1
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Zhang QB, Li F, Pan B, Yu L, Yue XG. Visible-Light-Mediated [2+2] Photocycloadditions of Alkynes. Chemistry 2024; 30:e202401501. [PMID: 38806409 DOI: 10.1002/chem.202401501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024]
Abstract
Visible-light-mediated [2+2] photocycloaddition reaction can be considered an ideal solution due to its green and sustainable properties, and is one of the most efficient methods to synthesize four-membered ring motifs. Although research on the [2+2] photocycloaddition of alkynes is challenging because of the diminished reactivity of alkynes, and the more significant ring strain of the products, remarkable achievements have been made in this field. In this article, we highlight the recent advances in visible-light-mediated [2+2] photocycloaddition reactions of alkynes, with focus on the reaction mechanism and the late-stage synthetic applications. Advances in obtaining cyclobutenes, azetines, and oxetene active intermediates continue to be breakthroughs in this fascinating field of research.
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Affiliation(s)
- Qing-Bao Zhang
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, CN, 262700, People's Republic of China
| | - Feng Li
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, CN, 262700, People's Republic of China
| | - Bin Pan
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, CN, 262700, People's Republic of China
| | - Lei Yu
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, CN, 262700, People's Republic of China
| | - Xiang-Guo Yue
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, CN, 262700, People's Republic of China
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2
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Wearing ER, Blackmun DE, Becker MR, Schindler CS. 1- and 2-Azetines via Visible Light-Mediated [2 + 2]-Cycloadditions of Alkynes and Oximes. J Am Chem Soc 2021; 143:16235-16242. [PMID: 34570970 DOI: 10.1021/jacs.1c07523] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Azetines, four-membered unsaturated nitrogen-containing heterocycles, hold great potential for drug design and development but remain underexplored due to challenges associated with their synthesis. We report an efficient, visible light-mediated approach toward 1- and 2-azetines relying on alkynes and the unique triplet state reactivity of oximes, specifically 2-isoxazolines. While 2-azetine products are accessible upon intermolecular [2 + 2]-cycloaddition via triplet energy transfer from a commercially available iridium photocatalyst, the selective formation of 1-azetines proceeds upon a second, consecutive, energy transfer process. Mechanistic studies are consistent with a stepwise reaction mechanism via N-O bond homolysis following the second energy transfer event to result in the formation of 1-azetine products. Characteristic for this method is its operational simplicity, mild conditions, and modular approach that allow for the synthesis of functionalized azetines and tetrahydrofurans (via in situ hydrolysis) from readily available precursors.
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Affiliation(s)
- Emily R Wearing
- University of Michigan, Department of Chemistry, Willard Henry Dow Laboratory, 930 North University Ave., Ann Arbor, Michigan 48109, United States
| | - Dominique E Blackmun
- University of Michigan, Department of Chemistry, Willard Henry Dow Laboratory, 930 North University Ave., Ann Arbor, Michigan 48109, United States
| | - Marc R Becker
- University of Michigan, Department of Chemistry, Willard Henry Dow Laboratory, 930 North University Ave., Ann Arbor, Michigan 48109, United States
| | - Corinna S Schindler
- University of Michigan, Department of Chemistry, Willard Henry Dow Laboratory, 930 North University Ave., Ann Arbor, Michigan 48109, United States
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3
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Osswald M, Fingerhut BP. Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of Drosophila melanogaster. J Phys Chem B 2021; 125:8690-8702. [PMID: 34323497 DOI: 10.1021/acs.jpcb.1c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of Drosophila melanogaster (D. melanogaster). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH- cofactor that facilitates reduction of the photoproduct. Microscopic details of the collective reaction coordinate of ET reactions are identified that involve the reorganization of the hydrogen bond network and structural relaxation of the active site. The simulations reveal complex active site relaxation dynamics involving distinguished amino acids (Lys246, His365, and His369), conformational reorganization of the hydroxyl group of the (6-4) photoproduct, and a strengthening of hydrogen bonds with immobilized water molecules. In particular, rotation of the Lys246 side chain is found to impose a double-well character along the reaction coordinate of the ET reaction. Our findings suggest that the primary ET reactions in the (6-4) photoproduct enzyme repair complex of D. melanogaster are governed by a complex multi-minima active site relaxation dynamics and potentially precede the equilibration of the protein. ET pathways mediated by the adenine moiety and the 5' side of the photoproduct are proposed to be relevant for triggering the catalytic (6-4) photoproduct reactivation.
