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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Guilbaud A, Ghanegolmohammadi F, Wang Y, Leng J, Kreymerman A, Gamboa Varela J, Garbern J, Elwell H, Cao F, Ricci-Blair E, Liang C, Balamkundu S, Vidoudez C, DeMott M, Bedi K, Margulies K, Bennett D, Palmer A, Barkley-Levenson A, Lee R, Dedon P. Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans. Nucleic Acids Res 2023; 51:10829-10845. [PMID: 37843128 PMCID: PMC10639045 DOI: 10.1093/nar/gkad822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/27/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to begin to define the landscape of DNA modifications in rat and human tissues. A basis set of 114 putative DNA adducts was identified in heart, liver, brain, and kidney in 1-26-month-old rats and 111 in human heart and brain by 'stepped MRM' LC-MS/MS. Subsequent targeted analysis of these species revealed species-, tissue-, age- and sex-biases. Structural characterization of 10 selected adductomic signals as known DNA modifications validated the method and established confidence in the DNA origins of the signals. Along with strong tissue biases, we observed significant age-dependence for 36 adducts, including N2-CMdG, 5-HMdC and 8-Oxo-dG in rats and 1,N6-ϵdA in human heart, as well as sex biases for 67 adducts in rat tissues. These results demonstrate the potential of adductomics for discovering the true spectrum of disease-driving DNA adducts. Our dataset of 114 putative adducts serves as a resource for characterizing dozens of new forms of DNA damage, defining mechanisms of their formation and repair, and developing them as biomarkers of aging and disease.
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Affiliation(s)
- Axel Guilbaud
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Farzan Ghanegolmohammadi
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yijun Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jiapeng Leng
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alexander Kreymerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jacqueline Gamboa Varela
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jessica Garbern
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hannah Elwell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fang Cao
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Elisabeth M Ricci-Blair
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cui Liang
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
| | - Seetharamsing Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
| | - Charles Vidoudez
- Harvard Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kenneth Bedi
- University of Pennsylvania Cardiovascular Institute, Philadelphia, PA, USA
| | | | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Richard T Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
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3
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Andrés CMC, de la Lastra JMP, Juan CA, Plou FJ, Pérez-Lebeña E. Chemical Insights into Oxidative and Nitrative Modifications of DNA. Int J Mol Sci 2023; 24:15240. [PMID: 37894920 PMCID: PMC10607741 DOI: 10.3390/ijms242015240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2'-deoxyribose oxidation products in DNA.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. AstrofísicoFco. Sánchez, 3, 38206 La Laguna, Spain
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén, 7, 47011 Valladolid, Spain;
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain;
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4
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Mu R, Li S, Wang T, Lu Z, Qin Q, Cheng SB, Yu D, Zhan J, Chen J. Electric Field Promoted Click Surface-Enhanced Raman Spectroscopy for Rapid and Specific Detection of DNA 2-Deoxyribose 5'-Aldehyde Oxidation Products in Plasma. Anal Chem 2023; 95:14324-14330. [PMID: 37713587 DOI: 10.1021/acs.analchem.3c02620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Rapid identification of DNA oxidative damage sites is of great significance for disease diagnosis. In this work, electric field-regulated click reaction surface-enhanced Raman spectroscopy (e-Click-SERS) was developed aiming at the rapid and specific analysis of furfural, the biomarker of oxidative damage to the 5-carbon site of DNA deoxyribose. In e-Click-SERS, cysteamine-modified porous Ag filaments (cys@p-Ag) were prepared and used as electrodes, amine-aldehyde click reaction sites, and SERS substrates. Cysteamine was controlled as an "end-on" conformation by setting the voltage of cys@p-Ag at -0.1 V, which ensures its activity in participating in the amine-aldehyde click reaction during the detection of furfural. Benefiting from this, the proposed e-Click-SERS method was found to be sensitive, rapid-responding, and interference-resistant in analyzing furfural from plasma. The method detection limits of furfural were 5 ng mL-1 in plasma, and the whole "extraction and detection" procedure was completed within 30 min with satisfactory recovery. Interference from 13 kinds of common plasma metabolites was investigated and found to not interfere with the analysis, according to the exclusive adaptation of the amine-aldehyde click reaction. Notably, the e-Click-SERS technique allows in situ analysis of biological samples, which offers great potential to be a point-of-care testing tool for detecting DNA oxidative damage.
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Affiliation(s)
- Run Mu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Shu Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Tong Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Zhengwei Lu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Qian Qin
- College of Medical Laboratory, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Shi-Bo Cheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Dexin Yu
- Department of Radiology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jinhua Zhan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jing Chen
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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5
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Narayanan S J J, Tripathi D, Verma P, Adhikary A, Dutta AK. Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials. ACS OMEGA 2023; 8:10669-10689. [PMID: 37008102 PMCID: PMC10061531 DOI: 10.1021/acsomega.2c06776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.
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Affiliation(s)
- Jishnu Narayanan S J
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Pooja Verma
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Achintya Kumar Dutta
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
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6
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Robert G, Wagner JR, Cadet J. Oxidatively generated tandem DNA modifications by pyrimidinyl and 2-deoxyribosyl peroxyl radicals. Free Radic Biol Med 2023; 196:22-36. [PMID: 36603668 DOI: 10.1016/j.freeradbiomed.2022.12.104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
Molecular oxygen sensitizes DNA to damage induced by ionizing radiation, Fenton-like reactions, and other free radical-mediated reactions. It rapidly converts carbon-centered radicals within DNA into peroxyl radicals, giving rise to a plethora of oxidized products consisting of nucleobase and 2-deoxyribose modifications, strand breaks and abasic sites. The mechanism of formation of single oxidation products has been extensively studied and reviewed. However, much evidence shows that reactive peroxyl radicals can propagate damage to vicinal components in DNA strands. These intramolecular reactions lead to the dual alteration of two adjacent nucleotides, designated as tandem or double lesions. Herein, current knowledge about the formation and biological implications of oxidatively generated DNA tandem lesions is reviewed. Thus far, most reported tandem lesions have been shown to arise from peroxyl radicals initially generated at pyrimidine bases, notably thymine, followed by reaction with 5'-flanking bases, especially guanine, although contiguous thymine lesions have also been characterized. Proper biomolecular processing is impaired by several tandem lesions making them refractory to base excision repair and potentially more mutagenic.
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Affiliation(s)
- Gabriel Robert
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada.
| | - Jean Cadet
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada.
