1
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Chatgilialoglu C, Barata-Vallejo S, Gimisis T. Radical Reactions in Organic Synthesis: Exploring in-, on-, and with-Water Methods. Molecules 2024; 29:569. [PMID: 38338314 PMCID: PMC10856544 DOI: 10.3390/molecules29030569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Radical reactions in water or aqueous media are important for organic synthesis, realizing high-yielding processes under non-toxic and environmentally friendly conditions. This overview includes (i) a general introduction to organic chemistry in water and aqueous media, (ii) synthetic approaches in, on, and with water as well as in heterogeneous phases, (iii) reactions of carbon-centered radicals with water (or deuterium oxide) activated through coordination with various Lewis acids, (iv) photocatalysis in water and aqueous media, and (v) synthetic applications bioinspired by naturally occurring processes. A wide range of chemical processes and synthetic strategies under different experimental conditions have been reviewed that lead to important functional group translocation and transformation reactions, leading to the preparation of complex molecules. These results reveal how water as a solvent/medium/reagent in radical chemistry has matured over the last two decades, with further discoveries anticipated in the near future.
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Affiliation(s)
- Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy
- Center of Advanced Technologies, Adam Mickiewicz University, 61-712 Poznan, Poland
| | - Sebastian Barata-Vallejo
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy
- Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Universidad de Buenos Aires, Junin 954, Buenos Aires CP 1113, Argentina
| | - Thanasis Gimisis
- Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
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2
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Chatgilialoglu C, Ferreri C, Krokidis MG, Masi A, Terzidis MA. On the relevance of hydroxyl radical to purine DNA damage. Free Radic Res 2021; 55:384-404. [PMID: 33494618 DOI: 10.1080/10715762.2021.1876855] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hydroxyl radical (HO•) is the most reactive toward DNA among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms. HO• is generated also by exogenous sources such as ionizing radiations. In this review we focus on the purine DNA damage by HO• radicals. In particular, emphasis is given on mechanistic aspects for the various lesion formation and their interconnections. Although the majority of the purine DNA lesions like 8-oxo-purine (8-oxo-Pu) are generated by various ROS (including HO•), the formation of 5',8-cyclopurine (cPu) lesions in vitro and in vivo relies exclusively on the HO• attack. Methodologies generally utilized for the purine lesions quantification in biological samples are reported and critically discussed. Recent results on cPu and 8-oxo-Pu lesions quantification in various types of biological specimens associated with the cellular repair efficiency as well as with distinct pathologies are presented, providing some insights on their biological significance.
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Affiliation(s)
- Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy.,Center for Advanced Technologies, Adam Mickiewicz University, Poznan, Poland
| | - Carla Ferreri
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, NCSR "Demokritos", Athens, Greece
| | - Annalisa Masi
- ISOF, Consiglio Nazionale delle Ricerche, Bologna, Italy.,Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Monterotondo, Italy
| | - Michael A Terzidis
- Department of Nutritional Sciences and Dietetics, International Hellenic University, Thessaloniki, Greece
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3
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Chatgilialoglu C, Eriksson LA, Krokidis MG, Masi A, Wang S, Zhang R. Oxygen Dependent Purine Lesions in Double-Stranded Oligodeoxynucleotides: Kinetic and Computational Studies Highlight the Mechanism for 5',8-Cyclopurine Formation. J Am Chem Soc 2020; 142:5825-5833. [PMID: 32129616 DOI: 10.1021/jacs.0c00945] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The reaction of HO• radical with DNA is intensively studied both mechanistically and analytically for lesions formation. Several aspects related to the reaction paths of purine moieties with the formation of 5',8-cyclopurines (cPu), 8-oxopurines (8-oxo-Pu), and their relationship are not well understood. In this study, we investigated the reaction of HO• radical with a 21-mer double-stranded oligodeoxynucleotide (ds-ODNs) in γ-irradiated aqueous solutions under various oxygen concentrations and accurately quantified the six purine lesions (i.e., four cPu and two 8-oxo-Pu) by LC-MS/MS analysis using isotopomeric internal standards. In the absence of oxygen, 8-oxo-Pu lesions are only ∼4 times more than cPu lesions. By increasing oxygen concentration, the 8-oxo-Pu and the cPu gradually increase and decrease, respectively, reaching a gap of ∼130 times at 2.01 × 10-4 M of O2. Kinetic treatment of the data allows to estimate the C5' radical competition between cyclization and oxygen trapping in ds-ODNs, and lastly the rate constants of the four cyclization steps. Tailored computational studies by means of dispersion-corrected DFT calculations were performed on the CGC and TAT in their double-strand models for each cPu diastereoisomer along with the complete reaction pathways of the cyclization steps. Our findings reveal unheralded reaction mechanisms that resolve the long-standing issues with C5' radical cyclization in purine moieties of DNA sequences.