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Affiliation(s)
- Mara Osswald
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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4
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Cellini A, Yuan Wahlgren W, Henry L, Pandey S, Ghosh S, Castillon L, Claesson E, Takala H, Kübel J, Nimmrich A, Kuznetsova V, Nango E, Iwata S, Owada S, Stojković EA, Schmidt M, Ihalainen JA, Westenhoff S. The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallogr D Struct Biol 2021; 77:1001-1009. [PMID: 34342273 PMCID: PMC8329860 DOI: 10.1107/s2059798321005830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Leticia Castillon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Valentyna Kuznetsova
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Eriko Nango
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St Louis Avenue, Chicago, IL 60625, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Janne A. Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
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Didier D, Reiners F. Uncommon Four-Membered Building Blocks - Cyclobutenes, Azetines and Thietes. CHEM REC 2021; 21:1144-1160. [PMID: 33734571 DOI: 10.1002/tcr.202100011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Strained ring systems have gained considerable importance over the last few years for their implication in natural product syntheses or in drug discovery programs. We present herein a recollection of our work on the construction and functionalization of unsaturated four-membered carbo- and heterocycles in the context of the literature, as well as their applications in further reactions.
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Affiliation(s)
- Dorian Didier
- Department of Chemistry, Ludwig-Maximilians Universität, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Felix Reiners
- Department of Chemistry, Ludwig-Maximilians Universität, Butenandtstraße 5-13, 81377, Munich, Germany
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6
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Franz S, Ignatz E, Wenzel S, Zielosko H, Putu E, Maestre-Reyna M, Tsai MD, Yamamoto J, Mittag M, Essen LO. Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii. Nucleic Acids Res 2019; 46:8010-8022. [PMID: 30032195 PMCID: PMC6125616 DOI: 10.1093/nar/gky621] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023] Open
Abstract
Photolyases and cryptochromes form an almost ubiquitous family of blue light photoreceptors involved in the repair and maintenance of DNA integrity or regulatory control. We found that one cryptochrome from the green alga Chlamydomonas reinhardtii (CraCRY) is capable of both, control of transcript levels and the sexual cycle of the alga in a positive (germination) and negative manner (mating ability), as well as catalyzing the repair of UV-DNA lesions. Its 1.6 Å crystal structure shows besides the FAD chromophore an aromatic tetrad that is indispensable in animal-like type I cryptochromes for light-driven change of their signaling-active redox state and formation of a stable radical pair. Given CraCRY’s catalytic activity as (6-4) photolyase in vivo and in vitro, we present the first co-crystal structure of a cryptochrome with duplex DNA comprising a (6-4) pyrimidine–pyrimidone lesion. This 2.9 Å structure reveals a distinct conformation for the catalytic histidine His1, H357, that challenges previous models of a single-photon driven (6-4) photolyase mechanism.
