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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering. Org Biomol Chem 2024; 22:3025-3034. [PMID: 38530278 DOI: 10.1039/d4ob00279b] [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: 03/27/2024]
Abstract
Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Clément Denhez
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, F-38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
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2
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide. Org Biomol Chem 2022; 20:2300-2307. [PMID: 35253821 DOI: 10.1039/d2ob00044j] [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: 11/21/2022]
Abstract
Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Clément Denhez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France. .,MaSCA, P3M, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
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3
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Clivio P. Inconsistencies in the specific nucleobase pairing motif prone to photodimerization in a MOF nanoreactor. Nat Commun 2021; 12:6981. [PMID: 34848719 PMCID: PMC8632898 DOI: 10.1038/s41467-021-27196-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/13/2021] [Indexed: 12/07/2022] Open
Affiliation(s)
- Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, F-51096, Reims Cedex, France.
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Peyrane F, Denhez C, Guillaume D, Clivio P. Anti Regiospecificity in the Photosensitized Cycloaddition of 4-Tetrazolouracil Nucleoside †. Photochem Photobiol 2021; 98:640-648. [PMID: 34655494 DOI: 10.1111/php.13541] [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: 09/09/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022]
Abstract
The [2 + 2] photocycloaddition of natural pyrimidine nucleobases is devoid of regioselectivity. Although modified pyrimidines have been developed to selectively obtain syn-cyclobutane isomers, the targeted formation of anti-cyclobutane isomers has not been addressed yet. Herein, using NMR analyses and DFT calculations, we demonstrate that the acetone photosensitized excitation of the 4-tetrazolouracil motif in the nucleoside series specifically provides anti-cyclobutane photoproducts in 51% yield. In addition, the cis stereomer formation is preferred over the trans-cyclobutane formation (71:29).
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - Clément Denhez
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, Reims, France.,MaSCA, P3M, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Dominique Guillaume
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, Reims, France
| | - Pascale Clivio
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, Reims, France
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5
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Coantic-Castex S, Martinez A, Harakat D, Guillaume D, Clivio P. The remarkable UV light invulnerability of thymine GNA dinucleotides. Chem Commun (Camb) 2019; 55:12571-12574. [PMID: 31577282 DOI: 10.1039/c9cc04355a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We herein demonstrate the UV resistance of glycol nucleic acid (GNA) dinucleotides. This resistance sustains the hypothesis of GNA as a nucleic acid prebiotic ancestor on early Earth, a time of intense solar UV light. Such photorobustness, due to the absence of intrastrand base stacking, could offer an opportunity for nanodevice development requiring challenging UV conditions.
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Affiliation(s)
- Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol'Agro, BP 1039, F-51687 Reims Cedex 2, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol'Agro, BP 1039, F-51687 Reims Cedex 2, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France.
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6
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Moriou C, Da Silva AD, Vianelli Prado MJ, Denhez C, Plashkevych O, Chattopadhyaya J, Guillaume D, Clivio P. C2′-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level. J Org Chem 2018; 83:2473-2478. [DOI: 10.1021/acs.joc.7b03186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Céline Moriou
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette 91198 Cedex, France
| | - Adilson D. Da Silva
- Departamento
de Quimica, ICE, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Marcos Joel Vianelli Prado
- Departamento
de Quimica, ICE, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Clément Denhez
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
- Université
de Reims Champagne Ardenne, Multiscale Molecular Modelling Platform, UFR Sciences Exactes et Naturelles, Reims F-51687 Cedex 2, France
| | - Oleksandr Plashkevych
- Institute of Cell & Molecular Biology, Program of Chemical Biology, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
| | - Jyoti Chattopadhyaya
- Institute of Cell & Molecular Biology, Program of Chemical Biology, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
| | - Dominique Guillaume
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
| | - Pascale Clivio
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
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7
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Lameiras P, Patis S, Jakhlal J, Castex S, Clivio P, Nuzillard JM. Small Molecule Mixture Analysis by Heteronuclear NMR under Spin Diffusion Conditions in Viscous DMSO-Water Solvent. Chemistry 2017; 23:4923-4928. [DOI: 10.1002/chem.201700636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, SFR CAP-Santé BP 1039; 51687 Reims Cedex 02 France
| | - Solène Patis
- Université de Reims Champagne-Ardenne; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, SFR CAP-Santé BP 1039; 51687 Reims Cedex 02 France
| | - Jouda Jakhlal
- Université de Reims Champagne-Ardenne; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, SFR CAP-Santé BP 1039; 51687 Reims Cedex 02 France
| | - Stéphanie Castex
- Université de Reims Champagne-Ardenne; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, SFR CAP-Santé BP 1039; 51687 Reims Cedex 02 France
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, SFR CAP-Santé BP 1039; 51687 Reims Cedex 02 France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne; Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, SFR CAP-Santé BP 1039; 51687 Reims Cedex 02 France
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8
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Jakhlal J, Coantic-Castex S, Denhez C, Petermann C, Martinez A, Harakat D, Guillaume D, Clivio P. 5'- vs. 3'-end sugar conformational control in shaping up dinucleotides. Chem Commun (Camb) 2016; 51:12381-3. [PMID: 26140549 DOI: 10.1039/c5cc04212g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 5'-end N-sugar puckering is currently believed to govern the intramolecular dinucleotide stacking. We demonstrate that if this 5'-conformation is indeed important in shaping up dinucleotide structures, the 3'-end sugar conformation can either potentiate or cancel the stacking capacity induced by the 5'-end N-sugar conformation.