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7
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Veerabhadrappa B, Sj S, Rao NN, Dyavaiah M. Loss of tRNA methyltransferase 9 and DNA damage response genes in yeast confers sensitivity to aminoglycosides. FEBS Lett 2023; 597:1149-1163. [PMID: 36708127 DOI: 10.1002/1873-3468.14591] [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: 10/14/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 01/29/2023]
Abstract
tRNA methyltransferase 9 (Trm9)-catalysed tRNA modifications have been shown to translationally enhance the DNA damage response (DDR). Here, we show that Saccharomyces cerevisiae trm9Δ, distinct DNA repair and spindle assembly checkpoint (SAC) mutants are differentially sensitive to the aminoglycosides tobramycin, gentamicin and amikacin, indicating DDR and SAC activation might rely on translation fidelity, under aminoglycoside stress. Further, we report that the DNA damage induced by aminoglycosides in the base excision repair mutants ogg1Δ and apn1Δ is mediated by reactive oxygen species, which induce the DNA adduct 8-hydroxy deoxyguanosine. Finally, the synergistic effect of tobramycin and the DNA-damaging agent bleomycin to sensitize trm9Δ and the DDR mutants mlh1Δ, rad51Δ, mre11Δ and sgs1Δ at significantly lower concentrations compared with wild-type suggests that cells with tRNA modification dysregulation and DNA repair gene defects can be selectively sensitized using a combination of translation inhibitors and DNA-damaging agents.
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Affiliation(s)
- Bhavana Veerabhadrappa
- Department of Biotechnology, R V College of Engineering - Visvesvaraya Technological University, Bengaluru, Karnataka, India.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Sudharshan Sj
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Nagashree N Rao
- Department of Biotechnology, R V College of Engineering - Visvesvaraya Technological University, Bengaluru, Karnataka, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
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8
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Guzman-Lopez EG, Reina M, Perez-Gonzalez A, Francisco-Marquez M, Hernandez-Ayala LF, Castañeda-Arriaga R, Galano A. CADMA-Chem: A Computational Protocol Based on Chemical Properties Aimed to Design Multifunctional Antioxidants. Int J Mol Sci 2022; 23:13246. [PMID: 36362034 PMCID: PMC9658414 DOI: 10.3390/ijms232113246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 10/12/2023] Open
Abstract
A computational protocol aimed to design new antioxidants with versatile behavior is presented. It is called Computer-Assisted Design of Multifunctional Antioxidants and is based on chemical properties (CADMA-Chem). The desired multi-functionality consists of in different methods of antioxidant protection combined with neuroprotection, although the protocol can also be used to pursue other health benefits. The dM38 melatonin derivative is used as a study case to illustrate the protocol in detail. This was found to be a highly promising candidate for the treatment of neurodegeneration, in particular Parkinson's and Alzheimer's diseases. This also has the desired properties of an oral-drug, which is significantly better than Trolox for scavenging free radicals, and has chelates redox metals, prevents the ●OH production, via Fenton-like reactions, repairs oxidative damage in biomolecules (lipids, proteins, and DNA), and acts as a polygenic neuroprotector by inhibiting catechol-O-methyl transferase (COMT), acetylcholinesterase (AChE) and monoamine oxidase B (MAOB). To the best of our best knowledge, CADMA-Chem is currently the only protocol that simultaneously involves the analyses of drug-like behavior, toxicity, manufacturability, versatile antioxidant protection, and receptor-ligand binding affinities. It is expected to provide a starting point that helps to accelerate the discovery of oral drugs with the potential to prevent, or slow down, multifactorial human health disorders.
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Affiliation(s)
- Eduardo Gabriel Guzman-Lopez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | - Miguel Reina
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Adriana Perez-Gonzalez
- CONACYT-Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | | | - Luis Felipe Hernandez-Ayala
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | - Romina Castañeda-Arriaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Mexico City 09310, Mexico
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9
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Formation Mechanism of Inter-Crosslink in DNA by Nitrogen Oxides Pollutants through A Diazonium Intermediate. Int J Mol Sci 2022; 23:ijms231810621. [PMID: 36142522 PMCID: PMC9502170 DOI: 10.3390/ijms231810621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Outdoor air pollution is a mixture of multiple atmospheric pollutants, among which nitrogen oxide (NOx) stands out due to its association with several diseases. NOx reactivity can conduct to DNA damage as severe as interstrand crosslinks (ICL) formation, that in turn is able to block DNA replication and transcription. Experimental studies have suggested that the ICL formation due to NOx is realized through a diazonium intermediate (DI). In this work, we have modeled the DI structure, including a DNA double-strand composed of two base pairs GC/CG, being diazotized as one of the guanine nucleotides. The structural stability of DNA with DI lesion was essayed through 500 ns molecular dynamics simulations. It was found that the DNA structure of the oligonucleotide is stable when the DI is present since the loss of a Guanine–Cytosine hydrogen bond is replaced by the presence of two cation-π interactions. Additionally, we have studied the mechanism of formation of a crosslink between the two guanine nucleobases from the modeled DI by carrying out DFT calculations at the M06-L/DNP+ level of theory. Our results show that the mechanism is thermodynamically favored by a strong stabilization of the ICL product, and the process is kinetically viable since its limiting stage is accessible.