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Affiliation(s)
- Sophie Franz
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Elisabeth Ignatz
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Sandra Wenzel
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Hannah Zielosko
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | | | - Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Taipei 115, Taiwan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
- LOEWE Center of Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
- To whom correspondence should be addressed. Tel: +49 6421/28 22032; Fax: +49 6421/28 22012;
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7
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Didier D, Baumann AN, Eisold M. Unsaturated four-membered N-heterocycles: From synthesis to applications. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.09.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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8
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Dokainish HM, Kitao A. Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases. J Phys Chem B 2018; 122:8537-8547. [PMID: 30124048 DOI: 10.1021/acs.jpcb.8b07048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Photolyases are ancient enzymes that harvest sunlight to repair DNA pyrimidine lesions such as pyrimidine(6-4)pyrimidone and cyclobutane dimers. Particularly, (6-4) photolyase ((6-4)PHR) plays an important role in maintaining genetic integrity by repairing thymine(6-4)thymine (T(6-4)T) and thymine(6-4)cytosine (T(6-4)C) photolesions. The majority of (6-4)PHR studies have been performed on the basis of the former's activity and assuming the equivalence of the two repair mechanisms, although the latter's activity remains poorly studied. Here, we describe investigations of the repair process of the T(6-4)C dimer using several computational methods from molecular dynamics (MD) simulations to large quantum mechanical/molecular mechanical approaches. Two possible mechanisms, the historically proposed azetidine four-member ring intermediate and the free NH3 formation pathways, were considered. The MD results predicted that important active site histidine residues employed for the repair of the T(6-4)C dimer have protonation states similar to those seen in the (6-4)PHR/T(6-4)T complex. More importantly, despite chemical differences between the two substrates, a similar repair mechanism was identified: His365 protonates NH2, resulting in formation/activation mechanism of a free NH3, inducing NH2 transfer to the 5' base, and ultimately leading to pyrimidine restoration. This reaction is thermodynamically favorable with a rate-limiting barrier of 20.4 kcal mol-1. In contrast, the azetidine intermediate is unfeasible, possessing an energy barrier of 60 kcal mol-1; this barrier is similar to that predicted for the oxetane intermediate in T(6-4)T repair. Although both substrates are repaired with comparable quantum yields, the reactive complex in T(6-4)C was shown to be a 3' base radical with a lower driving force for back electron transfer combined with higher energy barrier for catalysis. These results showed the similarity in the general repair mechanisms between the two substrates while emphasizing differences in the electron dynamics in the repair cycle.
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Affiliation(s)
- Hisham M Dokainish
- School of Life Science and Technology , Tokyo Institute of Technology , M6-13, 2-12-1 Ookayama , Meguro , Tokyo 152-8550 , Japan
| | - Akio Kitao
- School of Life Science and Technology , Tokyo Institute of Technology , M6-13, 2-12-1 Ookayama , Meguro , Tokyo 152-8550 , Japan
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9
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Hintze BJ, Richardson JS, Richardson DC. Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallogr D Struct Biol 2017; 73:852-859. [PMID: 28994414 PMCID: PMC5633910 DOI: 10.1107/s2059798317013729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or other syn purines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing a syn/anti 180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips. Seven examples are modeled as Watson-Crick base pairs but should be Hoogsteens (commonest at duplex termini), and three had the opposite issue. Syn/anti flips were also needed for some single-stranded purines. Five of the 20 convincing cases arose from an unmodeled alternate duplex running in the opposite direction. These are in semi-palindromic DNA sequences bound by a homodimeric protein and show flipped-purine-like difference peaks at residues where the palindrome is imperfect. This study documents types of incorrect modeling which are worth avoiding. However, the primary conclusions are that such mistakes are infrequent, the bias towards fitting anti purines is very slight, and the occurrence rate of Hoogsteen base pairs in DNA crystal structures remains unchanged from earlier estimates at ∼0.3%.
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10
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Yamamoto J, Plaza P, Brettel K. Repair of (6-4) Lesions in DNA by (6-4) Photolyase: 20 Years of Quest for the Photoreaction Mechanism. Photochem Photobiol 2017; 93:51-66. [PMID: 27992654 DOI: 10.1111/php.12696] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/09/2016] [Indexed: 01/05/2023]
Abstract
Exposure of DNA to ultraviolet (UV) light from the Sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Nature has developed unique flavoenzymes, called DNA photolyases, that utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. In this review, we focus on the chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and describe the major events along the quest for the reaction mechanisms, over the 20 years since the discovery of (6-4) photolyase.
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Affiliation(s)
- Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Pascal Plaza
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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11
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Knips A, Zacharias M. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage. Sci Rep 2017; 7:41324. [PMID: 28128222 PMCID: PMC5269681 DOI: 10.1038/srep41324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/16/2016] [Indexed: 01/31/2023] Open
Abstract
The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.