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Affiliation(s)
- J Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France.
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9
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Moriou C, Denhez C, Plashkevych O, Coantic-Castex S, Chattopadhyaya J, Guillaume D, Clivio P. A minute amount of s-puckered sugars is sufficient for (6-4) photoproduct formation at the dinucleotide level. J Org Chem 2014; 80:615-9. [PMID: 25496131 DOI: 10.1021/jo502230n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The di-2'-α-fluoro analogue of thymidylyl(3',5')thymidine, synthesized to probe the effect of a minimum amount of S conformer on the photoreactivity of dinucleotides, is endowed with only 3% and 8% of S sugar conformation at its 5'- and 3'-end, respectively. This analogue gives rise to the (6-4) photoproduct as efficiently as the dithymine dinucleotide (74% and 66% at the 5'- and 3'-end, respectively) under 254 nm. Our results suggest that the 5'-N, 3'-S conformer gives rise to the (6-4) photoproduct.
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Affiliation(s)
- Céline Moriou
- †Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Clément Denhez
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | | | - Stéphanie Coantic-Castex
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | | | - Dominique Guillaume
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Pascale Clivio
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
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10
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Pilles BM, Bucher DB, Liu L, Clivio P, Gilch P, Zinth W, Schreier WJ. Mechanism of the Decay of Thymine Triplets in DNA Single Strands. J Phys Chem Lett 2014; 5:1616-1622. [PMID: 26270105 DOI: 10.1021/jz500364g] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The decay of triplet states and the formation of cyclobutane pyrimidine dimers (CPDs) after UV excitation of the all-thymine oligomer (dT)18 and the locked dinucleotide TLpTL were studied by nanosecond IR spectroscopy. IR marker bands characteristic for the CPD lesion and the triplet state were observed from ∼1 ns (time resolution of the setup) onward. The amplitudes of the CPD marker bands remain constant throughout the time range covered (up to 10 μs). The triplet decays with a time constant of ∼10 ns presumably via a biradical intermediate (lifetime ∼60 ns). This biradical has often been invoked as an intermediate for CPD formation via the triplet channel. The present results lend strong support to the existence of this intermediate, yet there is no indication that its decay contributes significantly to CPD formation.
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Affiliation(s)
- Bert M Pilles
- †Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Dominik B Bucher
- †Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Lizhe Liu
- †Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Pascale Clivio
- §Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne Ardenne, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Peter Gilch
- ‡Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Wolfgang Zinth
- †Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Wolfgang J Schreier
- †Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
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Peyrane F, Clivio P. Sensitized photochemistry of di(4-tetrazolouracil) dinucleoside monophosphate as a route to dicytosine cyclobutane photoproduct precursors. Photochem Photobiol Sci 2014; 12:1366-74. [PMID: 23572020 DOI: 10.1039/c3pp25402j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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
The DNA cis-syn cyclobutane photoproduct formed between two adjacent cytosine residues is highly mutagenic and responsible for the tandem CC to TT transition. However, its instability has prevented its in vitro study, so far. With a view to prepare oligodeoxynucleotides containing the CC cyclobutane lesion, we have synthesized in good yield a ditetrazolouracil cyclobutane dinucleotide photoproduct as a stable precursor of this photoproduct. Our approach also overcomes the low photochemical reactivity of the cytosine-cytosine deoxydinucleoside monophosphate.
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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12
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Affiliation(s)
- Pascale Clivio
- UMR 6229, Institut de Chimie Moléculaire de Reims, CNRS-Université de Reims Champagne Ardenne , UFR Médecine-Pharmacie, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
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13
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Gourdain S, Petermann C, Harakat D, Clivio P. Highly efficient and facile synthesis of 5-azido-2'-deoxyuridine. Nucleosides Nucleotides Nucleic Acids 2011; 29:542-6. [PMID: 20589573 DOI: 10.1080/15257770.2010.487507] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Previously reported syntheses of the photoaffinity label 5-azido-2'-deoxyuridine are rather inefficient and involve the tedious preparation of a 5-nitro intermediate. To overcome these inconveniences, we have developed a new approach from the commercially available 5-bromo-2'-deoxyuridine nucleoside. Our synthetic route makes use of a benzylamination reduction sequence. Using this strategy, the 5-azido-2'-deoxyuridine photolabel is prepared in three steps and quantitative yields.