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10
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Paliwal K, Haldar P, Antharjanam PKS, Kumar M. Mixed Ligand Mononuclear Copper(II) Complex as a Promising Anticancer Agent: Interaction Studies with DNA/HSA, Molecular Docking, and In Vitro Cytotoxicity Studies. ACS OMEGA 2022; 7:21961-21977. [PMID: 35785271 PMCID: PMC9245097 DOI: 10.1021/acsomega.2c02354] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The isolated copper(II) complex [CuL(o-phen)]·H2O (1) [H2L = o-HO-C6H4C(H)=N-C6H4-SH-o, o-phen = 1,10-phenanthroline] was structurally characterized using single-crystal X-ray crystallography. 1 in CH3CN at liquid nitrogen temperature displayed a characteristic monomeric X-band electron paramagnetic resonance spectrum having a tetragonal character with g ∥ = 2.1479 and g ⊥ = 2.0691 and A ∥ ≈ 18.0 mT and A ⊥ ≤ 3.9 mT, respectively. 1 showed a strong binding affinity toward calf thymus DNA as reflected from its intrinsic binding constant (K b = 7.88 × 105 M-1), and its competitive displacement of ethidium bromide suggested an intercalative DNA-binding mode (K app = 1.32 × 106 M-1). This was confirmed from the viscosity study that showed an increase in the viscosity of DNA with an increasing concentration of 1. Complex 1 is highly efficient in promoting oxidative and hydrolytic DNA cleavage (k obs = 1.987 h-1). 1 showed a strong binding affinity with the carrier protein human serum albumin (HSA) (K a = 5.22 × 105 M-1). A high bimolecular quenching constant k q = 2.29 × 1013 M-1s-1 indicated a static quenching mechanism involved in the fluorescence quenching of HSA by 1. Fluorescence resonance energy transfer theory suggested that the distance (r = 3.52 nm) between 1 and HSA is very close. Molecular docking studies suggested that 1 primarily binds to HSA in subdomain IIA. A protein-ligand interaction profiler was used to visualize hydrophobic, hydrogen bonds, and π-cation interactions between HSA and 1. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay using HeLa and MDA-MB-231 cells showed a significant in vitro anticancer activity of 1 (IC50 2.63 and 2.68 μM, respectively). Nuclear staining assays suggested apoptotic cell death in HeLa cells treated with 1. The effect of 1 on the cytoskeletal actin filaments visualized using phalloidin staining showed extensive destruction of actin filaments. Flow cytometric analysis indicated that 1 inhibits the growth of HeLa cells through cell cycle arrest in the S phase. Western blot analysis showed upregulation in the expression of apoptotic marker proteins caspase 3, p53, and Bax. These results collectively indicate that 1 induces apoptosis by promoting DNA damage and has a high potential to act as an anticancer agent.
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Affiliation(s)
- Kumudini Paliwal
- Department
of Chemical Engineering, Birla Institute
of Technology and Science-Pilani, K. K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Paramita Haldar
- Department
of Chemical Engineering, Birla Institute
of Technology and Science-Pilani, K. K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | | | - Manjuri Kumar
- Department
of Chemical Engineering, Birla Institute
of Technology and Science-Pilani, K. K. Birla Goa Campus, Zuarinagar, Goa 403726, India
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11
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Chan W, Jin L. DNA-Protein Cross-Links Formed by Reacting Lysine with Apurinic/Apyrimidinic Sites in DNA and Human Cells: Quantitative Analysis by Liquid Chromatography-Tandem Mass Spectrometry Coupled with Stable Isotope Dilution. Anal Chem 2021; 94:803-810. [PMID: 34971314 DOI: 10.1021/acs.analchem.1c03356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Accumulating evidence suggests that DNA lesion-induced DNA-protein cross-links (DPCs) interrupt normal DNA metabolic processes, such as transcription, replication, and repair, resulting in profound biological consequences, including the development of many human diseases, such as cancers. Although apurinic/apyrimidinic (AP) sites are among the most predominant DNA lesions and are in close proximity to the histone proteins that they wrap around in the nucleosome, knowledge of the chemical structure or biological consequences of their associated DPCs is limited in part due to a lack of sensitive and selective analytical methods. We developed liquid chromatography-tandem mass spectrometry coupled with a stable isotope dilution method for rigorous quantitation of DPCs formed by reacting a DNA AP site with a lysine residue. In combination with chemical derivatization with fluorenylmethoxycarbonyl chloride to form a hydrophobic conjugate, the developed LC-MS/MS method allows sensitive detection of AP site-Lys cross-links down to sub-1 adduct per 106 nt. After validation using a synthetic AP site-lysine-cross-linked peptide and an oligodeoxyribonucleotide, the method was used to determine the concentration of AP site-lysine cross-links in hot acid-treated DNA and in human cells exposed to methyl methanesulfonate.
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Affiliation(s)
- Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Long Jin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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12
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Jin ZY, Fatima H, Zhang Y, Shao Z, Chen XJ. Recent Advances in Bio‐Compatible Oxygen Singlet Generation and Its Tumor Treatment. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202100176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zheng Yang Jin
- The First Affiliated Hospital of Wenzhou Medical University Wenzhou Zhejiang 325015 P. R. China
| | - Hira Fatima
- Western Australia School of Mines: Minerals Energy and Chemical Engineering (WASM‐MECE) Curtin University Perth Western Australia 6102 Australia
| | - Yue Zhang
- The First Affiliated Hospital of Wenzhou Medical University Wenzhou Zhejiang 325015 P. R. China
| | - Zongping Shao
- Western Australia School of Mines: Minerals Energy and Chemical Engineering (WASM‐MECE) Curtin University Perth Western Australia 6102 Australia
- State Key Laboratory of Materials‐Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University Nanjing Jiangsu 211816 P. R. China
| | - Xiang Jian Chen
- The First Affiliated Hospital of Wenzhou Medical University Wenzhou Zhejiang 325015 P. R. China
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13
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de la Lande A, Denisov S, Mostafavi M. The mystery of sub-picosecond charge transfer following irradiation of hydrated uridine monophosphate. Phys Chem Chem Phys 2021; 23:21148-21162. [PMID: 34528029 DOI: 10.1039/d0cp06482c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The early mechanisms by which ionizing rays damage biological structures by so-called direct effects are largely elusive. In a recent picosecond pulse radiolysis study of concentrated uridine monophosphate solutions [J. Ma, S. A. Denisov, J.-L. Marignier, P. Pernot, A. Adhikary, S. Seki and M. Mostafavi, J. Phys. Chem. Lett., 2018, 9, 5105], unexpected results were found regarding the oxidation of the nucleobase. The signature of the oxidized nucleobase could not be detected 5 ps after the electron pulse, but only the oxidized phosphate, raising intriguing questions about the identity of charge-transfer mechanisms that could explain the absence of U+. We address here this question by means of advanced first-principles atomistic simulations of solvated uridine monophosphate, combining Density Functional Theory (DFT) with polarizable embedding schemes. We contrast three very distinct mechanisms of charge transfer covering the atto-, femto- and pico-second timescales. We first investigate the ionization mechanism and subsequent hole/charge migrations on a timescale of attoseconds to a few femtoseconds under the frozen nuclei approximation. We then consider a nuclear-driven phosphate-to-oxidized-nucleobase electron transfer, showing that it is an uncompetitive reaction channel on the sub-picosecond timescale, despite its high exothermicity and significant electronic coupling. Finally, we show that non-adiabatic charge transfer is enabled by femtosecond nuclear relaxation after ionization. We show that electronic decoherence and the electronic coupling strength are the key parameters that determine the hopping probabilities. Our results provide important insight into the interplay between electronics and nuclear motions in the early stages of the multiscale responses of biological matter subjected to ionizing radiation.
