMR E3/LAN, F-38000 Grenoble, France
| | | | - Murat Saparbaev
- From the Groupe "Réparation de l'ADN," CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, F-94805 Villejuif Cedex, France,
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22
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Clavé G, Chatelain G, Filoramo A, Gasparutto D, Saint-Pierre C, Le Cam E, Piétrement O, Guérineau V, Campidelli S. Synthesis of a multibranched porphyrin-oligonucleotide scaffold for the construction of DNA-based nano-architectures. Org Biomol Chem 2014; 12:2778-83. [PMID: 24668242 DOI: 10.1039/c4ob00202d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.
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Affiliation(s)
- Guillaume Clavé
- CEA Saclay, IRAMIS, NIMBE, Laboratoire d'Innovation en Chimie des Surfaces et Nanosciences (LICSEN), F-91191 Gif sur Yvette, France.
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23
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Killelea T, Saint-Pierre C, Ralec C, Gasparutto D, Henneke G. Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5'-terminal Cy5 dyes. Electrophoresis 2014; 35:1938-46. [PMID: 24659099 DOI: 10.1002/elps.201400018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 11/10/2022]
Abstract
By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5'-indocarbo-cyanine 5 (5'-Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5'-Cy5-labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5'-Cy5-labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5'-carboxyfluorescein (5'-FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5'-labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5'-Cy5-labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5'-Cy5-labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3' to 5' exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.
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Affiliation(s)
- Tom Killelea
- IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Plouzané, France; Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, UMR 6197, Plouzané, France; CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Plouzané, France
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Silerme S, Bobyk L, Taverna-Porro M, Cuier C, Saint-Pierre C, Ravanat JL. DNA-Polyamine Cross-Links Generated upon One Electron Oxidation of DNA. Chem Res Toxicol 2014; 27:1011-8. [DOI: 10.1021/tx500063d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stéphanie Silerme
- Laboratoire Lésions des Acides
Nucléiques, Université Grenoble Alpes, INAC-SCIB, F-38000
Grenoble, France, CEA, INAC-SCIB, 17
rue des Martyrs, 38000 Grenoble cédex 9, France
| | - Laure Bobyk
- Laboratoire Lésions des Acides
Nucléiques, Université Grenoble Alpes, INAC-SCIB, F-38000
Grenoble, France, CEA, INAC-SCIB, 17
rue des Martyrs, 38000 Grenoble cédex 9, France
| | - Marisa Taverna-Porro
- Laboratoire Lésions des Acides
Nucléiques, Université Grenoble Alpes, INAC-SCIB, F-38000
Grenoble, France, CEA, INAC-SCIB, 17
rue des Martyrs, 38000 Grenoble cédex 9, France
| | - Camille Cuier
- Laboratoire Lésions des Acides
Nucléiques, Université Grenoble Alpes, INAC-SCIB, F-38000
Grenoble, France, CEA, INAC-SCIB, 17
rue des Martyrs, 38000 Grenoble cédex 9, France
| | - Christine Saint-Pierre
- Laboratoire Lésions des Acides
Nucléiques, Université Grenoble Alpes, INAC-SCIB, F-38000
Grenoble, France, CEA, INAC-SCIB, 17
rue des Martyrs, 38000 Grenoble cédex 9, France
| | - Jean-Luc Ravanat
- Laboratoire Lésions des Acides
Nucléiques, Université Grenoble Alpes, INAC-SCIB, F-38000
Grenoble, France, CEA, INAC-SCIB, 17
rue des Martyrs, 38000 Grenoble cédex 9, France
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25
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Lafaye C, Barbier E, Miscioscia A, Saint-Pierre C, Kraut A, Couté Y, Plo I, Gasparutto D, Ravanat JL, Breton J. DNA binding of the p21 repressor ZBTB2 is inhibited by cytosine hydroxymethylation. Biochem Biophys Res Commun 2014; 446:341-6. [DOI: 10.1016/j.bbrc.2014.02.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/25/2014] [Indexed: 01/01/2023]
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26
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Gines G, Saint-Pierre C, Gasparutto D. A multiplex assay based on encoded microbeads conjugated to DNA NanoBeacons to monitor base excision repair activities by flow cytometry. Biosens Bioelectron 2014; 58:81-4. [PMID: 24632132 DOI: 10.1016/j.bios.2014.02.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/03/2014] [Accepted: 02/14/2014] [Indexed: 02/07/2023]
Abstract
We reported here a new assay to detect base excision repair activities from purified enzymes, as well as in cell-free extracts. The multiplex format rests upon the encoding of magnetic beads with the fluorophore Alexa 488, thanks to a fast and original procedure. Fluorescently encoded microbeads are subsequently functionalized by lesion-containing DNA NanoBeacons labeled with the fluorophore/quencher pair Cyanine 5/BHQ2. Probes cleavage, induced by targeted enzymes leads to Cyanine 5 signal enhancement, which is finally quantified by flow cytometry. The multiplex assay was applied to the detection of restriction enzymes activities as well as base excision repair processes. Each test requires only 500fmol of DNA substrate, which constitutes great sensitivity compared to other BER functional assays. The present biosensor is able to detect both uracil DNA N-glycosylase (UNG) and AP-endonuclease 1 (APE1) within few nanograms of nuclear extract. Additionally, we demonstrated that the corresponding assay has potential application in DNA repair inhibitor search. Finally, the current multiplexed tool shows several advantages in comparison to other functional BER assays with no need of electrophoretic separation, straightforward, easy and reproducible functionalization of encoded microbeads and a high stability of DNA probes in cell-free extracts.