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Affiliation(s)
- Stephanie Gourdain
- Universite de Reims Champagne Ardenne, Institut de Chimie Moleculaire de Reims, Reims cedex, France
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14
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Gourdain S, Petermann C, Martinez A, Harakat D, Clivio P. Synthesis and Photochemical Behavior of the Tetrazolo Tautomer of 2-Azido-4-pyrimidinone-2′-deoxyriboside. J Org Chem 2011; 76:1906-9. [DOI: 10.1021/jo102316r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphanie Gourdain
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
| | - Christian Petermann
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
| | - Agathe Martinez
- UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol’Agro, BP 1039, 51687 Reims cedex 2, France
| | - Dominique Harakat
- UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol’Agro, BP 1039, 51687 Reims cedex 2, France
| | - Pascale Clivio
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
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15
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Asgatay S, Martinez A, Coantic-Castex S, Harakat D, Philippe C, Douki T, Clivio P. UV-induced TA photoproducts: formation and hydrolysis in double-stranded DNA. J Am Chem Soc 2010; 132:10260-1. [PMID: 20662506 DOI: 10.1021/ja1023173] [Citation(s) in RCA: 13] [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: 11/30/2022]
Abstract
Hydrolysis of TA photoproduct leads to two derivatives presenting different formation kinetic profiles depending on the oligomer content. The formation efficiency of TA photoproducts in UV-C-irradiated DNA slightly exceeds the formation of the trans,syn cyclobutane pyrimidine dimer at TT sites.
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Affiliation(s)
- Saâdia Asgatay
- Institut de Chimie Moléculaire de Reims, CNRS UMR 6229, UFR de Pharmacie, Université de Reims Champagne Ardenne, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France
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16
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Gourdain S, Martinez A, Petermann C, Harakat D, Clivio P. Unraveling the photochemistry of the 5-azido-2'-deoxyuridine photoaffinity label. J Org Chem 2009; 74:6885-7. [PMID: 19653622 DOI: 10.1021/jo901544a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UV irradiation of 5-azido-2'-deoxyuridine in water provides up to seven products. All likely result from a pivotal azirene, formed by the intramolecular rearrangement of the initially formed nitrene, that undergoes nucleophilic addition at its C5 position. This study strongly suggests that only nucleophilic amino acid residues in close proximity are cross-linkable in photolabeling experiments by using the 5-azidouracil photophore.
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Affiliation(s)
- Stéphanie Gourdain
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
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17
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Affiliation(s)
- Céline Desnous
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| | - Dominique Guillaume
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
| | - Pascale Clivio
- ICSN, UPR CNRS 2301, 1 Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France and UMR CNRS 6229, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
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18
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Schreier WJ, Kubon J, Regner N, Haiser K, Schrader TE, Zinth W, Clivio P, Gilch P. Thymine dimerization in DNA model systems: cyclobutane photolesion is predominantly formed via the singlet channel. J Am Chem Soc 2009; 131:5038-9. [PMID: 19309140 DOI: 10.1021/ja900436t] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UV-induced formation of cylcobutane pyrimidine dimers (CPD) in all thymine DNA models have been studied by femtosecond IR spectroscopy. CPDs are shown to form within approximately 1 ps during the decay of the initially excited (1)pi pi * state. The quantum yields phi(D)(ps) determined after the (1)pi pi * decay equal the final yield phi(D)(cw). This gives evidence for a predominance of the singlet channel in CPD formation.
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Affiliation(s)
- Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität Munchen, Oettingenstr. 67, 80538 Munchen, Germany
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19
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Asgatay S, Petermann C, Harakat D, Guillaume D, Taylor JS, Clivio P. Evidence that the (6-4) photolyase mechanism can proceed through an oxetane intermediate. J Am Chem Soc 2008; 130:12618-9. [PMID: 18763765 DOI: 10.1021/ja805214s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using the analogue of TpT methylated at the 3'-end N3 position (Tpm3T), we demonstrate that when the oxetane/(6-4) pathway is precluded, water addition occurs at the 3'-end C6 position of the oxetane intermediate to provide its opening. Photoreversal of this (6-4) photoproduct C6 hydrate brings the first experimental evidence that the (6-4) photolyase repair can proceed through an oxetane intermediate.
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Affiliation(s)
- Saâdia Asgatay
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
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20
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Desnous C, Babu BR, Moriou C, Mayo JUO, Favre A, Wengel J, Clivio P. The sugar conformation governs (6-4) photoproduct formation at the dinucleotide level. J Am Chem Soc 2007; 130:30-1. [PMID: 18069836 DOI: 10.1021/ja077095q] [Citation(s) in RCA: 32] [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: 11/29/2022]
Abstract
The LNA dinucleotide mimic of TpT whose two-sugar puckers are locked in the C3'-endo conformation selectively produces the corresponding cyclobutane pyrimidine dimer under 254 nm irradiation. In the natural series (TpT) the sugar puckers are in a major C2'-endo sugar conformation and the (6-4) photoproduct is also produced. Consequently, this study demonstrates that the C2'-endo conformation of the sugar pucker is necessary for (6-4) photoproduct formation.