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Affiliation(s)
- Alexander Knips
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
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12
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Dokainish HM, Kitao A. Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hisham M. Dokainish
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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13
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Knips A, Zacharias M. Influence of a cis,syn-cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations. Biopolymers 2016; 103:215-22. [PMID: 25382106 DOI: 10.1002/bip.22586] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/03/2014] [Indexed: 02/01/2023]
Abstract
The photo-induced formation of cis-syn-cyclobutane pyrimidine dimers (CPD) is a highly mutagenic and cancerogenic DNA lesion. In bacteria photolyases can efficiently reverse the dimer formation employing a light-driven reaction after looping out the CPD damaged bases into the enzyme active site. The exact mechanism how the repair enzyme identifies a damaged site within a large surplus of undamaged DNA is not fully understood. The CPD damage may alter the DNA structure and dynamics already in the absence of the repair enzyme which can facilitate the initial binding of a photolyase repair enzyme. To characterize the effect of a CPD damage, extensive comparative molecular dynamics (MD) simulations on duplex DNA with central regular or CPD damaged nucleotides were performed supplemented with simulations of the DNA-photolyase complex. Although no spontaneous flipping out transitions of the damaged bases were observed, the simulations showed significant differences in the conformational states of regular and CPD damage DNA. The isolated damaged DNA adopted transient conformations which resembled the global shape of the repair enzyme bound conformation more closely compared to regular B-DNA. In particular, these conformational changes were observed in most of helical and structural parameters where the protein bound DNA differs drastically from regular B-DNA. It is likely that the transient overlap of isolated DNA with the enzyme bound DNA conformation plays a decisive role for the specific and rapid initial recognition by the repair enzyme prior to the looping out process of the damaged DNA.
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Affiliation(s)
- Alexander Knips
- Physik-Department T38, Technische Universität München, James-Franck-Str. 1, D-85748, Garching, Germany
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14
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Douki T, Sage E. Dewar valence isomers, the third type of environmentally relevant DNA photoproducts induced by solar radiation. Photochem Photobiol Sci 2015; 15:24-30. [PMID: 26692437 DOI: 10.1039/c5pp00382b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
UV-induced DNA damage is the main initiating event in solar carcinogenesis. UV radiation is known to induce pyrimidine dimers in DNA, including cyclobutane dimers and (6-4) photoproducts which have been extensively studied. In contrast, much less attention has been paid to Dewar valence isomers, the photoisomerisation product of (6-4) photoproducts. Yet, the available data show that Dewar isomers can be produced by exposure to sunlight and may lead to mutations. Dewars are thus environmentally and biologically relevant. The present review summarizes currently available information on the formation, mutagenic properties and repair of this class of UV-induced DNA damage.
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Affiliation(s)
- T Douki
- Univ. Grenoble Alpes, INAC, LCIB, LAN, F-38000 Grenoble, France
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15
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Pulschen AA, Rodrigues F, Duarte RTD, Araujo GG, Santiago IF, Paulino-Lima IG, Rosa CA, Kato MJ, Pellizari VH, Galante D. UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology. Microbiologyopen 2015; 4:574-88. [PMID: 26147800 PMCID: PMC4554453 DOI: 10.1002/mbo3.262] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 03/18/2015] [Accepted: 03/27/2015] [Indexed: 11/17/2022] Open
Abstract
The Sairecabur volcano (5971 m), in the Atacama Desert, is a high-altitude extreme environment with high daily temperature variations, acidic soils, intense UV radiation, and low availability of water. Four different species of yeasts were isolated from this region using oligotrophic media, identified and characterized for their tolerance to extreme conditions. rRNA sequencing revealed high identity (>98%) to Cryptococcus friedmannii, Exophiala sp., Holtermanniella watticus, and Rhodosporidium toruloides. To our knowledge, this is the first report of these yeasts in the Atacama Desert. All isolates showed high resistance to UV-C, UV-B and environmental-UV radiation, capacity to grow at moderate saline media (0.75–2.25 mol/L NaCl) and at moderate to cold temperatures, being C. friedmannii and H. watticus able to grow in temperatures down to −6.5°C. The presence of pigments, analyzed by Raman spectroscopy, correlated with UV resistance in some cases, but there is evidence that, on the natural environment, other molecular mechanisms may be as important as pigmentation, which has implications for the search of spectroscopic biosignatures on planetary surfaces. Due to the extreme tolerances of the isolated yeasts, these organisms represent interesting eukaryotic models for astrobiological purposes.