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Affiliation(s)
- Guillaume Gines
- Laboratoire des Lésions des Acides Nucléiques, INAC/SCIB UMR_E3 CEA/UJF-Grenoble 1/CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex 9, France
| | - Christine Saint-Pierre
- Laboratoire des Lésions des Acides Nucléiques, INAC/SCIB UMR_E3 CEA/UJF-Grenoble 1/CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex 9, France
| | - Didier Gasparutto
- Laboratoire des Lésions des Acides Nucléiques, INAC/SCIB UMR_E3 CEA/UJF-Grenoble 1/CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex 9, France.
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27
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Gines G, Saint-Pierre C, Gasparutto D. On-bead fluorescent DNA nanoprobes to analyze base excision repair activities. Anal Chim Acta 2014; 812:168-75. [PMID: 24491778 DOI: 10.1016/j.aca.2013.12.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/18/2013] [Accepted: 12/28/2013] [Indexed: 12/25/2022]
Abstract
DNA integrity is constantly threatened by endogenous and exogenous agents that can modify its physical and chemical structure. Changes in DNA sequence can cause mutations sparked by some genetic diseases or cancers. Organisms have developed efficient defense mechanisms able to specifically repair each kind of lesion (alkylation, oxidation, single or double strand break, mismatch, etc). Here we report the adjustment of an original assay to detect enzymes' activity of base excision repair (BER), that supports a set of lesions including abasic sites, alkylation, oxidation or deamination products of bases. The biosensor is characterized by a set of fluorescent hairpin-shaped nucleic acid probes supported on magnetic beads, each containing a selective lesion targeting a specific BER enzyme. We have studied the DNA glycosylase alkyl-adenine glycosylase (AAG) and the human AP-endonuclease (APE1) by incorporating within the DNA probe a hypoxanthine lesion or an abasic site analog (tetrahydrofuran), respectively. Enzymatic repair activity induces the formation of a nick in the damaged strand, leading to probe's break, that is detected in the supernatant by fluorescence. The functional assay allows the measurement of DNA repair activities from purified enzymes or in cell-free extracts in a fast, specific, quantitative and sensitive way, using only 1 pmol of probe for a test. We recorded a detection limit of 1 μg mL(-1) and 50 μg mL(-1) of HeLa nuclear extracts for APE1 and AAG enzymes, respectively. Finally, the on-bead assay should be useful to screen inhibitors of DNA repair activities.
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Affiliation(s)
- Guillaume Gines
- Laboratoire des Lésions des Acides Nucléiques, SCIB-UMR E3 CEA-UJF/INAC/CEA Grenoble, Grenoble Cedex 09 38054, France
| | - Christine Saint-Pierre
- Laboratoire des Lésions des Acides Nucléiques, SCIB-UMR E3 CEA-UJF/INAC/CEA Grenoble, Grenoble Cedex 09 38054, France
| | - Didier Gasparutto
- Laboratoire des Lésions des Acides Nucléiques, SCIB-UMR E3 CEA-UJF/INAC/CEA Grenoble, Grenoble Cedex 09 38054, France.
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Prorok P, Saint-Pierre C, Gasparutto D, Fedorova OS, Ishchenko AA, Leh H, Buckle M, Tudek B, Saparbaev M. Highly mutagenic exocyclic DNA adducts are substrates for the human nucleotide incision repair pathway. PLoS One 2012; 7:e51776. [PMID: 23251620 PMCID: PMC3522590 DOI: 10.1371/journal.pone.0051776] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/12/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Oxygen free radicals induce lipid peroxidation (LPO) that damages and breaks polyunsaturated fatty acids in cell membranes. LPO-derived aldehydes and hydroxyalkenals react with DNA leading to the formation of etheno(ε)-bases including 1,N(6)-ethenoadenine (εA) and 3,N(4)-ethenocytosine (εC). The εA and εC residues are highly mutagenic in mammalian cells and eliminated in the base excision repair (BER) pathway and/or by AlkB family proteins in the direct damage reversal process. BER initiated by DNA glycosylases is thought to be the major pathway for the removal of non-bulky endogenous base damage. Alternatively, in the nucleotide incision repair (NIR) pathway, the apurinic/apyrimidinic (AP) endonucleases can directly incise DNA duplex 5' to a damaged base in a DNA glycosylase-independent manner. METHODOLOGY/PRINCIPAL FINDINGS Here we have characterized the substrate specificity of human major AP endonuclease 1, APE1, towards εA, εC, thymine glycol (Tg) and 7,8-dihydro-8-oxoguanine (8oxoG) residues when present in duplex DNA. APE1 cleaves oligonucleotide duplexes containing εA, εC and Tg, but not those containing 8oxoG. Activity depends strongly on sequence context. The apparent kinetic parameters of the reactions suggest that APE1 has a high affinity for DNA containing ε-bases but cleaves DNA duplexes at an extremely slow rate. Consistent with this observation, oligonucleotide duplexes containing an ε-base strongly inhibit AP site nicking activity of APE1 with IC(50) values in the range of 5-10 nM. MALDI-TOF MS analysis of the reaction products demonstrated that APE1-catalyzed cleavage of εA•T and εC•G duplexes generates, as expected, DNA fragments containing 5'-terminal ε-base residue. CONCLUSIONS/SIGNIFICANCE The fact that ε-bases and Tg in duplex DNA are recognized and cleaved by APE1 in vitro, suggests that NIR may act as a backup pathway to BER to remove a large variety of genotoxic base lesions in human cells.