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Affiliation(s)
- Céline Desnous
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France, Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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21
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Santini GPH, Pakleza C, Auffinger P, Moriou C, Favre A, Clivio P, Cognet JAH. Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries. J Phys Chem B 2007; 111:9400-9. [PMID: 17625827 DOI: 10.1021/jp0728656] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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: 11/29/2022]
Abstract
UV irradiation at 254 nm of 2'-O,5-dimethyluridylyl(3'-5')-2'-O,5-dimethyluridine (1a) and of natural thymidylyl(3'-5')thymidine (1b) generates the same photoproducts (CPD and (6-4)PP; responsible for cell death and skin cancer). The ratios of quantum yields of photoproducts obtained from 1a (determined herein) to that from 1b are in a proportion close to the approximately threefold increase of stacked dinucleotides for 1a compared with those of 1b (from previous circular dichroism results). 1a and 1b however are endowed with different predominant sugar conformations, C3'-endo (1a) and C2'-endo (1b). The present investigation of the stacked conformation of these molecules, by unrestrained state-of-the-art molecular simulation in explicit solvent and salt, resolves this apparent paradox and suggests the following main conclusions. Stacked dinucleotides 1a and 1b adopt the main characteristic features of a single-stranded A and B form, respectively, where the relative positions of the backbone and the bases are very different. Unexpectedly, the geometry of the stacking of two thymine bases, within each dinucleotide, is very similar and is in excellent agreement with photochemical and circular dichroism results. Analyses of molecular dynamics trajectories with conformational adiabatic mapping show that 1a and 1b explore two different regions of conformational space and possess very different flexibilities. Therefore, even though their base stacking is very similar, these molecules possess different geometrical, mechanical, and dynamical properties that may account for the discrepancy observed between increased stacking and increased photoproduct formations. The computed average stacked conformations of 1a and 1b are well-defined and could serve as starting models to investigate photochemical reactions with quantum dynamics simulations.
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Affiliation(s)
- Guillaume P H Santini
- Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033 CNRS, Université Pierre et Marie Curie, Genopole Campus 1, RN7, Evry 91030, France
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22
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Moriou C, Thomas M, Adeline MT, Martin MT, Chiaroni A, Pochet S, Fourrey JL, Favre A, Clivio P. Crystal structure and photochemical behavior in solution of the 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine. J Org Chem 2007; 72:43-50. [PMID: 17194080 DOI: 10.1021/jo061488a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [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: 11/28/2022]
Abstract
The 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine (TnsoT, 1) exhibits a preference for a C3'-endo conformation in the solution and solid states. Its photochemical behavior in solution is compared to that of its natural counterpart, thymidylyl(3'-5')thymidine (TpT, 2), to get further insight into the significance of the C3'-endo conformation on the photoproduct formation at the single-stranded dinucleotide level. Irradiation at 254 nm of 1 led to the same type of photoproducts as observed with 2. However, 1 was significantly more photoreactive than 2, and accordingly, the initial rate of photoproduct formation was enhanced in accordance with its propensity to base stack compared to 2. The corresponding quantum yields were determined and showed that the enhancement factor (1 compared to 2) is moderate for the cyclobutane pyrimidine dimer (CPD) (1.26) and much higher for the (6-4) photoproduct (1.8). These data strongly suggest that the CPD and (6-4) photoproduct arise from distinct minor stacked conformations.
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Affiliation(s)
- Céline Moriou
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France
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23
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Velez EV, Desnous C, Clivio P. Study of the pyrimidine nucleobase C5C6 bond reactivity under thio-michael/aldol tandem reaction conditions. J Heterocycl Chem 2006. [DOI: 10.1002/jhet.5570430442] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Peyrane F, Cesario M, Clivio P. Photochemical Ring Expansion of 4-Azidouracil: a Route to 5H-1,3,5-Triazepin-2,4-dione in the Nucleoside Series. J Org Chem 2006; 71:1742-5. [PMID: 16468839 DOI: 10.1021/jo0524066] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Under aqueous conditions, 4-azidouracil/tetrazolo[1,5-c]pyrimidin-5(6H)-one nucleosides undergo a very efficient photochemical nitrogen elimination and ring expansion to 1,3,5-triazepin-2,4-dione nucleosides whose structure has been confirmed by X-ray crystallography. In contrast, when the photolysis was attempted under anhydrous conditions in the presence of a nucleophile, a ring contraction reaction occurred, affording 2-oxoimidazolone nucleosides. A mechanism to account for the formation of ring expansion and contraction reactions and involving a carbodiimide intermediate is proposed which is reminiscent of the known photochemical behavior of 2-azidopyridines/tetrazolo[1,5-a]pyridines.
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, UPR 2301 CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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25
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Abstract
Treatment of 4-azido-2-pyrimidinone nucleoside 1 with MeOH/K2CO3 or ammonium hydroxide led to derivatives 2 and 3, respectively. Both compounds derived from a nucleophilic addition at the modified base 2-position. These results contrast with the previously reported sensitivity of the 4-azido-2-pyrimidinone nucleoside 6-position to nucleophiles.
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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26
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Peyrane F, Clivio P. β-Selective synthesis of 2′-deoxy-5,6-dihydro-4-thiouridine, a precursor of the unstable nucleoside product of ionising radiation damage 2′-deoxy-5,6-dihydrocytidine. Org Biomol Chem 2005; 3:1685-9. [PMID: 15858650 DOI: 10.1039/b502302e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 11/21/2022]
Abstract
4-Thio oxathiaphosphepane nucleosides - undergo a rearrangement in pyridine that leads selectively to the beta anomer of the 2'-deoxy-5,6-dihydro-4-thiouridine derivative . This diastereoselective reaction proceeds through a multistep mechanism initiated by the addition of pyridine at the C1'position of - and concomitant opening of the oxathiaphosphepane. This was confirmed by the trapping of the corresponding intermediate in the closely related DMAP series. In contrast, LR thiation of in pyridine leads to a new class of modified nucleosides containing an oxathiaphospholane moiety. The quantitative conversion of into the corresponding 5,6-dihydrocytosine derivative with NH3-MeOH is also reported.