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Affiliation(s)
- Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy.,Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", Agia Paraskevi Attikis 15310, Athens, Greece
| | - Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy
| | - Shudong Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Rubo Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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4
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5',8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance. Cells 2019; 8:cells8060513. [PMID: 31141888 PMCID: PMC6628319 DOI: 10.3390/cells8060513] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/18/2019] [Accepted: 05/22/2019] [Indexed: 12/14/2022] Open
Abstract
Purine 5′,8-cyclo-2′-deoxynucleosides (cPu) are tandem-type lesions observed among the DNA purine modifications and identified in mammalian cellular DNA in vivo. These lesions can be present in two diasteroisomeric forms, 5′R and 5′S, for each 2′-deoxyadenosine and 2′-deoxyguanosine moiety. They are generated exclusively by hydroxyl radical attack to 2′-deoxyribose units generating C5′ radicals, followed by cyclization with the C8 position of the purine base. This review describes the main recent achievements in the preparation of the cPu molecular library for analytical and DNA synthesis applications for the studies of the enzymatic recognition and repair mechanisms, their impact on transcription and genetic instability, quantitative determination of the levels of lesions in various types of cells and animal model systems, and relationships between the levels of lesions and human health, disease, and aging, as well as the defining of the detection limits and quantification protocols.
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5
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Shafirovich V, Kolbanovskiy M, Kropachev K, Liu Z, Cai Y, Terzidis MA, Masi A, Chatgilialoglu C, Amin S, Dadali A, Broyde S, Geacintov NE. Nucleotide Excision Repair and Impact of Site-Specific 5',8-Cyclopurine and Bulky DNA Lesions on the Physical Properties of Nucleosomes. Biochemistry 2019; 58:561-574. [PMID: 30570250 PMCID: PMC6373774 DOI: 10.1021/acs.biochem.8b01066] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The nonbulky 5',8-cyclopurine DNA lesions (cP) and the bulky, benzo[ a]pyrene diol epoxide-derived stereoisomeric cis- and trans- N2-guanine adducts (BPDE-dG) are good substrates of the human nucleotide excision repair (NER) mechanism. These DNA lesions were embedded at the In or Out rotational settings near the dyad axis in nucleosome core particles reconstituted either with native histones extracted from HeLa cells (HeLa-NCP) or with recombinant histones (Rec-NCP). The cP lesions are completely resistant to NER in human HeLa cell extracts. The BPDE-dG adducts are also NER-resistant in Rec-NCPs but are good substrates of NER in HeLa-NCPs. The four BPDE-dG adduct samples are excised with different efficiencies in free DNA, but in HeLa-NCPs, the efficiencies are reduced by a common factor of 2.2 ± 0.2 relative to the NER efficiencies in free DNA. The NER response of the BPDE-dG adducts in HeLa-NCPs is not directly correlated with the observed differences in the thermodynamic destabilization of HeLa-NCPs, the Förster resonance energy transfer values, or hydroxyl radical footprint patterns and is weakly dependent on the rotational settings. These and other observations suggest that NER is initiated by the binding of the DNA damage-sensing NER factor XPC-RAD23B to a transiently opened BPDE-modified DNA sequence that corresponds to the known footprint of XPC-DNA-RAD23B complexes (≥30 bp). These observations are consistent with the hypothesis that post-translational modifications and the dimensions and properties of the DNA lesions are the major factors that have an impact on the dynamics and initiation of NER in nucleosomes.