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Affiliation(s)
- Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay (UMR 8000), 15 Avenue Jean Perrin, 91405, France.
| | - Sergey Denisov
- Institut de Chimie Physique, CNRS, Université Paris Saclay (UMR 8000), 15 Avenue Jean Perrin, 91405, France.
| | - Mehran Mostafavi
- Institut de Chimie Physique, CNRS, Université Paris Saclay (UMR 8000), 15 Avenue Jean Perrin, 91405, France.
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14
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Lu R, Zhang H, Jiang YN, Wang ZQ, Sun L, Zhou ZW. Post-Translational Modification of MRE11: Its Implication in DDR and Diseases. Genes (Basel) 2021; 12:1158. [PMID: 34440334 PMCID: PMC8392716 DOI: 10.3390/genes12081158] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
Maintaining genomic stability is vital for cells as well as individual organisms. The meiotic recombination-related gene MRE11 (meiotic recombination 11) is essential for preserving genomic stability through its important roles in the resection of broken DNA ends, DNA damage response (DDR), DNA double-strand breaks (DSBs) repair, and telomere maintenance. The post-translational modifications (PTMs), such as phosphorylation, ubiquitination, and methylation, regulate directly the function of MRE11 and endow MRE11 with capabilities to respond to cellular processes in promptly, precisely, and with more diversified manners. Here in this paper, we focus primarily on the PTMs of MRE11 and their roles in DNA response and repair, maintenance of genomic stability, as well as their association with diseases such as cancer.
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Affiliation(s)
- Ruiqing Lu
- School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; (R.L.); (Y.-N.J.)
| | - Han Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College; Kunming 650118, China;
| | - Yi-Nan Jiang
- School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; (R.L.); (Y.-N.J.)
| | - Zhao-Qi Wang
- Leibniz Institute on Aging–Fritz Lipmann Institute (FLI), 07745 Jena, Germany;
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07745 Jena, Germany
| | - Litao Sun
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhong-Wei Zhou
- School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; (R.L.); (Y.-N.J.)
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15
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Bell M, Kumar A, Sevilla MD. Electron-Induced Repair of 2'-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study. Int J Mol Sci 2021; 22:ijms22041736. [PMID: 33572317 PMCID: PMC7916153 DOI: 10.3390/ijms22041736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′• > C1′• > C5′• > C3′• > C2′•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier.
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16
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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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17
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Ham YH, Chan KKJ, Madej D, Lam H, Chan W. Proteomics Study of DNA–Protein Crosslinks in Methylmethanesulfonate and Fe2+-EDTA-Exposed Human Cells. Chem Res Toxicol 2020; 33:2739-2744. [DOI: 10.1021/acs.chemrestox.0c00289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yat-Hing Ham
- Department of Chemistry and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - K. K. Jason Chan
- Department of Chemistry and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Dominik Madej
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Wan Chan
- Department of Chemistry and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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18
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Sarkar S, Gaddameedhi S. Solar ultraviolet-induced DNA damage response: Melanocytes story in transformation to environmental melanomagenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:736-751. [PMID: 32281145 PMCID: PMC9675355 DOI: 10.1002/em.22370] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/13/2020] [Accepted: 03/27/2020] [Indexed: 05/14/2023]
Abstract
Exposure to sunlight is both beneficial, as it heats the planet to a comfortable temperature, and potentially harmful, since sunlight contains ultraviolet radiation (UVR), which is deemed detrimental for living organisms. Earth's ozone layer plays a vital role in blocking most of the extremely dangerous UVC; however, low frequency/energy UVR (i.e., UVB and UVA) seeps through in minute amount and reaches the Earth's surface. Both UVB and UVA are physiologically responsible for a plethora of skin ailments, including skin cancers. The UVR is readily absorbed by the genomic DNA of skin cells, causing DNA bond distortion and UV-induced DNA damage. As a defense mechanism, the DNA damage response (DDR) signaling in skin cells activates nucleotide excision repair (NER), which is responsible for the removal of UVR-induced DNA photolesions and helps maintain the genomic integrity of the cells. Failure of proper NER function leads to mutagenesis and development of skin cancers. One of the deadliest form of skin cancers is melanoma which originates upon the genetic transformation of melanocytes, melanin producing skin cells. NER is a well-studied DNA repair system in the whole skin, as a tissue, but not much is known about it in melanocytes. Therefore, this review encapsulates NER in melanocytes, with a specific focus on its functional regulators and their cross talks due to skin heterogeneity and divulging the potential knowledge gap in the field.
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Affiliation(s)
- Soumyadeep Sarkar
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA
| | - Shobhan Gaddameedhi
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA
- Sleep and Performance Research Center, Washington State University, Spokane, WA
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19
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Cao B, Wu X, Zhou J, Wu H, Liu L, Zhang Q, DeMott MS, Gu C, Wang L, You D, Dedon PC. Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage. Nucleic Acids Res 2020; 48:6715-6725. [PMID: 32484547 PMCID: PMC7337925 DOI: 10.1093/nar/gkaa473] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
DNA damage and epigenetic marks are well established to have profound influences on genome stability and cell phenotype, yet there are few technologies to obtain high-resolution genomic maps of the many types of chemical modifications of DNA. Here we present Nick-seq for quantitative, sensitive, and accurate mapping of DNA modifications at single-nucleotide resolution across genomes. Pre-existing breaks are first blocked and DNA modifications are then converted enzymatically or chemically to strand-breaks for both 3'-extension by nick-translation to produce nuclease-resistant oligonucleotides and 3'-terminal transferase tailing. Following library preparation and next generation sequencing, the complementary datasets are mined with a custom workflow to increase sensitivity, specificity and accuracy of the map. The utility of Nick-seq is demonstrated with genomic maps of site-specific endonuclease strand-breaks in purified DNA from Eschericia coli, phosphorothioate epigenetics in Salmonella enterica Cerro 87, and oxidation-induced abasic sites in DNA from E. coli treated with a sublethal dose of hydrogen peroxide. Nick-seq applicability is demonstrated with strategies for >25 types of DNA modification and damage.