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Affiliation(s)
- Frederic Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
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27
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Coin F, Auriol J, Tapias A, Clivio P, Vermeulen W, Egly JM. Phosphorylation of XPB helicase regulates TFIIH nucleotide excision repair activity. EMBO J 2004; 23:4835-46. [PMID: 15549133 PMCID: PMC535092 DOI: 10.1038/sj.emboj.7600480] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 10/20/2004] [Indexed: 11/08/2022] Open
Abstract
Nucleotide excision repair (NER) removes damage from DNA in a tightly regulated multiprotein process. The xeroderma pigmentosum group B (XPB) helicase subunit of TFIIH functions in NER and transcription. The serine 751 (S751) residue of XPB was found to be phosphorylated in vivo. This phosphorylation inhibits NER and the microinjection of a phosphomimicking XPB-S751E mutant is unable to correct the NER defect of XP-B cells. Conversely, XPB-S751 dephosphorylation or its substitution with alanine (S751A) restores NER both in vivo and in vitro. Surprisingly, phospho/dephosphorylation of S751 spares TFIIH-dependent transcription. Finally, the phosphorylation of XPB-S751 does not impair the TFIIH unwinding of the DNA around the lesion, but rather prevents the 5' incision triggered by the ERCC1-XPF endonuclease. These data support an additional role for XPB in promoting the incision of the damaged fragment and reveal a point of NER regulation on TFIIH without interference in its transcription activity.
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Affiliation(s)
- Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
| | - Jérome Auriol
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
| | - Angel Tapias
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
| | - Pascale Clivio
- Institut de Chimie des Substances Naturelles du CNRS, ICSN-CNRS, Gif sur Yvette, France
| | - Wim Vermeulen
- Department of Genetics, Medical Genetic Cluster, Erasmus MC, Rotterdam, The Netherlands
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, CU Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, CU de Strasbourg, France. Tel.: +33 388 65 34 47; Fax: +33 388 65 32 01; E-mail:
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Ortiz Mayo JU, Dupradeau FY, Guillaume D, Fourrey JL, Clivio P. Gamma-radiolysis DNA products: synthesis of 6-(alpha-thyminyl)-5,6-dihydro-4-thiothymine derivatives. J Org Chem 2004; 69:4797-801. [PMID: 15230605 DOI: 10.1021/jo0401570] [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: 11/28/2022]
Abstract
Far-UV photolysis of 4-thiothymidylyl(3'-5')thymidine led to the formation of three stable derivatives: one resulting from a combination between a 3'-end methylene radical and a 5'-end C(4) radical [4-(alpha-thyminyl) derivative] and two formed after a combination between a 3'-end methylene radical and a 5'-end C(6) radical [6-(alpha-thyminyl) derivative]. In the latter series, two stereochemical pathways took place during the reaction between the methylene and C(6) radicals. The major pathway occurred when the 5'-base glycosidic bond had an anti conformation leading to an S configuration of the C(6) Tp-end. The minor pathway, which had never been reported before in this series, involved a 5'-base in a syn conformation leading consequently to the R configuration at the C(6) Tp-end. The 5,6-dihydrothymine moiety of these two adducts presented a 5,6-trans diaxial substitution that resulted from the epimerization, at the 5,6-dihydropyrimidine 5-position, of a less stable cis-disubstituted intermediate.
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Affiliation(s)
- Javier Ulises Ortiz Mayo
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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29
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Guérineau V, Matus SKA, Halgand F, Laprévote O, Clivio P. Studies on the chemical synthesis of oligodeoxynucleotides containing the s 5T(6-4)T photoproduct: side reactions derived from the methylsulfenyl thiol protection elucidated by MALDI mass spectrometry. Org Biomol Chem 2004; 2:899-907. [PMID: 15007420 DOI: 10.1039/b314831a] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Attempts to incorporate the phosphoramidite of the thymine-thymine (6-4) photoproduct C5 thiol analogue (s(5)T(6-4)T PP), whose sulfur atom was protected with the methylsulfenyl group, into oligodeoxynucleotides (ODNs), are reported. Using matrix-assisted laser desorption-ionisation mass spectrometry (MALDI-MS) coupled to enzymatic digestion, accurate mass measurements and tandem mass spectrometry experiments, we demonstrated that ODNs containing the (2-cyanoethylthio)(5)T(6-4)T PP were obtained. Supported by model reactions, these results were explained 1) by the incorporation, during oligonucleotide synthesis, of the sulfur deprotected phosphoramidite that arose from a Michaelis-Arbusov-type rearrangement, and 2) the Michael addition to the thiol of acrylonitrile released upon the cyanoethyl phosphotriester deprotection. To avoid the formation of the cyanoethyl adduct, the phosphotriester deprotection was carried out in the presence of a thiol in excess. This afforded the ODN containing the h(5)T(6-4)T PP.