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Affiliation(s)
- Vladimir Shafirovich
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Marina Kolbanovskiy
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Konstantin Kropachev
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Zhi Liu
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Yuquin Cai
- Department of Biology, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Michael A. Terzidis
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Shantu Amin
- Department of Pharmacology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Alexander Dadali
- Bronx College of the City University of New York, Bronx, NY 10453, United States
| | - Suse Broyde
- Department of Biology, New York University, 31 Washington Place, New York, NY 10003-5180, United States
| | - Nicholas E. Geacintov
- Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003-5180, United States
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6
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Bowry VW, Chatgilialoglu C. Radical Arene Addition vs Radical Reduction: Why Organometal Hydride Chain Reactions Stop and How To Make Them Go. J Org Chem 2018; 83:10037-10050. [PMID: 30028610 DOI: 10.1021/acs.joc.8b01387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonideal kinetic chain analysis was used to examine the kinetic limitations of free-radical synthesis. Homolytic aromatic substitution (HAS: ArH + R• → ArR + H•) occurs in a chain-terminating side reaction to the tributyltin hydride ( SnH) reduction chain (RX + SnH + ( i•)cat. → RH + SnX). Kinetic modeling of premixed and slow reagent addition reactions have clarified the mechanisms of SM HAS, with the azo initiator ( iNN i) acting not only as radical source but also (as an H• acceptor) as the redox catalyst for aromatization, and/or as a postaddition oxidant. Refractory halides and other hitherto baffling anomalies may arise from the build up of ipso (rather than ortho)-cycloadduct radicals in the steady-state radical population. The implications of these findings for "tin-free" radical chains (and emerging photoredox methods) are considered via historical and recent examples of the effects of chain-degrading radical transfer (to substrate, product, solvent, initiator, and/or reagent ligands) on the reagent's chain.
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Affiliation(s)
- Vincent W Bowry
- ISOF, Consiglio Nazionale delle Ricerche , Via P. Gobetti 101 , Bologna 40129 , Italy
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7
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Chatgilialoglu C, Ferreri C, Landais Y, Timokhin VI. Thirty Years of (TMS)3SiH: A Milestone in Radical-Based Synthetic Chemistry. Chem Rev 2018; 118:6516-6572. [DOI: 10.1021/acs.chemrev.8b00109] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Carla Ferreri
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Yannick Landais
- University of Bordeaux, Institute of Molecular Sciences, UMR-CNRS 5255, 351 cours de la libération, 33405 Talence Cedex, France
| | - Vitaliy I. Timokhin
- Department of Biochemistry, University of Wisconsin-Madison, 1552 University Avenue, Madison, Wisconsin 53726, United States
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8
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Kropachev K, Ding S, Terzidis MA, Masi A, Liu Z, Cai Y, Kolbanovskiy M, Chatgilialoglu C, Broyde S, Geacintov NE, Shafirovich V. Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system. Nucleic Acids Res 2014; 42:5020-32. [PMID: 24615810 PMCID: PMC4041128 DOI: 10.1093/nar/gku162] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The hydroxyl radical is a powerful oxidant that generates DNA lesions including the
stereoisomeric R and S
5′,8-cyclo-2′-deoxyadenosine (cdA) and
5′,8-cyclo-2′-deoxyguanosine (cdG) pairs that have been detected in cellular
DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the
human nucleotide excision repair (NER) apparatus. The relative NER efficiencies of all
four cyclopurines were measured and compared in identical human HeLa cell extracts for the
first time under identical conditions, using identical sequence contexts. The cdA and cdG
lesions were excised with similar efficiencies, but the efficiencies for both
5′R cyclopurines were greater by a factor of ∼2 than for the
5′S lesions. Molecular modeling and dynamics simulations have
revealed structural and energetic origins of this difference in NER-incision efficiencies.
These lesions cause greater DNA backbone distortions and dynamics relative to unmodified
DNA in 5′R than in 5′S stereoisomers,
producing greater impairment in van der Waals stacking interaction energies in the
5′R cases. The locally impaired stacking interaction energies
correlate with relative NER incision efficiencies, and explain these results on a
structural basis in terms of differences in dynamic perturbations of the DNA backbone
imposed by the R and S covalent 5′,8 bonds.