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Affiliation(s)
- Bo Cao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaolin Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| | - Jieliang Zhou
- KK Research Center, KK Women's and Children's Hospital, 229899, Singapore
| | - Hang Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Lili Liu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Qinghua Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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20
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Douki T. Oxidative Stress and Genotoxicity in Melanoma Induction: Impact on Repair Rather Than Formation of DNA Damage? Photochem Photobiol 2020; 96:962-972. [PMID: 32367509 DOI: 10.1111/php.13278] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/21/2020] [Indexed: 12/22/2022]
Abstract
Keratinocytes and melanocytes, two cutaneous cell types located within the epidermis, are the origin of most skin cancers, namely carcinomas and melanomas. These two types of tumors differ in many ways. First, carcinomas are almost 10 times more frequent than melanomas. In addition, the affected cellular pathways, the mutated genes and the metastatic properties of the tumors are not the same. This review addresses another specificity of melanomas: the role of photo-oxidative stress. UVA efficiently produces reactive oxygen species in melanocytes, which results in more frequent oxidatively generated DNA lesions than in other cell types. The question of the respective contribution of UVB-induced pyrimidine dimers and UVA-mediated oxidatively generated lesions to mutagenesis in melanoma remains open. Recent results based on next-generation sequencing techniques strongly suggest that the mutational signature associated with pyrimidine dimers is overwhelming in melanomas like in skin carcinomas. UVA-induced oxidative stress may yet be indirectly linked to the genotoxic pathways involved in melanoma through its ability to hamper DNA repair activities.
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Affiliation(s)
- Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble, France
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21
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Dong Y, Wang Y, Zhuang P, Fu X, Zheng Y, Sanche L. Role of Transient Anions in Chemoradiation Therapy: Base Modifications, Cross-Links, and Cluster Damages Induced to Cisplatin-DNA Complexes by 1–20 eV Electrons. J Phys Chem B 2020; 124:3315-3325. [DOI: 10.1021/acs.jpcb.0c00946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yaxiao Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Puxiang Zhuang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Xianzhi Fu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
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22
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Yun BH, Guo J, Bellamri M, Turesky RJ. DNA adducts: Formation, biological effects, and new biospecimens for mass spectrometric measurements in humans. MASS SPECTROMETRY REVIEWS 2020; 39:55-82. [PMID: 29889312 PMCID: PMC6289887 DOI: 10.1002/mas.21570] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Hazardous chemicals in the environment and diet or their electrophilic metabolites can form adducts with genomic DNA, which can lead to mutations and the initiation of cancer. In addition, reactive intermediates can be generated in the body through oxidative stress and damage the genome. The identification and measurement of DNA adducts are required for understanding exposure and the causal role of a genotoxic chemical in cancer risk. Over the past three decades, 32 P-postlabeling, immunoassays, gas chromatography/mass spectrometry, and liquid chromatography/mass spectrometry (LC/MS) methods have been established to assess exposures to chemicals through measurements of DNA adducts. It is now possible to measure some DNA adducts in human biopsy samples, by LC/MS, with as little as several milligrams of tissue. In this review article, we highlight the formation and biological effects of DNA adducts, and highlight our advances in human biomonitoring by mass spectrometric analysis of formalin-fixed paraffin-embedded tissues, untapped biospecimens for carcinogen DNA adduct biomarker research.
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Affiliation(s)
- Byeong Hwa Yun
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Jingshu Guo
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Robert J. Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
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23
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Quiñones JL, Thapar U, Wilson SH, Ramsden DA, Demple B. Oxidative DNA-protein crosslinks formed in mammalian cells by abasic site lyases involved in DNA repair. DNA Repair (Amst) 2020; 87:102773. [PMID: 31945542 PMCID: PMC7065521 DOI: 10.1016/j.dnarep.2019.102773] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 01/15/2023]
Abstract
Free radical attack on C1' of deoxyribose forms the oxidized abasic (AP) site 2-deoxyribonolactone (dL). In vitro, dL traps the major base excision DNA repair enzyme DNA polymerase beta (Polβ) in covalent DNA-protein crosslinks (DPC) via the enzyme's N-terminal lyase activity acting on 5'-deoxyribose-5-phosphate residues. We previously demonstrated formation of Polβ-DPC in cells challenged with oxidants generating significant levels of dL. Proteasome inhibition under 1,10-copper-ortho-phenanthroline (CuOP) treatment significantly increased Polβ-DPC accumulation and trapped ubiquitin in the DPC, with Polβ accounting for 60-70 % of the total ubiquitin signal. However, the identity of the remaining oxidative ubiquityl-DPC remained unknown. In this report, we surveyed whether additional AP lyases are trapped in oxidative DPC in mammalian cells in culture. Poly(ADP-ribose) polymerase 1 (PARP1), Ku proteins, DNA polymerase λ (Polλ), and the bifunctional 8-oxoguanine DNA glycosylase 1 (OGG1), were all trapped in oxidative DPC in mammalian cells. We also observed significant trapping of Polλ, PARP1, and OGG1 in cells treated with the alkylating agent methylmethane sulfonate (MMS), in addition to dL-inducing agents. Ku proteins, in contrast, followed a pattern of trapping similar to that for Polβ: MMS failed to produce Ku-DPC, while treatment with CuOP or (less effectively) H2O2 gave rise to significant Ku-DPC. Unexpectedly, NEIL1 and NEIL3 were trapped following H2O2 treatment, but not detectably in cells exposed to CuOP. The half-life of all the AP lyase-DPC ranged from 15-60 min, consistent with their active repair. Accordingly, CuOP treatment under proteasome inhibition significantly increased the observed levels of DPC in cultured mammalian cells containing PARP1, Ku protein, Polλ, and OGG1 proteins. As seen for Polβ, blocking the proteasome led to the accumulation of DPC containing ubiquitin. Thus, the ubiquitin-dependent proteolytic mechanisms that control Polβ-DPC removal may also apply to a broad array of oxidative AP lyase-DPC, preventing their toxic accumulation in cells.
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Affiliation(s)
- Jason L Quiñones
- Department of Pharmacological Sciences, Stony Brook University, Renaissance School of Medicine, Basic Science Tower 8-140, Stony Brook, New York, 11794, USA
| | - Upasna Thapar
- Department of Pharmacological Sciences, Stony Brook University, Renaissance School of Medicine, Basic Science Tower 8-140, Stony Brook, New York, 11794, USA
| | - Samuel H Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC, 27709-2233, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Stony Brook University, Renaissance School of Medicine, Basic Science Tower 8-140, Stony Brook, New York, 11794, USA.