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Affiliation(s)
- Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS, avenue de la Terrasse, F-91 198 Gif-sur-Yvette cedex, France
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30
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Abstract
The synthesis and conformational analysis of 2'-O,5-dimethyluridylyl(3'-5')-2'-O,5-dimethyluridine (1a), the analogue of thymidylyl(3'-5')thymidine (TpT; 1b) in which a methoxy group replaces each 2'-alpha-hydrogen atom, are described. In comparison with TpT, such modification increases the population of the C3'-endo conformer of the sugar ring puckering at the 5'- and 3'-ends from 30 to 75% and from 37 to 66%, respectively. Photolyses of 1a and TpT at 254 nm are qualitatively comparable (the cis-syn cyclobutane pyrimidine dimer and the (6-4) photoproduct are formed), although it is significantly faster in the case of 1a. These results are explained by the increased propensity of the modified dinucleotide to adopt a base-stacked conformation geometry reminiscent of that for TpT.
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Affiliation(s)
- Tomasz Ostrowski
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France
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31
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Peyrane F, Fourrey JL, Clivio P. Thiation of 2'-deoxy-5,6-dihydropyrimidine nucleosides with Lawesson's reagent: characterisation of oxathiaphosphepane intermediates. Chem Commun (Camb) 2003:736-7. [PMID: 12703798 DOI: 10.1039/b211405d] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Treatment of 2'-deoxy-3',5'-dithexyldimethylsilyl-5,6-dihydrouridine with Lawesson's reagent led to the expected C4-thiolated derivative together with a number of oxathiaphosphepane isomers which resulted from the heat reversible incorporation of an AnPS2 unit within the 2'-deoxyribose moiety explaining the subsequent anomerisation of the 5,6-dihydropyrimidine nucleosides.
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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32
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Matus SKA, Fourrey JL, Clivio P. Synthesis of the TT pyrimidine (6–4) pyrimidone photoproduct–thio analogue phosphoramidite building block. Org Biomol Chem 2003; 1:3316-20. [PMID: 14584795 DOI: 10.1039/b305067j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [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
The phosphoramidite building block synthesis of the thio analogue at the 5,6-dihydropyrimidine C5 position of the thymidylyl(3'-5')thymidine (6-4) photoproduct 1 is presented. This compound was readily obtained from the appropriately protected dinucleotide P-methyl-5'-O-dimethoxytritylthymidilyl(3' --> 5')-4-thiothymidine 2 after irradiation at 366 nm, then S-sulfenylmethylation of the thiol function of the resulting (6-4) adduct, and phosphitylation of the 3'-hydroxyl group.
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Affiliation(s)
- Sandra Karina Angulo Matus
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif sur Yvette, France
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33
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Dupradeau FY, Sonnet P, Guillaume D, Senn HM, Clivio P. Ab initio study of the (5R)- and (5S)-TT pyrimidine h5(6-4) pyrimidone photoproducts. Implications on the design of new biologically relevant analogues. J Org Chem 2002; 67:9140-5. [PMID: 12492313 DOI: 10.1021/jo020604g] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A computational study of a series of N(1)- and/or C(6)-alkyl-5,6-dihydrothymine diastereomers at theory levels up to MP4(SDTQ)/6-31G//HF/6-31G and MP2/6-311G//HF/6-31G has demonstrated the respective importance of the substituents at positions 1, 5, and 6 on the energetically favored conformation of each isomer. Results obtained both in the gas and condensed phase indicate that unsubstitution of the N(1)-position favors a half-chair conformation with the C(5) -and C(6)-substituents in the equatorial position. On the other hand, in the case of the (6S)-1,6-dimethyl-5,6-dihydrothymine, the C(6)-substituent adopts the axial position to minimize its van der Waals interactions with the N(1)-substituent. Furthermore, if the configuration at the C(5)-dihydrothymine position has no resultant influence on the total molecular free energy, when a pyrimidone substituent is introduced at the dihydrothymine C(6)-position, additional repulsive forces between the C(5)- and C(6)-substituents make the diaxially substituted half-chair conformation the most energetically favorable one. These results indicate that the observed C(6)-axially substituted conformation of the thymine-thymine pyrimidine h(5)(6-4) pyrimidone photoproducts is not necessarily induced by the macrocyclic structure. They also nicely explain the formation mechanism of these photoproduct derivatives, and allow the prediction of the conformation of new analogues.
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Clivio P, Fourrey JL, Gasche J, Favre A. DNA photodamage mechanistic studies: characterization of a thietane intermediate in a model reaction relevant to "6-4 lesions". J Am Chem Soc 2002. [DOI: 10.1021/ja00014a065] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Clivio P, Fourrey JL, Szabo T, Stawinski J. Photochemistry of Di(deoxyribonucleoside) Methylphosphonates Containing N3-Methyl-4-thiothymine. J Org Chem 2002. [DOI: 10.1021/jo00103a018] [Citation(s) in RCA: 25] [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] [Indexed: 11/29/2022]
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37
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Thomas M, Guillaume D, Fourrey JL, Clivio P. Further insight in the photochemistry of DNA: structure of a 2-imidazolone (5-4) pyrimidone adduct derived from the mutagenic pyrimidine (6-4) pyrimidone photolesion by UV irradiation. J Am Chem Soc 2002; 124:2400-1. [PMID: 11890764 DOI: 10.1021/ja011292m] [Citation(s) in RCA: 17] [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: 11/30/2022]
Abstract
Pyrimidine (6-4) pyrimidone photoproducts represent one of the major mutagenic and carcinogenic class of DNA damage produced by UV exposure. At present, besides their conversion to their Dewar valence isomer, (6-4) photoproducts are generally believed to be photostable, and the observed biological properties of Paterno-Büchi-derived photoproducts are, thus far, exclusively attributed to these two types of compounds. Using a model system (2) relevant to DNA photochemistry, we have observed that the 5'-base moiety of the (6-4) thymine dimer 3, under far-UV radiation, is able to undergo a ring contraction leading to a 2-oxoimidazoline, 1. This unprecedented secondary photochemical reaction constitutes the first report of a major photomodification affecting (6-4) photoproducts and strongly questions the biological stability of the (6-4) adducts under UV light with 2-imidazolone (5-4) pyrimidone adducts being possibly another source of endogenous DNA damage.