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Affiliation(s)
- Paulina Prorok
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Diorio C, Lemieux J, Cote MA, Provencher L, Nadeau-Larochelle C, Jacob S, Demers E, Tremblay-Lemay R, Saint-Pierre C, Beauchemin M, Barabe F, Laflamme C. Evaluation of Ile655Val HER2 polymorphism associated with cardiac toxicity following the administration of trastuzumab in women with breast cancer. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
634 Background: Trastuzumab is well tolerated without major side effects except for cardiac toxicity. Although a number of clinical parameters have been associated with trastuzumab-associated cardiac toxicity (TACT), there is some indication that genetic variation of the HER2 gene may play a toxic role in a population of metastatic breast cancer patients. However, this finding needs confirmation and we looked at a population of non-metastatic breast cancer. This study aimed to evaluate the association between cardiac toxicity and HER2 [Ile655Val] polymorphism in non-metastatic breast cancer patients treated with trastuzumab. Methods: The Ile655Val HER2 polymorphism was assessed in 73 women using TaqMan technology. For this study, the genotyping was performed using DNA extracted from normal breast tissue located at more than 1 cm of any other lesions. Charts review was used to collect information on TACT which was defined as any decline in LVEF > 10 % from the baseline to < 55 % or a decline in LVEF > 5 % to < 50 % (lower limit of normal). The Fisher exact test was used to evaluate the association between cardiac toxicity and HER2 polymorphism. Results: No deviation from the Hardy-Weinberg equilibrium has been observed for the allele and genotype frequencies. The distribution of HER2 polymorphism was 3 Val/Val (4%), 18 Ile/Val (25%) and 52 Ile/Ile (71%). In this population, 19% (14/73) developed a cardiac toxicity. We found that 29% (6/21) of Ile/Val or Val/Val carriers compared to 15% (8/52) of Ile/Ile carriers showed TACT, but this association did not reach statistical significance (P = 0.21). Conclusions: HER2 Ile655Val polymorphism may be an efficient marker of TACT considering this tendency with this small cohort of patients. Larger sample is needed to strengthen this conclusion, since this result may influence on prescribing decision for adjuvant chemotherapy and anti-HER2 therapy in HER2 positive patients.
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Affiliation(s)
- Caroline Diorio
- URESP, Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada
| | - Julie Lemieux
- CHA-Hopital du St Sacrement, Quebec City, QC, Canada
| | | | | | | | - Simon Jacob
- CHA-Hopital du St Sacrement, Quebec City, QC, Canada
| | - Eric Demers
- CHA-Hopital du St Sacrement, Quebec City, QC, Canada
| | | | | | | | - Frederic Barabe
- Centre de recherche en infectiologie du CHUL, Quebec City, QC, Canada
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30
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Diorio C, Lemieux J, Côté MA, Provencher L, Nadeau-Larochelle C, Jacob S, Demers E, Tremblay-Lemay R, Saint-Pierre C, Beauchemin M, Barabé F, Laflamme C. P1-12-12: Evaluation of Ile655Val HER2 Polymorphism Associated with Cardiac Toxicity Following the Administration of Trastuzumab in Women with Non-Metastatic Breast Cancer. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-p1-12-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Trastuzumab is well tolerated without major side effects except for cardiac toxicity. Although a number of clinical parameters have been associated with trastuzumab-associated cardiac toxicity (TACT), there is some indication that genetic variation of the HER2 gene may be associated with TACT in a population of metastatic breast cancer patients. However, this finding needs confirmation and we looked at a population of non-metastatic breast cancer.
Purpose: This study aimed to evaluate the association between cardiac toxicity and HER2 [Ile655Val] polymorphism in non-metastatic breast cancer patients treated with trastuzumab.
Method: The Ile655Val HER2 polymorphism was assessed in 41 women using TaqMan technology. For this study, the genotyping was performed using DNA extracted from normal breast tissue located at more than 1 cm of any other lesions. Charts review was used to collect information on TACT which was defined as a decrease in the left ventricular ejection fraction (LVEF) of ≥15% or ≥10% with a resulting LVEF < 50% or any follow-up LVEF of < 45%. The Fisher exact test was used to evaluate the association between cardiac toxicity and HER2 polymorphism.
Results: No deviation from the Hardy-Weinberg equilibrium has been observed for the allele and genotype frequencies. The distribution of HER2 polymorphism was 10 Ile/Val (24%) and 31 Ile/Ile (76%). In this population, 22% (9/41) developed a cardiac toxicity. The Val655Ile genotype was associated with cardiac toxicity (0.03). In this preliminary study, 50% (5/10) of Ile/Val carriers compared to 13% (4/31) of Ile/Ile carriers showed TACT.