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24
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Nakamura J, Nakamura M. DNA-protein crosslink formation by endogenous aldehydes and AP sites. DNA Repair (Amst) 2020; 88:102806. [PMID: 32070903 DOI: 10.1016/j.dnarep.2020.102806] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/19/2022]
Abstract
Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the blockage of DNA replication and transcription. Both DNA lesions and endogenous products with carbonyl functional groups can produce DPC in genomic DNA under normal physiological conditions. For example, formaldehyde, the most abundant endogenous human carcinogen, and apurinic/apyrimidinic (AP) sites, the most common type of endogenous DNA lesions, has been shown to crosslink proteins and/or DNA through their carbonyl functional groups. Unfortunately, compared to other types of DNA damage, DPC have been less studied and understood. However, a recent advancement has allowed researchers to determine accurate yields of various DNA lesions including formaldehyde-derived DPC with high sensitivity and specificity, paving the way for new developments in this field of research. Here, we review the current literature and remaining unanswered questions on DPC formation by endogenous formaldehyde and various aldehydic 2-deoxyribose lesions.
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Affiliation(s)
- Jun Nakamura
- Laboratory of Laboratory Animal Science, Graduate School of Life and Environmental Biosciences, Osaka Prefecture University, Izumisano, Osaka, Japan.
| | - Mai Nakamura
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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25
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Gao L, Tong X, Ye T, Gao H, Zhang Q, Yan C, Yu Y, Fei Y, Zhou X, Shao Y. G‐Quadruplex‐Based Photooxidase Driven by Visible Light. ChemCatChem 2019. [DOI: 10.1002/cctc.201901481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Xingyu Tong
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
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Khorsandgolchin G, Sanche L, Cloutier P, Wagner JR. Strand Breaks Induced by Very Low Energy Electrons: Product Analysis and Mechanistic Insight into the Reaction with TpT. J Am Chem Soc 2019; 141:10315-10323. [PMID: 31244176 DOI: 10.1021/jacs.9b03295] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Numerous experimental studies show that 5-15 eV electrons induce strand breaks in DNA at energies below the ionization threshold of DNA components. In this energy range, DNA damage arises principally by the formation of transient negative ions, decaying into dissociative electron attachment (DEA) and electronic excitation of dissociative states. Here, we carried out LC-MS/MS analysis of the degradation products arising from bombardment of TpT, a DNA model compound, irradiated with very low energy electrons (vLEEs; ∼1.8 eV). The formation of thymidine 5'-monophosphate (TMP5') together with 2',3'-dideoxythymidine (ddT3') can be explained by cleavage of the C3'-O bond of TpT, whereas thymidine 3'-monophosphate (TMP3') and 2',5'-dideoxythymidine (ddT5') are formed by cleavage of the C5'-O bond. The formation of ddT3' and ddT5' decreased upon irradiation of either TMP5' or TMP3', and even further in the case of thymidine, underlining the critical role of the phosphate group. Interestingly, the yield of TMP5' and TMP3' was higher than that of the corresponding ddT3' and ddT5' products, suggesting alternative fates of C3' and C5'-centered sugar radicals. In contrast, the release of thymine from TpT was minor (<20%) and did not result in the formation of expected products from DEA-mediated cleavage at the N-glycosidic bond. Lastly, vLEE induced the conversion of thymine to 5,6-dihydrothymine (5,6-dhT) within TpT, a reaction likely involving thymine anion radicals. In summary, we show that a major pathway of vLEEs involves DEA-mediated cleavage of the C3'-O and C5'-O bonds of TpT, resulting in the formation of specific fragments, which represent a prompt single strand break in DNA.
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Affiliation(s)
- Ghazal Khorsandgolchin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
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Emerging Technologies in Mass Spectrometry-Based DNA Adductomics. High Throughput 2019; 8:ht8020013. [PMID: 31091740 PMCID: PMC6630665 DOI: 10.3390/ht8020013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/19/2019] [Accepted: 05/09/2019] [Indexed: 12/11/2022] Open
Abstract
The measurement of DNA adducts, the covalent modifications of DNA upon the exposure to the environmental and dietary genotoxicants and endogenously produced electrophiles, provides molecular evidence for DNA damage. With the recent improvements in the sensitivity and scanning speed of mass spectrometry (MS) instrumentation, particularly high-resolution MS, it is now feasible to screen for the totality of DNA damage in the human genome through DNA adductomics approaches. Several MS platforms have been used in DNA adductomic analysis, each of which has its strengths and limitations. The loss of 2′-deoxyribose from the modified nucleoside upon collision-induced dissociation is the main transition feature utilized in the screening of DNA adducts. Several advanced data-dependent and data-independent scanning techniques originated from proteomics and metabolomics have been tailored for DNA adductomics. The field of DNA adductomics is an emerging technology in human exposure assessment. As the analytical technology matures and bioinformatics tools become available for analysis of the MS data, DNA adductomics can advance our understanding about the role of chemical exposures in DNA damage and disease risk.
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Hardie ME, Gautam SD, Murray V. The genome-wide sequence preference of ionising radiation-induced cleavage in human DNA. Mol Biol Rep 2019; 46:3731-3745. [PMID: 31037547 DOI: 10.1007/s11033-019-04815-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/11/2019] [Indexed: 12/26/2022]
Abstract
For ionising radiation (IR)-induced cellular toxicity, DNA cleavage is thought to be a crucial step. In this paper, the genome-wide DNA sequence preference of gamma radiation-induced cleavage was investigated in purified human DNA. We utilised Illumina short read technology and over 80 million double-strand breaks (DSBs) were analysed in this study. The frequency of occurrence of individual nucleotides at the 50,000 most frequently cleaved sites was calculated and C nucleotides were found to be most prevalent at the cleavage site, followed by G and T, with A being the least prevalent. 5'-C*C and 5'-CC* dinucleotides (where * is the cleavage site) were found to be the present at the highest frequency at the cleavage site; while it was 5'-CC*C for trinucleotides and 5'-GCC*C and 5'-CC*CC for tetranucleotides. The frequency of occurrence of individual nucleotides at the most frequently cleaved sites was determined and the nucleotides in the sequence 5'-GGC*MH (where M is A or C, H is any nucleotide except G) were found to occur most frequently for DNA that was treated with endonuclease IV (to remove blocking 3'-phosphoglycolate termini); and 5'-GSC*MH (where S is G or C) for non-endonuclease IV-treated DNA. It was concluded that GC-rich sequences were preferentially targeted for cleavage by gamma irradiation. This was the first occasion that an extensive examination of the genome-wide DNA sequence preference of IR-induced DSBs has been performed.