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Affiliation(s)
- Konstantin Kropachev
- Department of Chemistry New York University, 100 Washington Square East, New York, NY 10003, USA, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA and Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
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9
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Chatgilialoglu C, Ferreri C, Masi A, Sansone A, Terzidis MA, Tsakos M. A problem solving approach for the diastereoselective synthesis of (5′S)- and (5′R)-5′,8-cyclopurine lesions. Org Chem Front 2014. [DOI: 10.1039/c4qo00133h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Insight into reaction mechanism and product formation a C8-purine radical in RNA: a theoretical perspective. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1355-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Terzidis MA, Chatgilialoglu C. Radical Cascade Protocol for the Synthesis of (5'S)- and (5'R)-5',8-Cyclo-2'-deoxyguanosine Derivatives. Aust J Chem 2013. [DOI: 10.1071/ch12494] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The reaction of the appropriately substituted 8-bromo-2′-deoxyguanosine with Bu3SnH/2,2′-azobisisobutyronitrile (AIBN) can be favourably tuned to give the analogous 5′,8-cyclo-2′-deoxyguanosine derivatives in good yields, thus providing easy access to modified nucleosides that constitute an important DNA lesion. A large excess of AIBN is necessary. The creation of the new C5′–C8 bond is a non-chain radical cascade protocol.
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12
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Recent advances in cyclonucleosides: C-cyclonucleosides and spore photoproducts in damaged DNA. Molecules 2012; 17:11630-54. [PMID: 23023688 PMCID: PMC6268316 DOI: 10.3390/molecules171011630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 12/04/2022] Open
Abstract
Cyclonucleosides which are fixed in a specific conformation around the glycosyl bond by a carbon and heteroatom chain constitute a unique category of nucleoside derivatives. Because they are structural analogs, cyclonucleosides and oligodeoxynucleotides containing them would be useful tools for investigating the biological functions and conformations of DNA, RNA as well as their steric interactions with proteins. C-Cyclonucleosides bridged by a carbon chain between the base and sugar moieties are the most attractive from the synthetic points of view as well as for use as biological tools. In this review, recent progress of the synthesis of C-cyclonucleosides is surveyed. Among the C-cyclonucleosides, 5′,8-C-cyclodeoxyadenosine is one of the well-known derivatives of which the first practical synthesis was reported over 30 years ago. Recently, 5′,8-C-cyclodeoxyadenosine has attracted considerable interest as a biomarker, since its formation in oxidatively-damaged DNA is considered to be related to various diseases and aging. Another important analogue of cyclonucleosides is a unique thymidine phosphate dimer, a so-called spore photoproduct, which has been found in photo-damaged DNA. Recent advances in the synthesis, mechanism-studies, and stereochemical preference of repairing enzymes related to 5′,8-C-cyclodeoxyadenosine and spore photoproducts are also reviewed.
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Zaliznyak T, Lukin M, de los Santos C. Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER. Chem Res Toxicol 2012; 25:2103-11. [PMID: 22928555 DOI: 10.1021/tx300193k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cellular respiration and ionizing radiation generate 5',8-cyclo-2'-deoxyribonucleosides, a special type of DNA damage that involves two modifications in the same nucleotide. These lesions evade the action of base excision glycosylases, and their removal is a function of the nucleotide excision repair pathway. Diastereomeric 5',8-cyclo-2'-deoxyadenosine blocks mammalian DNA replication, diminishes the levels of DNA transcription, and induces transcriptional mutagenesis. Using solution state NMR spectroscopy and restrained molecular dynamics simulations, we have determined the structure of an undecameric DNA duplex having a centrally located (5'S)-5',8-cyclo-2'-deoxyadenosine residue paired to T. The damaged duplex structure is a right-handed helix having Watson-Crick base-pair alignments throughout, and 2-deoxyribose puckers within the B-form conformation. Only small structural perturbations are observed at the lesion-containing and 5'-flanking base pair. The 2-deoxyribose of the damaged nucleotide adopts the O4'-exo conformation, and the S-cdA·T base pair is propeller twisted. The 5'-lesion-flanking base is tilted forming a significantly buckled base pair with its partner guanine. Analysis of UV-melting curves indicates mild thermal and thermodynamic destabilization on the damaged duplex. The S-cdA·T duplex structure shows many similarities to and some intriguing differences from the recently reported structure of an S-cdG·dC duplex³¹ that suggest different lesion site dynamics.