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Affiliation(s)
- André A Pulschen
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Rodrigues
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Rubens T D Duarte
- Microbiology, Immunology and Parasitology Department, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Gabriel G Araujo
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil.,Brazilian Synchrotron Light Laboratory, Campinas, Brazil
| | - Iara F Santiago
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ivan G Paulino-Lima
- NASA Postdoctoral Program Fellow at NASA Ames Research Center, Moffett Field, California
| | - Carlos A Rosa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Massuo J Kato
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | | | - Douglas Galante
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil.,Brazilian Synchrotron Light Laboratory, Campinas, Brazil
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16
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Karentz D. Beyond xeroderma pigmentosum: DNA damage and repair in an ecological context. A tribute to James E. Cleaver. Photochem Photobiol 2014; 91:460-74. [PMID: 25395165 DOI: 10.1111/php.12388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/29/2014] [Indexed: 12/12/2022]
Abstract
The ability to repair DNA is a ubiquitous characteristic of life on Earth and all organisms possess similar mechanisms for dealing with DNA damage, an indication of a very early evolutionary origin for repair processes. James E. Cleaver's career (initiated in the early 1960s) has been devoted to the study of mammalian ultraviolet radiation (UVR) photobiology, specifically the molecular genetics of xeroderma pigmentosum and other human diseases caused by defects in DNA damage recognition and repair. This work by Jim and others has influenced the study of DNA damage and repair in a variety of taxa. Today, the field of DNA repair is enhancing our understanding of not only how to treat and prevent human disease, but is providing insights on the evolutionary history of life on Earth and how natural populations are coping with UVR-induced DNA damage from anthropogenic changes in the environment such as ozone depletion.
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Affiliation(s)
- Deneb Karentz
- Department of Biology, University of San Francisco, San Francisco, CA
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17
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Douki T, Meador JA, Bérard I, Wack A. N4-methylation of cytosine drastically favors the formation of (6-4) photoproducts in a TCG context. Photochem Photobiol 2014; 91:102-8. [PMID: 25319211 DOI: 10.1111/php.12365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/13/2014] [Indexed: 11/27/2022]
Abstract
Methylation of cytosine is a common biological process both in prokaryotic and eukaryotic cells. In addition to 5-methylcytosine (5mC), some bacterial species contain in their genome N(4) -methylcytosine (N4mC). Methylation at C5 has been shown to enhance the formation of pyrimidine dimeric photoproducts but nothing is known of the effect of N4 methylation on UV-induced DNA damage. In the present work, we compared the yield and the nature of bipyrimidine photoproducts induced in a series of trinucleotides exhibiting a TXG sequence where X is either T, C, 5mC or N4mC. HPLC associated to tandem mass spectrometry was used to quantify cyclobutane pyrimidine dimers (CPD), (6-4) photoproducts (64PP) and their Dewar valence isomer. Methylation at position N4 was found to drastically increase the reactivity of C upon exposure to both UVC and UVB and to favor the formation of 64PP. In contrast methylation at C5 increased the yield of CPD at the expense of 64PP. In addition, enhancement of photoreactivity by C5 methylation was much higher in the UVB than in the UVC range. These results show the drastic effect of the methylation site on the photochemistry of cytosine.