Conclusion: HER2 Ile655Val polymorphism may be an efficient marker of TACT considering this tendency with this small cohort of patients. Larger sample is needed to strengthen this conclusion, since this result may influence on prescribing decision for adjuvant chemotherapy and anti-HER2 therapy in HER2 positive patients.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-12-12.
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Affiliation(s)
- C Diorio
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - J Lemieux
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - M-A Côté
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - L Provencher
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - C Nadeau-Larochelle
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - S Jacob
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - É Demers
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - R Tremblay-Lemay
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - C Saint-Pierre
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - M Beauchemin
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - F Barabé
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
| | - C Laflamme
- 1Centre de Recherche FRSQ du CHA Universitaire de Québec, Quebec City, QC, Canada; Hôpital du Saint-Sacrement, Quebec City, QC, Canada; Université Laval, Quebec City, QC, Canada; Centre Hospitalié de l'Université Laval, Quebec City, QC, Canada; Centre Hospitalier Affilie Universitaire de Quebec, Quebec City, QC, Canada
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Flaender M, Sicoli G, Aci-Seche S, Reignier T, Maurel V, Saint-Pierre C, Boulard Y, Gambarelli S, Gasparutto D. A triple spin-labeling strategy coupled with DEER analysis to detect DNA modifications and enzymatic repair. Chembiochem 2011; 12:2560-3. [PMID: 21984076 DOI: 10.1002/cbic.201100550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 12/20/2022]
Abstract
In a spin: Spin-labeled oligonucleotides produced by click chemistry can be studied by EPR, by using a DEER sequence. This was used to test a complex triple-labeling strategy with damaged DNA. Extensive and accurate analysis of DNA structure and enzymatic repair processes were performed after digestion by EndoIV. Modified DNA structures and DNA-protein interactions can now be readily studied.
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Affiliation(s)
- Mélanie Flaender
- Institut Nanoscience et Cryogénie, Laboratoire de Chimie Inorganique et Biologique, UMR-E n°3 CEA-UJF, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
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Redrejo-Rodríguez M, Saint-Pierre C, Couve S, Mazouzi A, Ishchenko AA, Gasparutto D, Saparbaev M. New insights in the removal of the hydantoins, oxidation product of pyrimidines, via the base excision and nucleotide incision repair pathways. PLoS One 2011; 6:e21039. [PMID: 21799731 PMCID: PMC3143120 DOI: 10.1371/journal.pone.0021039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/17/2011] [Indexed: 11/30/2022] Open
Abstract
Background Oxidative damage to DNA, if not repaired, can be both miscoding and blocking. These genetic alterations can lead to mutations and/or cell death, which in turn cause cancer and aging. Oxidized DNA bases are substrates for two overlapping repair pathways: base excision (BER) and nucleotide incision repair (NIR). Hydantoin derivatives such as 5-hydroxyhydantoin (5OH-Hyd) and 5-methyl-5-hydroxyhydantoin (5OH-5Me-Hyd), major products of cytosine and thymine oxidative degradation pathways, respectively, have been detected in cancer cells and ancient DNA. Hydantoins are blocking lesions for DNA polymerases and excised by bacterial and yeast DNA glycosylases in the BER pathway. However little is known about repair of pyrimidine-derived hydantoins in human cells. Methodology/Principal Findings Here, using both denaturing PAGE and MALDI-TOF MS analyses we report that the bacterial, yeast and human AP endonucleases can incise duplex DNA 5′ next to 5OH-Hyd and 5OH-5Me-Hyd thus initiating the NIR pathway. We have fully reconstituted the NIR pathway for these lesions in vitro using purified human proteins. Depletion of Nfo in E. coli and APE1 in HeLa cells abolishes the NIR activity in cell-free extracts. Importantly, a number of redundant DNA glycosylase activities can excise hydantoin residues, including human NTH1, NEIL1 and NEIL2 and the former protein being a major DNA glycosylase activity in HeLa cells extracts. Conclusions/Significance This study demonstrates that both BER and NIR pathways can compete and/or back-up each other to remove hydantoin DNA lesions in vivo.