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Affiliation(s)
- Megan E Hardie
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Shweta D Gautam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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Chan W, Ham YH, Jin L, Chan HW, Wong YL, Chan CK, Chung PY. Quantification of a Novel DNA–Protein Cross-Link Product Formed by Reacting Apurinic/Apyrimidinic Sites in DNA with Cysteine Residues in Protein by Liquid Chromatography-Tandem Mass Spectrometry Coupled with the Stable Isotope-Dilution Method. Anal Chem 2019; 91:4987-4994. [DOI: 10.1021/acs.analchem.8b04306] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Du H, Wang P, Li L, Amato NJ, Wang Y. Cytotoxic and Mutagenic Properties of C1' and C3'-Epimeric Lesions of 2'-Deoxyribonucleosides in Human Cells. ACS Chem Biol 2019; 14:478-485. [PMID: 30768892 DOI: 10.1021/acschembio.8b01126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genomic integrity is constantly challenged by exposure to environmental and endogenous genotoxic agents. Reactive oxygen species (ROS) represent one of the most common types of DNA damaging agents. While ROS mainly induce single-nucleobase lesions, epimeric 2-deoxyribose lesions can also be induced upon hydrogen atom abstraction from the C1', C3', or C4' carbon and the subsequent incorrect chemical repair of the resulting carbon-centered radicals. Herein, we investigated the replicative bypass of the C1'- and C3'-epimeric lesions of the four 2'-deoxynucleosides in HEK293T human embryonic kidney epithelial cells. Our results revealed distinct bypass efficiencies and mutagenic properties of these two types of epimeric lesions. Replicative bypasses of all C1'-epimeric lesions except α-dA are mutagenic in HEK293T cells, and their mutagenic properties are further modulated by translesion synthesis (TLS) DNA polymerases. By contrast, none of the four C3'-epimeric lesions are mutagenic, and the replicative bypass of these lesions is not compromised upon depletion of polymerase η, ι, κ, or ζ. Together, our results provide important new knowledge about the cytotoxic and mutagenic properties of C1' and C3' epimeric lesions, and reveal the roles of TLS DNA polymerases in bypassing these lesions in human cells.
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Affiliation(s)
- Hua Du
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Nicholas J. Amato
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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31
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Pérez-González A, Castañeda-Arriaga R, Álvarez-Idaboy JR, Reiter RJ, Galano A. Melatonin and its metabolites as chemical agents capable of directly repairing oxidized DNA. J Pineal Res 2019; 66:e12539. [PMID: 30417425 DOI: 10.1111/jpi.12539] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/26/2018] [Accepted: 11/05/2018] [Indexed: 12/24/2022]
Abstract
Oxidative stress mediates chemical damage to DNA yielding a wide variety of products. In this work, the potential capability of melatonin and several of its metabolites to repair directly (chemically) oxidative lesions in DNA was explored. It was found that all the investigated molecules are capable of repairing guanine-centered radical cations by electron transfer at very high rates, that is, diffusion-limited. They are also capable of repairing C-centered radicals in the sugar moiety of 2'-deoxyguanosine (2dG) by hydrogen atom transfer. Although this was identified as a rather slow process, with rate constants ranging from 1.75 to 5.32 × 102 M-1 s-1 , it is expected to be fast enough to prevent propagation of the DNA damage. Melatonin metabolites 6-hydroxymelatonin (6OHM) and 4-hydroxymelatonin (4OHM) are also predicted to repair OH adducts in the imidazole ring. In particular, the rate constants corresponding to the repair of 8-OH-G adducts were found to be in the order of 104 M-1 s-1 and are assisted by a water molecule. The results presented here strongly suggest that the role of melatonin in preventing DNA damage might be mediated by its capability, combined with that of its metabolites, to directly repair oxidized sites in DNA through different chemical routes.
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Affiliation(s)
- Adriana Pérez-González
- CONACYT, Universidad Autónoma Metropolitana - Iztapalapa, Iztapalapa, México City, México
| | - Romina Castañeda-Arriaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, México City, México
| | - Juan Raúl Álvarez-Idaboy
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México City, México
| | - Russel J Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, Texas
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Iztapalapa, México City, México
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Di Mascio P, Martinez GR, Miyamoto S, Ronsein GE, Medeiros MHG, Cadet J. Singlet Molecular Oxygen Reactions with Nucleic Acids, Lipids, and Proteins. Chem Rev 2019; 119:2043-2086. [DOI: 10.1021/acs.chemrev.8b00554] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Glaucia R. Martinez
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, 81531-990 Curitiba, PR, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Graziella E. Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Marisa H. G. Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508-000, São Paulo, SP Brazil
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4 Québec, Canada
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Cadet J, Douki T. Formation of UV-induced DNA damage contributing to skin cancer development. Photochem Photobiol Sci 2018; 17:1816-1841. [PMID: 29405222 DOI: 10.1039/c7pp00395a] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto-oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280-320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (64PPs). Less energetic but 20-times more intense UVA (320-400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8-oxo-7,8-dihydroguanine (8-oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8-oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV-induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, 3001 12e Avenue Nord, Université de Sherbrooke, Sherbrooke, Québec JIH 5N4, Canada.
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Pouget JP, Georgakilas AG, Ravanat JL. Targeted and Off-Target (Bystander and Abscopal) Effects of Radiation Therapy: Redox Mechanisms and Risk/Benefit Analysis. Antioxid Redox Signal 2018; 29:1447-1487. [PMID: 29350049 PMCID: PMC6199630 DOI: 10.1089/ars.2017.7267] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE Radiation therapy (from external beams to unsealed and sealed radionuclide sources) takes advantage of the detrimental effects of the clustered production of radicals and reactive oxygen species (ROS). Research has mainly focused on the interaction of radiation with water, which is the major constituent of living beings, and with nuclear DNA, which contains the genetic information. This led to the so-called target theory according to which cells have to be hit by ionizing particles to elicit an important biological response, including cell death. In cancer therapy, the Poisson law and linear quadratic mathematical models have been used to describe the probability of hits per cell as a function of the radiation dose. Recent Advances: However, in the last 20 years, many studies have shown that radiation generates "danger" signals that propagate from irradiated to nonirradiated cells, leading to bystander and other off-target effects. CRITICAL ISSUES Like for targeted effects, redox mechanisms play a key role also in off-target effects through transmission of ROS and reactive nitrogen species (RNS), and also of cytokines, ATP, and extracellular DNA. Particularly, nuclear factor kappa B is essential for triggering self-sustained production of ROS and RNS, thus making the bystander response similar to inflammation. In some therapeutic cases, this phenomenon is associated with recruitment of immune cells that are involved in distant irradiation effects (called "away-from-target" i.e., abscopal effects). FUTURE DIRECTIONS Determining the contribution of targeted and off-target effects in the clinic is still challenging. This has important consequences not only in radiotherapy but also possibly in diagnostic procedures and in radiation protection.