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Affiliation(s)
- Martial Thomas
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91 190 Gif sur Yvette, France
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Thomas M, Clivio P, Guillaume D, Fourrey JL. Synthesis and photochemical behaviour of a T-T dimer containing an amide linkage. Nucleosides Nucleotides Nucleic Acids 2001; 20:927-9. [PMID: 11563146 DOI: 10.1081/ncn-100002460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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
A T-T dimer characterized by an amide linkage to replace the phosphodiester backbone has been synthesized using a modified radical strategy. The new synthetic approach makes use of a thymidin-3'-yl phosphorodithioate derivative as a precursor of 3'-allyl-3'-deoxythymidine. Standard chemical transformations of this derivative led to the desired T-T dimer incorporating an amide bond. The latter was irradiated with 254 nm wavelength light to yield mainly cyclobutane and [6-4] photoadducts.
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Affiliation(s)
- M Thomas
- Institut de Chimie de Chimie des Substances Naturelles, CNRS 91198 Gif-sur-Yvette, France
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Saintomé C, Clivio P, Fourrey JL, Woisard A, Laugâa P, Favre A. Synthesis of 4-Thiothymine Based Photolabels as New Tools for Nucleic Acids Structural Studies in Solution: Formation of Long-Range Photo-Cross-Links within a Hammerhead Ribozyme Domain. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00024-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Favre A, Saintomé C, Fourrey JL, Clivio P, Laugâa P. Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions. J Photochem Photobiol B 1998; 42:109-24. [PMID: 9540218 DOI: 10.1016/s1011-1344(97)00116-4] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the past few years thionucleobases have been extensively used as intrinsic photolabels to probe the structure in solution of folded RNA molecules and to identify contacts within nucleic acids and/or between nucleic acids and proteins, in complex nucleoprotein assemblies. These thio residues such as 4-thiouracil found in E. coli tRNA and its non-natural congeners 4-thiothymine, 6-thioguanine and 6-mercaptopurine absorb light at wavelengths longer than 320 nm and, thus, can be selectively photoactivated. Synthetic or enzymatic procedures have been established, allowing the random or site-specific incorporation of thionucleotide(s) within a RNA (DNA) chain which, in most cases, retains unaltered structural and biological properties. Owing to the high photoreactivity of their triplet state (intersystem yield close to unity), 4-thiouracil and 4-thiothymine derivatives exhibit a high photocrosslinking ability towards pyrimidines (particularly thymine) but also purines. From the nature of the photoproducts obtained in base or nucleotide mixtures and in dinucleotides, the main photochemical pathway was identified as a (2 + 2) photoaddition of the excited C-S bond onto the 5, 6 double bond of pyrimidines yielding thietane intermediates whose structure could be characterized. Depending on the mutual orientation of these bonds in the thietanes, their subsequent dark rearrangement yielded, respectively, either the 5-4 or 6-4 bipyrimidine photoadduct. A similar mechanism appears to be involved in the formation of the unique photoadduct formed between 4-thiothymidine and adenosine. The higher reactivity of thymine derived acceptors can be explained by an additional pathway which involves hydrogen abstraction from the thymine methyl group, followed by radical recombination, leading to methylene linked bipyrimidines. The high photocrosslinking potential of thionucleosides inserted in nucleic acid chains has been used to probe RNA-RNA contacts within the ribosome permitting, in particular, the elucidation of the path of mRNA throughout the small ribosomal subunit. Functional interactions between the mRNA spliced sites and U RNAs could be detected within the spliceosome. Analysis of the photocrosslinks obtained within small endonucleolytic ribozymes in solution led to a tertiary folded pseudo-knot structure for the HDV ribozyme and allowed the construction of a Y form of a hammerhead ribozyme, which revealed to be in close agreement with the structure observed in crystals. Thionucleosides incorporated in nucleic acids crosslink efficiently amino-acid residues of proteins in contact with them. Despite the fact that little is known about the nature of the photoadducts formed, this approach has been extensively used to identify protein components interacting at a defined nucleic acid site and applied to various systems (replisome, spliceosome, transcription complexes and ribosomes).