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Affiliation(s)
- Modesto Redrejo-Rodríguez
- Groupe Réparation de l'ADN, CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Christine Saint-Pierre
- Laboratoire Lésions des Acides Nucléiques, SCIB/UMR E3 CEA-UJF, INAC, CEA, Grenoble, France
| | - Sophie Couve
- Groupe Réparation de l'ADN, CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Abdelghani Mazouzi
- Groupe Réparation de l'ADN, CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Alexander A. Ishchenko
- Groupe Réparation de l'ADN, CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Didier Gasparutto
- Laboratoire Lésions des Acides Nucléiques, SCIB/UMR E3 CEA-UJF, INAC, CEA, Grenoble, France
- * E-mail: (DG); (MS)
| | - Murat Saparbaev
- Groupe Réparation de l'ADN, CNRS UMR8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
- * E-mail: (DG); (MS)
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Sicoli G, Mathis G, Aci-Sèche S, Saint-Pierre C, Boulard Y, Gasparutto D, Gambarelli S. Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling. Nucleic Acids Res 2009; 37:3165-76. [PMID: 19304747 PMCID: PMC2691821 DOI: 10.1093/nar/gkp165] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 02/05/2009] [Accepted: 03/01/2009] [Indexed: 12/23/2022] Open
Abstract
Double electron-electron resonance (DEER) was applied to determine nanometre spin-spin distances on DNA duplexes that contain selected structural alterations. The present approach to evaluate the structural features of DNA damages is thus related to the interspin distance changes, as well as to the flexibility of the overall structure deduced from the distance distribution. A set of site-directed nitroxide-labelled double-stranded DNA fragments containing defined lesions, namely an 8-oxoguanine, an abasic site or abasic site analogues, a nick, a gap and a bulge structure were prepared and then analysed by the DEER spectroscopic technique. New insights into the application of 4-pulse DEER sequence are also provided, in particular with respect to the spin probes' positions and the rigidity of selected systems. The lesion-induced conformational changes observed, which were supported by molecular dynamics studies, confirm the results obtained by other, more conventional, spectroscopic techniques. Thus, the experimental approaches described herein provide an efficient method for probing lesion-induced structural changes of nucleic acids.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Gérald Mathis
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Samia Aci-Sèche
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Christine Saint-Pierre
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Yves Boulard
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Didier Gasparutto
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - Serge Gambarelli
- Laboratoire de Résonance Magnétique, Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France
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Vitale S, Fauquant C, Lascoux D, Schauer K, Saint-Pierre C, Michaud-Soret I. A ZnS4 Structural Zinc Site in the Helicobacter pylori Ferric Uptake Regulator. Biochemistry 2009; 48:5582-91. [DOI: 10.1021/bi9004396] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sylvia Vitale
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), and Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Caroline Fauquant
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), and Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - David Lascoux
- Laboratoire de Spectrométrie de Masse des Protéines, Institut de Biologie Structurale, Jean-Pierre Ebel (UMR 5075 CNRS/CEA/UJF), F-38027 Grenoble Cedex 1, France
| | - Kristine Schauer
- Unité Pathogenèse de Helicobacter, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Christine Saint-Pierre
- Laboratoire des Lésions des Acides Nucléiques, DSM/INAC/Service de Chimie Inorganique et Biologique, UMR E-3 CEA/UJF CNRS FRE 3200, 17 rue des Martyrs, Grenoble F-38054 Cedex 9, France
| | - Isabelle Michaud-Soret
- CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), and Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
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Verbyla A, Saint-Pierre C, Peterson C, Ross A, Appels R. Fourier modelling, analysis and interpretation of high-resolution mixograph data. J Cereal Sci 2007. [DOI: 10.1016/j.jcs.2006.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bellon S, Gasparutto D, Saint-Pierre C, Cadet J. Guanine-thymine intrastrand cross-linked lesion containing oligonucleotides: from chemical synthesis to in vitro enzymatic replication. Org Biomol Chem 2006; 4:3831-7. [PMID: 17024291 DOI: 10.1039/b609460k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An intrastrand cross-link lesion, in which two neighboring nucleobases are covalently tethered, has been site-specifically synthesized into defined sequence oligonucleotides in order to perform in vitro replication studies using either bacterial replicative or translesional synthesis polymerases. The investigated tandem base lesion that involves a cross-link between the methylene group of thymine and the C8 of an adjacent guanine residue has been prepared by UV-photolysis under anaerobic condition of the photolabile precursor 5-(phenylthiomethyl)-2'-deoxyuridine that has been site-specifically incorporated into a 9-mer oligonucleotide. After ligation, the lesion-containing modified oligonucleotide was used as a DNA template in primer extension reactions catalyzed by several DNA polymerases including the fragment Klenow exo-(Kf-) of E. coli polymerase I, the Thermus aquaticus polymerase (Taq pol) and the E. coli translesional DNA polymerase Pol IV (dinB). It was found that the primer extension reaction was stopped after the incorporation of the correct nucleotide dAMP opposite the 3'-thymine residue of guanine(C8-CH2) thymine lesion by Kf- and Pol IV; however it was noted that the efficiency of the nucleotide incorporation was reduced. In contrast, the Taq polymerase was totally blocked at the nucleotide preceding the tandem lesion. These results are strongly suggestive that the present intrastrand cross-link lesion, if not repaired, would constitute a blocking lesion for prokaryotic DNA polymerases, being likely lethal for the cell.
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Affiliation(s)
- Sophie Bellon
- Service de Chimie Inorganique et Biologique UMR E3 CEA UJF, Département de Recherche Fondamentale sur la Matière Condensée, CEA Grenoble, 17 Avenue des Martyrs, F-38054, Grenoble Cedex 9, France
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Simon P, Gasparutto D, Gambarelli S, Saint-Pierre C, Favier A, Cadet J. Formation of isodialuric acid lesion within DNA oligomers via one-electron oxidation of 5-hydroxyuracil: characterization, stability and excision repair. Nucleic Acids Res 2006; 34:3660-9. [PMID: 16885239 PMCID: PMC1540730 DOI: 10.1093/nar/gkl496] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
5-Hydroxyuracil is a major oxidized nucleobase that can be generated by the action of •OH radical and one-electron oxidants. The latter modified base that exhibits a low ionization potential is highly susceptible to further degradation upon exposure to various oxidants. Emphasis was placed in thiswork on the formation and characterization of one-electron oxidation products of 5-hydroxyuracil within DNA fragments of defined sequence. For this purpose, 5-hydroxyuracil containing single- and double-stranded oligonucleotides of various lengths were synthesized and then exposed to the oxidizing action of iridium salts. Isodialuric acid was found to be formed almost quantitatively by a one-electron oxidation mechanism for which relevant information was inferred from a freeze-quenched ESR study. Information on the stability of isodialuric acid thus formed and its conversion products in aqueous solutions was also gained from experiments performed at acidic, neutral and alkali pH’s. Moreover, biochemical features dealing with the substrate specificity of several bacterial and yeast base excision repair enzymes to remove isodialuric acid from site-specifically modified DNA fragments were determined.