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Affiliation(s)
- Tatiana Zaliznyak
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8651, USA
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14
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Abstract
Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates. Hydrated electron and H atom also add to the heterocyclic bases. These reactions lead to adduct radicals, further reactions of which yield numerous products. These include DNA base and sugar products, single- and double-strand breaks, 8,5'-cyclopurine-2'-deoxynucleosides, tandem lesions, clustered sites and DNA-protein cross-links. Reaction conditions and the presence or absence of oxygen profoundly affect the types and yields of the products. There is mounting evidence for an important role of free radical-induced DNA damage in the etiology of numerous diseases including cancer. Further understanding of mechanisms of free radical-induced DNA damage, and cellular repair and biological consequences of DNA damage products will be of outmost importance for disease prevention and treatment.
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Affiliation(s)
- Miral Dizdaroglu
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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15
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Huang H, Das R, Basu AK, Stone MP. Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT. Chem Res Toxicol 2012; 25:478-90. [PMID: 22309170 PMCID: PMC3285119 DOI: 10.1021/tx2005053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Indexed: 02/08/2023]
Abstract
Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, are induced in DNA by ionizing radiation. They are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. If not repaired, the S-8,5'-cyclo-2'-deoxyguanosine lesion (S-cdG) induces Pol V-dependent mutations at a frequency of 34% in Escherichia coli. Most are S-cdG → A transitions, suggesting mis-incorporation of dTTP opposite the lesion during replication bypass, although low levels of S-cdG → T transversions, arising from mis-incorporation of dATP, are also observed. We report the structures of 5'-d(GTGCXTGTTTGT)-3'·5'-d(ACAAACAYGCAC)-3', where X denotes S-cdG and Y denotes either dA or dT, corresponding to the situation following mis-insertion of either dTTP or dATP opposite the S-cdG lesion. The S-cdG·dT mismatch pair adopts a wobble base pairing. This provides a plausible rationale for the S-cdG → A transitions. The S-cdG·dA mismatch pair differs in conformation from the dG·dA mismatch pair. For the S-cdG·dA mismatch pair, both S-cdG and dA intercalate, but no hydrogen bonding is observed between S-cdG and dA. This is consistent with the lower levels of S-cdG → T transitions in E. coli.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in
Molecular Toxicology, and Center for Structural Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235,
United States
| | - Rajat
S. Das
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Michael P. Stone
- Department of Chemistry, Center in
Molecular Toxicology, and Center for Structural Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235,
United States
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16
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Recent applications of the (TMS)3SiH radical-based reagent. Molecules 2012; 17:527-55. [PMID: 22269866 PMCID: PMC6268903 DOI: 10.3390/molecules17010527] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 12/29/2011] [Accepted: 01/02/2012] [Indexed: 12/29/2022] Open
Abstract
This review article focuses on the recent applications of tris(trimethylsilyl)silane as a radical-based reagent in organic chemistry. Numerous examples of the successful use of (TMS)(3)SiH in radical reductions, hydrosilylation and consecutive radical reactions are given. The use of (TMS)(3)SiH allows reactions to be carried out under mild conditions with excellent yields of products and remarkable chemo-, regio-, and stereoselectivity. The strategic role of (TMS)(3)SiH in polymerization is underlined with emphasis on the photo-induced radical polymerization of olefins and photo-promoted cationic polymerization of epoxides.
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17
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Huang H, Das RS, Basu AK, Stone MP. Structure of (5'S)-8,5'-cyclo-2'-deoxyguanosine in DNA. J Am Chem Soc 2011; 133:20357-68. [PMID: 22103478 PMCID: PMC3279155 DOI: 10.1021/ja207407n] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the β, γ, and χ torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG·dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC·dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG·dC and 3'- neighbor dT·dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.