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Affiliation(s)
- Thierry Douki
- University Grenoble Alpes, INAC-LCIB, LAN, Grenoble, France; CEA, INAC-SCIB, LAN, Grenoble, France
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18
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Meador JA, Baldwin AJ, Pakulski JD, Jeffrey WH, Mitchell DL, Douki T. The significance of the Dewar valence photoisomer as a UV radiation-induced DNA photoproduct in marine microbial communities. Environ Microbiol 2014; 16:1808-20. [PMID: 24517516 DOI: 10.1111/1462-2920.12414] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/11/2014] [Accepted: 01/27/2014] [Indexed: 11/28/2022]
Abstract
Induction of pyrimidine dimers in DNA by solar UV radiation has drastic effects on microorganisms. To better define the nature of these DNA photoproducts in marine bacterioplankton and eukaryotes, a study was performed during a cruise along a latitudinal transect in the Pacific Ocean. The frequency of all possible cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts (64PPs) and their related Dewar valence isomers (DEWs) was determined by high-performance liquid chromatography-mass spectrometry. Studied samples were bacterioplankton and eukaryotic fractions isolated from sea water either collected before sunrise or exposed to ambient sunlight from sunrise to sunset. Isolated DNA dosimeters were also exposed to daily sunlight for comparison purposes. A first major result was the observation in all samples of large amounts of DEWs, a class of photoproducts rarely considered outside photochemical studies. Evidence was obtained for a major role of UVA in the formation of these photoisomerization products of 64PPs. Considerations on the ratio between the different classes of photoproducts in basal and induced DNA damage suggests that photoenzymatic repair (PER) is an important DNA repair mechanism used by marine microorganisms occupying surface seawater in the open ocean. This result emphasizes the biological role of DEWs which are very poor substrate for PER.
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Affiliation(s)
- Jarah A Meador
- Center for Radiological Research, Columbia University, New York, NY, USA
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19
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Singh I, Lian Y, Li L, Georgiadis MM. The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:752-9. [PMID: 24598744 PMCID: PMC3949526 DOI: 10.1107/s1399004713032987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/05/2013] [Indexed: 11/12/2022]
Abstract
The spore photoproduct lesion (SP; 5-thymine-5,6-dihydrothymine) is the dominant photoproduct found in UV-irradiated spores of some bacteria such as Bacillus subtilis. Upon spore germination, this lesion is repaired in a light-independent manner by a specific repair enzyme: the spore photoproduct lyase (SP lyase). In this work, a host-guest approach in which the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) serves as the host and DNA as the guest was used to determine the crystal structures of complexes including 16 bp oligonucleotides with and without the SP lesion at 2.14 and 1.72 Å resolution, respectively. In contrast to other types of thymine-thymine lesions, the SP lesion retains normal Watson-Crick hydrogen bonding to the adenine bases of the complementary strand, with shorter hydrogen bonds than found in the structure of the undamaged DNA. However, the lesion induces structural changes in the local conformation of what is otherwise B-form DNA. The region surrounding the lesion differs significantly in helical form from B-DNA, and the minor groove is widened by almost 3 Å compared with that of the undamaged DNA. Thus, these unusual structural features associated with SP lesions may provide a basis for recognition by the SP lyase.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yajun Lian
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| | - Lei Li
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University at Indianapolis, Indianapolis, IN 46202, USA
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20
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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21
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Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore. Proc Natl Acad Sci U S A 2013; 110:7217-22. [PMID: 23589886 DOI: 10.1073/pnas.1302377110] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The (6-4) photolyases use blue light to reverse UV-induced (6-4) photoproducts in DNA. This (6-4) photorepair was thought to be restricted to eukaryotes. Here we report a prokaryotic (6-4) photolyase, PhrB from Agrobacterium tumefaciens, and propose that (6-4) photolyases are broadly distributed in prokaryotes. The crystal structure of photolyase related protein B (PhrB) at 1.45 Å resolution suggests a DNA binding mode different from that of the eukaryotic counterparts. A His-His-X-X-Arg motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. The PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore and a [4Fe-4S] cluster bound to the catalytic domain. A significant part of the Fe-S fold strikingly resembles that of the large subunit of eukaryotic and archaeal primases, suggesting that the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. Our study presents a unique prokaryotic (6-4) photolyase and proposes that the prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family.
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22
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Fingerhut BP, Oesterling S, Haiser K, Heil K, Glas A, Schreier WJ, Zinth W, Carell T, de Vivie-Riedle R. ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization. J Chem Phys 2012; 136:204307. [PMID: 22667560 DOI: 10.1063/1.4720090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.
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Affiliation(s)
- Benjamin P Fingerhut
- Department of Chemistry, Ludwig-Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany.