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Affiliation(s)
| | - Didier Gasparutto
- To whom the correspondence should be addressed. Tel: +33 4 38 78 45 58; Fax: +33 4 38 78 50 90;
| | - Serge Gambarelli
- Laboratoire de Résonance Magnétique, Département de Recherche Fondamentale sur la Matière CondenséeService de Chimie Inorganique et Biologique, UMR E3 CEA-UJF, CEA-Grenoble, F-38054 Grenoble Cedex 9, France
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Gasparutto D, Michel T, Ramirez-Fuentes T, Saint-Pierre C, Cadet J. Epoxide adducts at the guanine residue within single-stranded DNA chains: reactivity and stability studies. Nucleosides Nucleotides Nucleic Acids 2005; 24:545-52. [PMID: 16247987 DOI: 10.1081/ncn-200061805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Emphasis was placed in this work on the assessment of structural and biological features of nucleobase adducts that result from the reaction of DNA with epoxide derivatives. Thus we have prepared and characterized a set of site-specifically modified oligonucleotides at N7-position of a guanine residue, upon reaction with diepoxibutane, with the purpose of further investigating some of their biochemical features. The stability of the lesion-containing DNA fragments has also been investigated and clearly shows that the latter modified oligomers may be used as substrates for in vitro enzymatic assays, aimed at determining the biological effects within cell of these chemically induced DNA damage.
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Affiliation(s)
- D Gasparutto
- Laboratoire des Lesions des Acides Nucléiques, Service Chimie Inorganique Biologique-UMR CEA-UJF, DRFMC CEA-Grenoble, Grenoble Cedex 9, France.
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Gasparutto D, Saint-Pierre C, Jaquinod M, Favier A, Cadet J. MALDI-TOF mass spectrometry as a powerful tool to study enzymatic processing of DNA lesions inserted into oligonucleotides. Nucleosides Nucleotides Nucleic Acids 2003; 22:1583-6. [PMID: 14565471 DOI: 10.1081/ncn-120023039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
MALDI-TOF mass spectrometry measurements, coupled with either exonuclease or DNA N-glycosylases digestions of lesion-containing oligonucleotides, were used to assess biochemical features of several oxidative DNA damage. The latter analytical approach was shown to be an informative and efficient alternative technique to conventional electrophoresis and chromatographic analyses.
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Affiliation(s)
- D Gasparutto
- Laboratoire des Lésions des Acides Nucléiques, Service Chimie Inorganique Biologique-UMR 5046, DRFMC, CEA-Grenoble, Grenoble Cedex, France.
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Ravanat JL, Saint-Pierre C, Cadet J. One-electron oxidation of the guanine moiety of 2'-deoxyguanosine: influence of 8-oxo-7,8-dihydro-2'-deoxyguanosine. J Am Chem Soc 2003; 125:2030-1. [PMID: 12590514 DOI: 10.1021/ja028608q] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) on riboflavin and UVA-mediated one-electron oxidation of an aqueous aerated solution of 2'-deoxyguanosine (dGuo) has been studied. Using labeled experiments, we have demonstrated that, despite not being able to detect significant amounts of 8-oxodGuo upon one-electron oxidation of dGuo, 8-oxodGuo is indeed produced but is further rapidly degraded to oxidized nucleosides. Evidence is provided showing that an efficient electron transfer reaction from 8-oxodGuo to the guanine radical cation or rather its deprotonated form occurs, giving rise to the specific decomposition of 8-oxodGuo together with the restitution of dGuo. It could be concluded that 8-oxodGuo efficiently protects dGuo from decomposition by the one-electron oxidation reaction.
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Affiliation(s)
- Jean-Luc Ravanat
- Laboratoire "Lésions des Acides Nucléiques", Service de Chimie Inorganique et Biologique, UMR 5046, DRFMC, CEA Grenoble, F-38054 Grenoble Cedex 9, France.