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Affiliation(s)
- Hai Huang
- Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Rajat S. Das
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Ashis K. Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
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Chatgilialoglu C, Ferreri C, Terzidis MA. Purine 5′,8-cyclonucleoside lesions: chemistry and biology. Chem Soc Rev 2011; 40:1368-82. [DOI: 10.1039/c0cs00061b] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Fagan V, Bonham S, Carty MP, Aldabbagh F. One-pot double intramolecular homolytic aromatic substitution routes to dialicyclic ring fused imidazobenzimidazolequinones and preliminary analysis of anticancer activity. Org Biomol Chem 2010; 8:3149-56. [PMID: 20485753 DOI: 10.1039/c003511d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Bu(3)SnH/1,1'-azobis(cyclohexanecarbonitrile) (ACN)-mediated five, six, and seven-membered double alkyl radical cyclizations onto imidazo[5,4-f]benzimidazole and imidazo[4,5-f]benzimidazole are described. The quinone derivatives evaluated show selective toxicity towards human cervical (HeLa) and prostate (DU145) cancer cell lines (with negligible toxicity towards a normal human cell line, GM00637). Only the Fremy oxidation of the 6-aminoimidazo[5,4-f]benzimidazole gave iminoquinone, which showed high specificity towards the prostate cancer cell line (DU145).
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Affiliation(s)
- Vincent Fagan
- School of Chemistry, National University of Ireland, Galway, Ireland
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Nowak J, Skalski B, Gdaniec Z, Milecki J. Synthesis of an acyclic nucleoside analog of highly fluorescent luminarosine. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2008.10.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8,5'-Cyclopurine-2'-deoxynucleosides in DNA: mechanisms of formation, measurement, repair and biological effects. DNA Repair (Amst) 2008; 7:1413-25. [PMID: 18603018 DOI: 10.1016/j.dnarep.2008.06.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 06/06/2008] [Accepted: 06/09/2008] [Indexed: 01/19/2023]
Abstract
8,5'-Cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine (cdG) are among the major lesions formed in DNA by hydroxyl radical attack on 2'-deoxyadenosine and 2'-deoxyguanosine, respectively, followed by intramolecular cyclization between C5' and C8. Mechanisms of formation of these unique tandem lesions were elucidated. The 8,5'-cyclization causes an unusual puckering of the sugar moiety giving rise to significant distortion in the DNA double helix. Methodologies were developed for the measurement of these lesions in DNA by mass spectrometry coupled either with gas chromatography or high performance liquid chromatography. Both techniques allowed identification and quantification of both R- and S-diastereomers of cdA and cdG in DNA in vitro and in vivo. Because of the 8,5'-covalent bond between the sugar and base moieties in the same nucleoside, cdA and cdG are repaired by nucleotide excision repair rather than by base excision repair. Thus, these lesions may play a role in diseases with defective nucleotide excision repair. Their biological effects include blocking DNA polymerases, inhibition of gene expression, transcriptional mutagenesis among others. Accumulation of cdA and cdG was observed in tissues in vivo in connection to disease and environmental conditions, suggesting an important role for these lesions in disease processes including carcinogenesis and neuronal death.
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Boussicault F, Kaloudis P, Caminal C, Mulazzani QG, Chatgilialoglu C. The Fate of C5′ Radicals of Purine Nucleosides under Oxidative Conditions. J Am Chem Soc 2008; 130:8377-85. [DOI: 10.1021/ja800763j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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The 8,5'-cyclopurine-2'-deoxynucleosides: candidate neurodegenerative DNA lesions in xeroderma pigmentosum, and unique probes of transcription and nucleotide excision repair. DNA Repair (Amst) 2008; 7:1168-79. [PMID: 18495558 DOI: 10.1016/j.dnarep.2008.03.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is a commonly held view that oxidatively induced DNA lesions are repaired by the base excision repair (BER) pathway, whereas DNA lesions induced by UV light and other "bulky" chemical adducts are repaired by the nucleotide excision repair (NER) pathway. While this distinction is generally accurate, the 8,5'-cyclopurine deoxynucleosides represent an important exception, in that they are formed in DNA by the hydroxyl radical, but are specifically repaired by NER, not by BER. They are also strong blocks to nucleases and polymerases, including RNA polymerase II in human cells. In this review, I will discuss the evidence that these lesions are in part responsible for the neurodegeneration that occurs in some XP patients, and what additional evidence would be necessary to prove such a role. I will also consider other DNA lesions that might be involved in XP neurologic disease. Finally, I will also discuss how our recent studies of these lesions have generated novel insights into the process of transcriptional mutagenesis in human cells, as well as the value of studying these lesions not only for a better understanding of NER but also for other aspects of human health and disease.