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Affiliation(s)
- A Favre
- Institut Jacques Monod, CNRS-Université Paris VII, France
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Clivio P, Guillaume D, Adeline MT, Hamon J, Riche C, Fourrey JL. Synthesis and Photochemical Behavior of Peptide Nucleic Acid Dimers and Analogues Containing 4-Thiothymine: Unprecedented (5−4) Photoadduct Reversion. J Am Chem Soc 1998. [DOI: 10.1021/ja971983b] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Clivio P, Fourrey JL. Photochemistry of the thio-analogue of the DNA (6-4) photoproduct Dewar valence isomer: Structure of a new photoproduct. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(97)10511-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Saintomé C, Clivio P, Favre A, Fourrey JL. Photochemistry of 4-Thiothymine Derivatives in the Presence of N-9-Substituted-Adenine Derivatives: Formation of N-6-Formamidopyrimidines. J Org Chem 1997; 62:8125-8130. [PMID: 11671921 DOI: 10.1021/jo971162p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UV irradiation of aqueous solutions containing either 4-thiothymin-1-ylacetic acid (1b) and adenosine (2a), 4-thiothymidine (1a) and adenin-9-ylacetic acid (2b), or 1b and 2b led to 4,5-diamino-6-formamidopyrimidine (N-6-Fapy-Ade) derivatives as observed after irradiation of a mixture of 1a and 2a (J. Am. Chem. Soc. 1996, 118, 8142-8143). These new observations demonstrate that the replacement of one or both nucleoside sugar residues by a carboxymethyl group does not affect the regioselective course of the photochemical reaction. The thermal decomposition of 3a that resulted from irradiation of 1a in the presence of 2a, was examined along with its behavior under mild alkaline conditions. Finally, irradiation of N-3-methyl-4-thiothymidine (6a) in the presence of adenosine gave the N-3-methylcytidine derivative 7.
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Affiliation(s)
- Carole Saintomé
- Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France, and Institut Jacques Monod, CNRS-Université Paris VII, 2 Place Jussieu, 75251 Paris Cedex 05, France
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Affiliation(s)
- Pascale Clivio
- Institut de Chimie des Substances Naturelles, CNRS 91198 Gif-sur-Yvette Cedex, France Laboratoire de Chimie Thérapeutique (URA 1310) Faculté de Pharmacie, Université René Descartes 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Dominique Guillaume
- Institut de Chimie des Substances Naturelles, CNRS 91198 Gif-sur-Yvette Cedex, France Laboratoire de Chimie Thérapeutique (URA 1310) Faculté de Pharmacie, Université René Descartes 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Marie-Thérèse Adeline
- Institut de Chimie des Substances Naturelles, CNRS 91198 Gif-sur-Yvette Cedex, France Laboratoire de Chimie Thérapeutique (URA 1310) Faculté de Pharmacie, Université René Descartes 4, Avenue de l'Observatoire, 75006 Paris, France
| | - Jean-Louis Fourrey
- Institut de Chimie des Substances Naturelles, CNRS 91198 Gif-sur-Yvette Cedex, France Laboratoire de Chimie Thérapeutique (URA 1310) Faculté de Pharmacie, Université René Descartes 4, Avenue de l'Observatoire, 75006 Paris, France
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Saintomé C, Clivio P, Favre A, Fourrey JL, Laugâa P. Site specific photo-crosslinking of single stranded oligonucleotides by a complementary sequence equipped with an internal photoactive probe. Chem Commun (Camb) 1997. [DOI: 10.1039/a606330f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Saintomé C, Clivio P, Favre A, Fourrey JL, Riche C. RNA Photolabeling Mechanistic Studies: X-ray Crystal Structure of the Photoproduct Formed between 4-Thiothymidine and Adenosine upon Near UV Irradiation. J Am Chem Soc 1996. [DOI: 10.1021/ja961329g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carole Saintomé
- Institut de Chimie des Substances Naturelles CNRS, 91198 Gif-sur-Yvette Cedex, France Institut Jacques Monod, CNRS-Université Paris VII 2 Place Jussieu, 75251 Paris Cedex O5, France
| | - Pascale Clivio
- Institut de Chimie des Substances Naturelles CNRS, 91198 Gif-sur-Yvette Cedex, France Institut Jacques Monod, CNRS-Université Paris VII 2 Place Jussieu, 75251 Paris Cedex O5, France
| | - Alain Favre
- Institut de Chimie des Substances Naturelles CNRS, 91198 Gif-sur-Yvette Cedex, France Institut Jacques Monod, CNRS-Université Paris VII 2 Place Jussieu, 75251 Paris Cedex O5, France
| | - Jean-Louis Fourrey
- Institut de Chimie des Substances Naturelles CNRS, 91198 Gif-sur-Yvette Cedex, France Institut Jacques Monod, CNRS-Université Paris VII 2 Place Jussieu, 75251 Paris Cedex O5, France
| | - Claude Riche
- Institut de Chimie des Substances Naturelles CNRS, 91198 Gif-sur-Yvette Cedex, France Institut Jacques Monod, CNRS-Université Paris VII 2 Place Jussieu, 75251 Paris Cedex O5, France
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Burlina F, Clivio P, Fourrey JL, Riche C, Thomas M. Convenient chemical resolution of a bicyclic hydroxylactone of synthetic interest. Tetrahedron Lett 1994. [DOI: 10.1016/0040-4039(94)88268-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Saintomé C, Clivio P, Fourrey JL, Woisard A, Favre A. Development of new nucleic acid photoaffinity probes: Synthesis of 4-thiothymine labelled nucleoside analogues. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)75986-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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