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23
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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24
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Condic-Jurkic K, Smith AS, Zipse H, Smith DM. The Protonation States of the Active-Site Histidines in (6-4) Photolyase. J Chem Theory Comput 2012; 8:1078-91. [PMID: 26593369 DOI: 10.1021/ct2005648] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active sites of the (6-4) photolyases contain two conserved histidine residues, which, in the Drosophila melanogaster enzyme, correspond to His365 and His369. While there are nine combinations in which the three possible protonation states of the two histidines (with protons on Nδ (HID), Nε (HIE), or both Nδ and Nε (HIP)) can be paired, there is presently no consensus as to which of these states is present, let alone mechanistically relevant. EPR hyperfine couplings for selected protons of the FADH(•) radical have previously been used to address this issue. Our QM/MM calculations show, however, that the experimental couplings are equally well reproduced by each of the nine combinations. Since the EPR results seemingly cannot be used to unequivocally assign the protonation states, the pKa values of the two histidines were calculated using the popular PROPKA, H++, and APBS approaches, in various environments and for several lesions. These techniques consistently indicate that, at pH = 7, both His365 and His369 should be neutral, although His369 is found to be more prone to becoming protonated. In a comparative approach, a series of molecular dynamics simulations was performed with all nine combinations, employing various reference crystal structures and different oxidation states of the FAD cofactor. The overall result of this approach is in agreement with our pKa results. Consequently, although the introduction of the reduced cofactor results in an increased stability for selected protonated states, particularly the His365═HID and His369═HIP combination, the neutral combination His365═HID and His365═HIE stands out as the most relevant state for the activity of the enzyme.
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Affiliation(s)
- Karmen Condic-Jurkic
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.,Excellence Cluster, Engineering of Advanced Materials, University Erlangen-Nürnberg, Nägelsbachstrasse 49b, 91052 Erlangen, Germany
| | - Ana-Sunčana Smith
- Institute of Theoretical Physics, University Erlangen-Nürnberg, Staudtstrasse 9, 91058 Erlangen, Germany.,Excellence Cluster, Engineering of Advanced Materials, University Erlangen-Nürnberg, Nägelsbachstrasse 49b, 91052 Erlangen, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians Universität, Butenandtstrasse 13, 82131 München, Germany
| | - David M Smith
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.,Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
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25
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Fingerhut BP, Heil K, Kaya E, Oesterling S, de Vivie-Riedle R, Carell T. Mechanism of UV-induced Dewar lesion repair catalysed by DNA (6-4) photolyase. Chem Sci 2012. [DOI: 10.1039/c2sc20122d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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26
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Haiser K, Fingerhut BP, Heil K, Glas A, Herzog TT, Pilles BM, Schreier WJ, Zinth W, de Vivie-Riedle R, Carell T. Mechanismus der UV-induzierten Bildung von Dewar-Schäden in DNA. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106231] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Haiser K, Fingerhut BP, Heil K, Glas A, Herzog TT, Pilles BM, Schreier WJ, Zinth W, de Vivie-Riedle R, Carell T. Mechanism of UV-induced formation of Dewar lesions in DNA. Angew Chem Int Ed Engl 2011; 51:408-11. [PMID: 22109845 DOI: 10.1002/anie.201106231] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Indexed: 11/11/2022]
Abstract
The importance of a backbone: The mechanism of formation of Dewar lesions has been investigated by using femtosecond IR spectroscopy and ab initio calculations of the exited state. The 4π electrocyclization is rather slow, occurs with an unusual high quantum yield, and--surprisingly--is controlled by the phosphate backbone.