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Jacobsen MI, Meier C. Synthesis of C8-modified 2''-deoxyadenosine with carcinogenic arylamines. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1217-20. [PMID: 18066755 DOI: 10.1080/15257770701527976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The synthesis of phosphoramidites of C8-modified 2'-deoxyadenosine with carcinogenic arylamines p-anisidine and 4-aminobiphenyl is described. Two different methods were studied related to the glycon and base protection groups.
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Affiliation(s)
- M I Jacobsen
- Department of Chemistry, Organic Chemistry, Faculty of Science, University of Hamburg, Martin-Luther-King Platz 6, D-20146 Hamburg, Germany
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26
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Chatgilialoglu C, Timokhin VI. Silyl Radicals in Chemical Synthesis. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2008. [DOI: 10.1016/s0065-3055(08)00002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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27
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Chatgilialoglu C, Bazzanini R, Jimenez LB, Miranda MA. (5'S)- and (5'R)-5',8-cyclo-2'-deoxyguanosine: mechanistic insights on the 2'-deoxyguanosin-5'-yl radical cyclization. Chem Res Toxicol 2007; 20:1820-4. [PMID: 17988100 DOI: 10.1021/tx700282x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The two diastereomeric forms (5'S) and (5'R) of 5',8-cyclo-2'-deoxyguanosine have been synthesized and fully characterized. They have been used as references for the investigation of gamma-irradiation of 2'-deoxyguanosine and photolysis of 8-bromo-2'-deoxyguanosine in aqueous solutions. The observed (5'R)/(5'S) ratio of 8:1 was obtained in both sets of experiments. The mechanism of the cyclization reaction is discussed in some detail, and the diastereomeric outcome is rationalized in terms of favorable hydrogen-bonded structures in the pro-(5'R) conformation.
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Manetto A, Georganakis D, Leondiadis L, Gimisis T, Mayer P, Carell T, Chatgilialoglu C. Independent generation of C5'-nucleosidyl radicals in thymidine and 2'-deoxyguanosine. J Org Chem 2007; 72:3659-66. [PMID: 17425368 DOI: 10.1021/jo062518c] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of the C5' tert-butyl ketone of thymidine 1a and 2'-deoxyguanosine 2 is achieved by reaction of 5'-C-cyano derivatives with tert-butyl lithium followed by acid hydrolysis. The 5'R configuration is assigned by X-ray crystal structure determination of an opportunely protected derivative of 1a. The (5'S)-isomers of both nucleosides are not stable, and a complete decomposition occurs in the reaction medium. The photochemistry of 1a and 2 effectively produced the thymidin-5'-yl radical and the 2'-deoxyguanosin-5'-yl radical, respectively. In the thymidine system, the C5' radical is fully quenched in the presence of a physiological concentration of thiols. In the 2'-deoxyguanosine system, the C5' radical undergoes intramolecular attack onto the C8-N7 double bond of guanine leading ultimately to the 5',8-cyclo-2'-deoxyguanosine derivative. The cyclization of the 2'-deoxyguanosin-5'-yl radical occurs with a rate constant of ca. 1x10(6) s-1 and is highly stereoselective affording only the (5'S)-diastereomer.
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Affiliation(s)
- Antonio Manetto
- ISOF, Consiglio Nazionale delle Ricerche Via P. Gobetti 101, 40129 Bologna, Italy
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Navacchia ML, Montevecchi PC. Sulfanyl radical promoted C4′–C5′ bond scission of 5′-oxo-3′,4′-didehydro-2′,3′-dideoxynucleosides. Org Biomol Chem 2006; 4:3754-6. [PMID: 17024279 DOI: 10.1039/b609995e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Treatment of C5'-aldehydes, under mildly basic conditions leads to the formation of 3',4'-didehydroaldehydes, and furfural. Sulfanyl radical addition eventually gives rise to the lactones, through C4'-C5' bond scission of the 1,2-dioxetane intermediates.
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