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Ravanat JL, Douki T, Duez P, Gremaud E, Herbert K, Hofer T, Lasserre L, Saint-Pierre C, Favier A, Cadet J. Cellular background level of 8-oxo-7,8-dihydro-2'-deoxyguanosine: an isotope based method to evaluate artefactual oxidation of DNA during its extraction and subsequent work-up. Carcinogenesis 2002; 23:1911-8. [PMID: 12419840 DOI: 10.1093/carcin/23.11.1911] [Citation(s) in RCA: 238] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The measurement of oxidative damage to cellular DNA is a challenging analytical problem requiring highly sensitive and specific methods. In addition, artefactual DNA oxidation during its extraction and subsequent work-up may give rise to overestimated levels of oxidized DNA bases. In the present study, we have used (18)O-labelled 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) as an internal standard to evaluate the extent of artefactual DNA oxidation during the critical steps preceding the measurement. The labelled oxidized purine nucleoside was specifically generated in cellular DNA using the recently available generator of (18)O-labelled singlet oxygen. Artefactual DNA oxidation that could take place during the work-up increases the level of 8-oxodGuo but not of the (18)O-oxidized nucleoside. Therefore, the ratio between the two compounds, as measured by high performance liquid chromatography coupled to tandem mass spectrometry, allows an unambiguous comparison of different methodologies. The comparison of different DNA extraction protocols led to the conclusion that artefactual DNA oxidation during the extraction step could be minimized if: (i) nuclei are isolated after cell lysis; (ii) desferrioxamine, a transition metal chelator is added to the different extraction buffers; and (iii) sodium iodide (or alternatively guanidine thiocyanate) is used for DNA precipitation. It was also demonstrated that sodium iodide does not decompose the targeted oxidized purine nucleoside. In addition, three different DNA digestion protocols were evaluated and they were found to give rise to similar results. Using the best-studied protocol, the steady-state cellular background level of 8-oxodGuo, in a lymphocyte cell line, was determined to be approximately 0.5 lesions/10(6) DNA nucleosides.
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Affiliation(s)
- Jean-Luc Ravanat
- Laboratoire Lésions des Acides Nucléiques, DRFMC/SCIB UMR 5046 CEA Grenoble, 17 Avenue des Martyrs, F-38054 Grenoble Cedex 9, France.
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Gonzalez de Peredo A, Saint-Pierre C, Latour JM, Michaud-Soret I, Forest E. Conformational changes of the ferric uptake regulation protein upon metal activation and DNA binding; first evidence of structural homologies with the diphtheria toxin repressor. J Mol Biol 2001; 310:83-91. [PMID: 11419938 DOI: 10.1006/jmbi.2001.4769] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fur (ferric uptake regulation protein) is a bacterial global regulator that uses iron as a cofactor to bind to specific DNA sequences. It has been suggested that metal binding induces a conformational change in the protein, which is subsequently able to recognize DNA. This mechanism of activation has been investigated here using selective chemical modification monitored by mass spectrometry. The reactivity of each lysine residue of the Fur protein was studied, first in the apo form of the protein, then after metal activation and finally after DNA binding. Of particular interest is Lys76, which was shown to be highly protected from modification in the presence of target DNA. Hydrogen-deuterium exchange experiments were performed to map with higher resolution the conformational changes induced by metal binding. On the basis of these results, together with a secondary structure prediction, the presence in Fur of a non-classical helix-turn-helix motif is proposed. Experimental results show that activation upon metal binding induces conformational modification of this specific motif. The recognition helix, interacting directly with the major groove of the DNA, would include the domain [Y55-F61]. This helix would be followed by a small "wing" formed between two beta strands, containing Lys76, which might interact directly with DNA. These results suggest that Fur and DtxR (diphtheria toxin repressor), another bacterial repressor, share not only the function of being iron concentration regulators, and the structure of their DNA-binding domain.
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Affiliation(s)
- A Gonzalez de Peredo
- Laboratoire de Spectrométrie de Masse des Protéines, Institut de Biologie Structurale, (UMR 5075 CEA/CNRS/UJF), Grenoble Cedex 1, F-38027, France
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Legros V, Jolivet-Reynaud C, Battail-Poirot N, Saint-Pierre C, Forest E. Characterization of an anti-Borrelia burgdorferi OspA conformational epitope by limited proteolysis of monoclonal antibody-bound antigen and mass spectrometric peptide mapping. Protein Sci 2000; 9:1002-10. [PMID: 10850810 PMCID: PMC2144631 DOI: 10.1110/ps.9.5.1002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Lyme borreliosis is a multisystem disorder caused by the spirochete Borrelia burgdorferi that is transmitted to humans by the tick Ixodes dammini. The immune response against the 31 kDa OspA, which is one of the most abundant B. burgdorferi proteins, appears to be critical in preventing infection and tissue inflammation. Detailed knowledge of the immunological and molecular characteristics of the OspA protein is important for the development of reliable diagnostic assays. In this study, we characterized a new conformational epitope present within the middle part of B. burgdorferi OspA. Our approach used enzymatic proteolyses of the immune complex followed by mass spectrometric identification of the peptides bound to the antibody. It appears to be one of the first reports on the characterization of a discontinuous epitope using mass spectrometry.