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Affiliation(s)
- Karin Haiser
- Faculty of Physics, Center for Integrative Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
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28
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Domratcheva T. Neutral Histidine and Photoinduced Electron Transfer in DNA Photolyases. J Am Chem Soc 2011; 133:18172-82. [DOI: 10.1021/ja203964d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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29
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Ai YJ, Liao RZ, Chen SL, Hua WJ, Fang WH, Luo Y. Repair of DNA Dewar photoproduct to (6-4) photoproduct in (6-4) photolyase. J Phys Chem B 2011; 115:10976-82. [PMID: 21834563 DOI: 10.1021/jp204128k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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Affiliation(s)
- Yue-Jie Ai
- Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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30
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Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T. Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion. Chemistry 2011; 17:9651-7. [PMID: 21780197 DOI: 10.1002/chem.201100177] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 05/05/2011] [Indexed: 11/11/2022]
Abstract
UV light is one of the major causes of DNA damage. In spore DNA, due to an unusual packing of the genetic material, a special spore photoproduct lesion (SP lesion) is formed, which is repaired by the enzyme spore photoproduct lyase (Spl), a radical S-adenosylmethionine (SAM) enzyme. We report here the synthesis and DNA incorporation of a DNA SP lesion analogue lacking the phosphodiester backbone. The oligonucleotides were used for repair studies and they were cocrystallized with a polymerase enzyme as a template to clarify the configuration of the SP lesion and to provide information about the base-pairing properties of the lesion. The structural analysis together with repair studies allowed us to clarify the identity of the preferentially repaired lesion diastereoisomer.
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Affiliation(s)
- Korbinian Heil
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Munich, Germany
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31
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Münzel M, Szeibert C, Glas AF, Globisch D, Carell T. Discovery and synthesis of new UV-induced intrastrand C(4-8)G and G(8-4)C photolesions. J Am Chem Soc 2011; 133:5186-9. [PMID: 21425860 DOI: 10.1021/ja111304f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
UV irradiation of cellular DNA leads to the formation of a number of defined mutagenic DNA lesions. Here we report the discovery of new intrastrand C(4-8)G and G(8-4)C cross-link lesions in which the C(4) amino group of the cytosine base is covalently linked to the C(8) position of an adjacent dG base. The structure of the novel lesions was clarified by HPLC-MS/MS data for UV-irradiated DNA in combination with chemical synthesis and direct comparison of the synthetic material with irradiated DNA. We also report the ability to generate the lesions directly in DNA with the help of a photoactive precursor that was site-specifically incorporated into DNA. This should enable detailed chemical and biochemical investigations of these lesions.
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Affiliation(s)
- Martin Münzel
- Center for Integrated Protein Science (CIPS(M)) at the Department of Chemistry, Ludwig-Maximilians-University Munich , Butenandtstrasse 5-13, 81377 Munich, Germany
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32
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Ai YJ, Liao RZ, Chen SF, Luo Y, Fang WH. Theoretical studies on photoisomerizations of (6-4) and Dewar photolesions in DNA. J Phys Chem B 2011; 114:14096-102. [PMID: 20961081 DOI: 10.1021/jp107873w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (CI) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S(2) ((1)ππ*) and the S(0) states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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Affiliation(s)
- Yue-Jie Ai
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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33
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Heil K, Pearson D, Carell T. Chemical investigation of light induced DNA bipyrimidine damage and repair. Chem Soc Rev 2010; 40:4271-8. [PMID: 21076781 DOI: 10.1039/c000407n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In all organisms, genetic information is stored in DNA and RNA. Both of these macromolecules are damaged by many exogenous and endogenous events, with UV irradiation being one of the major sources of damage. The major photolesions formed are the cyclobutane pyrimidine dimers (CPD), pyrimidine-pyrimidone-(6-4)-photoproducts, Dewar valence isomers and, for dehydrated spore DNA, 5-(α-thyminyl)-5,6-dihydrothymine (SP). In order to be able to investigate how nature's repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential. This tutorial review provides an overview of synthetic procedures by which these oligonucleotides can be generated, either through phosphoramidite chemistry or direct irradiation of DNA. Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided.
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Affiliation(s)
- Korbinian Heil
- Center for Integrative Protein Science CiPSM at the Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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Brettel K, Byrdin M. Reaction mechanisms of DNA photolyase. Curr Opin Struct Biol 2010; 20:693-701. [PMID: 20705454 DOI: 10.1016/j.sbi.2010.07.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH° occur in overall 1ns. Whereas the kinetics of FADH° was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH° to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.
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Affiliation(s)
- Klaus Brettel
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, 91191 Gif-sur-Yvette, France.
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