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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] [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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Vasilyeva SV, Kuznetsova AA, Baranovskaya EE, Kuznetsov NA, Lomzov AA, Pyshnyi DV. Synthesis of the new nucleoside 5'-alpha-iminophosphates using Staudinger reaction. Bioorg Chem 2022; 127:105987. [DOI: 10.1016/j.bioorg.2022.105987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
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Detection of the thietane precursor in the UVA formation of the DNA 6-4 photoadduct. Nat Commun 2020; 11:3599. [PMID: 32680990 PMCID: PMC7368040 DOI: 10.1038/s41467-020-17333-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
Notwithstanding the central biological role of the (6-4) photoadduct in the induction of skin cancer by sunlight, crucial mechanistic details about its formation have evaded characterization despite efforts spanning more than half a century. 4-Thiothymidine (4tT) has been widely used as an important model system to study its mechanism of formation, but the excited-state precursor, the intermediate species, and the time scale leading to the formation of the (6-4) photoadduct have remained elusive. Herein, steady-state and time-resolved spectroscopic techniques are combined with new and reported quantum-chemical calculations to demonstrate the excited state leading to the formation of the thietane intermediate, its rate, and the formation of the (6-4) photoadduct using the 5’-TT(4tT)T(4tT)TT-3’ DNA oligonucleotide. Efficient, sub-1 ps intersystem crossing leads to the population of a triplet minimum of the thietane intermediate in as short as 3 ps, which intersystem crosses to its ground state and rearranges to form the (6-4) photoadduct. The mechanisms of formation of the (6-4) photoproducts in DNA damage by sunlight is still debated. Here the authors show, by optical spectroscopies and computations, the details of the formation of a (6-4) photoadduct via the thietane intermediate in a single-stranded DNA oligonucleotide.
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Yan H, Zhu K, Teng M, Li X. A newly identified photolyase from Arthrospira platensis possesses a unique methenyltetrahydrofolate chromophore-binding pattern. FEBS Lett 2019; 594:740-750. [PMID: 31675429 DOI: 10.1002/1873-3468.13657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 01/03/2023]
Abstract
Cyclobutane pyrimidine dimers (CPD), as a common DNA damage caused by UV radiation, often lead to skin cancer. Here, we identified a photolyase from the alga Arthrospira platensis (designated as Ap-phr), which has been regarded as a safe organism for humans for centuries, that can efficiently repair CPD lesions in ssDNA and dsDNA in vitro. The 1.6 Å resolution crystal structure of Ap-phr revealed that it possesses a unique methenyltetrahydrofolate chromophore-binding pattern with high energy transfer efficiency. Our study of Ap-phr highlights its potential use in cosmetic, industrial and aesthetic medicine applications.
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Affiliation(s)
- Hui Yan
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Kongfu Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
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Martínez-Fernández L, Improta R. Sequence dependence on DNA photochemistry: a computational study of photodimerization pathways in TpdC and dCpT dinucleotides. Photochem Photobiol Sci 2018; 17:586-591. [PMID: 29624198 DOI: 10.1039/c8pp00040a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The excited states involved in the main photodimerization paths in TpdC and dCpT are mapped by PCM/TD-M052X calculations, considering different dinucleotide conformers. As for TT steps, a cyclobutane pyrimidine dimer (CPD) is formed on the PES of the lowest energy exciton, delocalized over two stacked pyrimidines; 6-4 pyrimidine-pyrimidone (64-PP) adduct's formation involves instead a 5'-ter → 3'-ter charge transfer state. For dCpT, 64-PP dimerization occurs via a two-step reaction, which proceeds through an oxetane intermediate. For TpdC, instead, the final 64-PP product is obtained in a single step and it is as stable as the CPD photoproduct, explaining the relatively large yield of 64-PP found experimentally for TC steps in DNA.
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Affiliation(s)
- Lara Martínez-Fernández
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy. and LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Roberto Improta
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy. and LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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Domratcheva T, Schlichting I. Spiers Memorial Lecture. Introductory lecture: the impact of structure on photoinduced processes in nucleic acids and proteins. Faraday Discuss 2018; 207:9-26. [PMID: 29583144 DOI: 10.1039/c8fd00058a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light is an important environmental variable and most organisms have evolved means to sense, exploit or avoid it and to repair detrimental effects on their genome. In general, light absorption is the task of specific chromophores, however other biomolecules such as oligonucleotides also do so which can result in undesired outcomes such as mutations and cancer. Given the biological importance of light-induced processes and applications for imaging, optogenetics, photodynamic therapy or photovoltaics, there is a great interest in understanding the detailed molecular mechanisms of photoinduced processes in proteins and nucleic acids. The processes are typically characterized by time-resolved spectroscopic approaches or computation, inferring structural information on transient species from stable ground state structures. Recently, however, structure determination of excited states or other short-lived species has become possible with the advent of X-ray free-electron lasers. This review gives an overview of the impact of structure on the understanding of photoinduced processes in macromolecules, focusing on systems presented at this Faraday Discussion meeting.
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Affiliation(s)
- Tatiana Domratcheva
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
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Conti I, Martínez-Fernández L, Esposito L, Hofinger S, Nenov A, Garavelli M, Improta R. Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6-4 Thymine-Thymine Photodimerization in a DNA Duplex. Chemistry 2017; 23:15177-15188. [PMID: 28809462 DOI: 10.1002/chem.201703237] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 11/09/2022]
Abstract
The T-T photodimerization paths leading to the formation of cyclobutane pyrimidine dimer (CPD) and 6-4 pyrimidine pyrimidone (64-PP), the two main DNA photolesions, have been resolved for a T-T step in a DNA duplex by two complementary state-of-the-art quantum mechanical approaches: QM(CASPT2//CASSCF)/MM and TD-DFT/PCM. Based on the analysis of several different representative structures, we define a new-ensemble of cooperating geometrical and electronic factors (besides the distance between the reacting bonds) ruling T-T photodimerization in DNA. CPD is formed by a barrierless path on an exciton state delocalized over the two bases. Large interbase stacking and shift values, together with a small pseudorotation phase angle for T at the 3'-end, favor this reaction. The oxetane intermediate, leading to a 64-PP adduct, is formed on a singlet T→T charge-transfer state and is favored by a large interbase angle and slide values. A small energy barrier (<0.3 eV) is associated to this path, likely contributing to the smaller quantum yield observed for this process. Eventually, a clear directionality is always shown by the electronic excitation characterizing the singlet photoactive state driving the photodimerization process: an exciton that is more localized on T3 and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale "T. Montanari", Università di Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | | | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Siegfried Hofinger
- TU Wien, Zentraler Informatikdienst, Wiedner Hauptstrasse 8-10, 1040, Wien, Austria.,Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49331-1295, USA
| | - Artur Nenov
- Dipartimento di Chimica Industriale "T. Montanari", Università di Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "T. Montanari", Università di Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy.,LIDYL, CEA, CNRS, Université Paris, Saclay, 91191, Gif-sur-Yvette, France
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