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Affiliation(s)
- V Legros
- Institut de Biologie Structurale (CEA-CNRS-UJF), Laboratoire de Spectrométrie de Masse des Protéines, Grenoble, France
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Gonzalez de Peredo A, Saint-Pierre C, Adrait A, Jacquamet L, Latour JM, Michaud-Soret I, Forest E. Identification of the two zinc-bound cysteines in the ferric uptake regulation protein from Escherichia coli: chemical modification and mass spectrometry analysis. Biochemistry 1999; 38:8582-9. [PMID: 10387106 DOI: 10.1021/bi9902283] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective chemical modification of thiol groups combined with mass spectrometry analysis was used to characterize cysteine ligands in the zinc-binding site of the Fur protein. Fur is a metalloregulatory protein involved in the regulation of almost all bacterial genes related to iron uptake in Gram-negative bacteria such as Escherichia coli. In addition to the iron site, Fur also possesses a tight-binding zinc site that likely comprises two cysteines. Using a new procedure, we confirm the involvement of two cysteines in zinc binding and identify them within the two pairs of cysteines present in the protein. The protein was treated under nondenaturing conditions with iodoacetamide, and the progressive alkylation of the thiol groups monitored by quenching the reaction at different times and measuring the extent of alkylation by mass spectrometry. Complementary experiments were carried out in the absence or presence of EDTA, a strong zinc chelator, to determine which of the cysteines were protected from alkylation by the zinc atom. Enzymatic digestion of the modified protein and analysis of the peptide mixture by mass spectrometry enabled fast identification of reactive and protected thiol groups. Two cysteines, Cys92 and Cys95, were thus assigned as zinc ligands. Examination of the sequence comprising the zinc site indicates that it may belong to a new type of structural zinc site. Furthermore, Cys132 was shown to be the fastest reacting cysteine, implying it is a surface-exposed residue.
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Affiliation(s)
- A Gonzalez de Peredo
- Laboratoire de Spectrométrie de Masse des Protéines, Institut de Biologie Structurale, 38027 Grenoble Cedex 1, France
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Lasko B, Lau CY, Saint-Pierre C, Reddington JL, Martel A, Anstey RJ. Efficacy and safety of oral levofloxacin compared with clarithromycin in the treatment of acute sinusitis in adults: a multicentre, double-blind, randomized study. The Canadian Sinusitis Study Group. J Int Med Res 1998; 26:281-91. [PMID: 10399110 DOI: 10.1177/030006059802600602] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Adult patients with acute sinusitis (n = 236) were randomized in a double-blind study to levofloxacin 500 mg orally once daily (n = 119) or clarithromycin 500 mg orally twice daily (n = 117) for 10-14 days. Between 2 and 5 days after therapy participants were evaluated as cured (no symptoms), improved (symptoms improved, no further therapy required), or failed (further therapy required). Clinical response rates (cured plus improved) for clinically evaluable patients were 93.9% for levofloxacin (n = 98) and 93.5% for clarithromycin (n = 93). The proportion of patients evaluated as cured was higher in the levofloxacin (40.8%) than in the clarithromycin arm (29.0%) and individual symptoms showed higher rates of resolution. Of patients receiving levofloxacin and clarithromycin, 22.5% and 39.3%, respectively, experienced adverse events related or possibly related to the study therapy. This study showed that, in the treatment of acute sinusitis, daily levofloxacin therapy is as effective as twice-daily clarithromycin therapy with more complete clearing of symptoms and a more tolerable side-effect profile.
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Affiliation(s)
- B Lasko
- Janssen-Ortho Inc., Toronto, Ontario, Canada
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Dubois J, Saint-Pierre C, Tremblay C. Efficacy of clarithromycin vs. amoxicillin/clavulanate in the treatment of acute maxillary sinusitis. Ear Nose Throat J 1993; 72:804-10. [PMID: 8313865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A new macrolide drug, clarithromycin (Biaxin) was compared with amoxicillin/clavulanate (Augmentin) in a single-blind (investigator-blind), randomized, multicenter study of 497 outpatients with acute maxillary sinusitis; treatment was 500 mg clarithromycin bid (n = 246) or 500 mg amoxicillin/clavulanate tid (n = 251). Pathogens included Streptococcus pneumoniae in 22% of patients, Staphylococcus aureus in 16%, Haemophilus influenzae in 10%, and Moraxella catarrhalis in 7%. For evaluable patients, clinical success (cure or improvement) was noted for 97% (128/132) of clarithromycin recipients and 93% (119/128) amoxicillin/clavulanate recipients. Clinically significant improvement in signs and symptoms was comparable between groups. Bacteriologic cure rates were 87% (115/132) and 90% (115/128), respectively. Respective pathogen eradication rates were 87% (125/143) and 90% (125/139). Adverse events not due to concurrent conditions occurred in 41% of the former and 46% of the latter group; most were mild to moderate gastrointestinal upsets (21% and 38%, respectively; P < 0.001). We conclude that clarithromycin appears to be as effective as amoxicillin/clavulanate in acute maxillary sinusitis and may cause fewer gastrointestinal upsets.
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Affiliation(s)
- J Dubois
- Centre Hospitalier Hotel-Dieu, Sherbrooke, Quebec, Canada
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Abstract
Rats fed laboratory chow or elemental diet 3 were given fractions of 240 rads of 60Co gamma-radiation abdominally (1200 rads/week) until all animals had died. Changes in appetite, body weight, and mortality were monitored as a function of the cumulative dose received. More radiation was needed in the diet-fed group to achieve both 0 and 100% mortality, a difference of 37% at the mean lethal dose level. Both groups developed similar progressive anorexia but the diet-fed animals lost weight more slowly. Data indicate that basic intestinal radio-resistance is enhanced by feeding the elemental diet.
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