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Affiliation(s)
- Jean-Pierre Pouget
- 1 Institut de Recherche en Cancérologie de Montpellier (IRCM) , INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Alexandros G Georgakilas
- 2 DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens , Athens, Greece
| | - Jean-Luc Ravanat
- 3 Univ. Grenoble Alpes , CEA, CNRS INAC SyMMES UMR 5819, Grenoble, France
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35
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Yao W, Ma X, Li S, Gao Y, Nian F, Zhou L. Theoretical study of mechanism and kinetics for the reaction of hydroxyl radical with 2′-deoxycytidine. Struct Chem 2018. [DOI: 10.1007/s11224-018-1122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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36
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Monien BH, Sachse B, Meinl W, Abraham K, Lampen A, Glatt H. Hemoglobin adducts of furfuryl alcohol in genetically modified mouse models: Role of endogenous sulfotransferases 1a1 and 1d1 and transgenic human sulfotransferases 1A1/1A2. Toxicol Lett 2018; 295:173-178. [DOI: 10.1016/j.toxlet.2018.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 11/28/2022]
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Keratinocyte stem cells are more resistant to UVA radiation than their direct progeny. PLoS One 2018; 13:e0203863. [PMID: 30208100 PMCID: PMC6135485 DOI: 10.1371/journal.pone.0203863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 08/29/2018] [Indexed: 12/16/2022] Open
Abstract
The epidermis undergoes constant renewal during its lifetime. This is possible due to a special population of keratinocyte stem cells (KSCs) located at the basal layer. These cells are surrounded by their direct progeny, keratinocyte progenitors or transient amplifying cells (TAs), which arise from cell division. Skin is exposed every day to sun radiation; in particular, UVA radiation penetrates through the epidermis and induces damage to KSCs and TAs. Although keratinocytes in the basal layer are the most likely skin carcinomas and/or photoaging cells of origin, surprisingly few studies have addressed the specific responses of these cells to UV radiation. In this study, we showed for the first time that keratinocyte stem cells were more resistant to UVA irradiation than their direct progeny, transient amplifying cells. Using both the MTT assay and clonogenic assay, we found that KSCs were more photo-resistant compared to TAs after exposure to different doses of UVA (from 0 to 50 J/cm2). Moreover, KSCs had a greater ability to reconstruct human epidermis (RHE) after UVA exposure compared with TAs. Finally, investigations of DNA repair using the comet assay showed that DNA single-strand breaks and thymine dimers were repaired quicker and more efficiently in KSCs compared with TAs. In a previous work, we showed that the same stem cell population was more resistant to ionizing radiation, another carcinogenic agent. Collectively, our results combined with other observations demonstrate that keratinocyte stem cells, which are responsible for epidermal renewal throughout life, are equipped with an efficient arsenal against several genotoxic agents. Our future work will try to identify the factors or signaling pathways that are responsible for this differential photo-sensitivity and DNA repair capacity between KSCs and TAs.
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38
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Belostotskii AM. Nanosecond-Scale Isomerization of the 4'-Carboxonium Cation Oxidatively Produced in Pyrimidine Units of DNA. J Org Chem 2018; 83:11604-11613. [PMID: 30153025 DOI: 10.1021/acs.joc.8b01580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The long-standing puzzle of the chemistry producing the Stubbe-Kozarich abasic site, which is the minor product in the oxidation of 2'-deoxycytidine units of DNA by Fe(II)-bleomycin, has been computationally solved in this study. Scrupulous DFT-based calculations that included extensive screening of the potential energy surface of model-solvated nucleotides and the elucidation of the chemical structure of the located nucleotide cations via natural bond orbital analysis demonstrated that the 2'-deoxycytidine unit bearing the 2'-deoxyribose ring 2e-oxidized at the 4'-position undergoes carboxonium ion- iminium ion (C═O+-C → C═N+) isomerization. This 1,2-elimination of the carbonyl group 4'-C═O from the carboxonium cation fragment is associated with minimal spatial reorganization of the molecule and appears to be an ultrafast reaction. The calculated barrier Δ G0# of 2.7 kcal mol-1 for this isomerization is lower than that reported for the addition of water to oxocarbenium ions. Thus, this unusual nucleotide transformation is the key chemical reaction that yields the Stubbe-Kozarich product. Such a product cannot be formed for purine nucleotide units in DNA. The isomerization of 4'-dehydro-2'-deoxyribose-4'-carboxonium cations formed in these DNA units is slower because it destroys the purine aromaticity, and the cations are intercepted by water molecules before they isomerize.
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39
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Galano A, Reiter RJ. Melatonin and its metabolites vs oxidative stress: From individual actions to collective protection. J Pineal Res 2018; 65:e12514. [PMID: 29888508 DOI: 10.1111/jpi.12514] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/05/2018] [Indexed: 12/11/2022]
Abstract
Oxidative stress (OS) represents a threat to the chemical integrity of biomolecules including lipids, proteins, and DNA. The associated molecular damage frequently results in serious health issues, which justifies our concern about this phenomenon. In addition to enzymatic defense mechanisms, there are compounds (usually referred to as antioxidants) that offer chemical protection against oxidative events. Among them, melatonin and its metabolites constitute a particularly efficient chemical family. They offer protection against OS as individual chemical entities through a wide variety of mechanisms including electron transfer, hydrogen transfer, radical adduct formation, and metal chelation, and by repairing biological targets. In fact, many of them including melatonin can be classified as multipurpose antioxidants. However, what seems to be unique to the melatonin's family is their collective effects. Because the members of this family are metabolically related, most of them are expected to be present in living organisms wherever melatonin is produced. Therefore, the protection exerted by melatonin against OS may be viewed as a result of the combined antioxidant effects of the parent molecule and its metabolites. Melatonin's family is rather exceptional in this regard, offering versatile and collective antioxidant protection against OS. It certainly seems that melatonin is one of the best nature's defenses against oxidative damage.
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Affiliation(s)
- Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, México City, México
| | - Russel J Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX, USA
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40
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Saifi IJ, Neelofar K, Ajmal M, Siddiqi SS. Biophysical and immunological characterization of 2-dRib modified HSA and its implications in diabetes mellitus. Int J Biol Macromol 2018; 113:294-299. [DOI: 10.1016/j.ijbiomac.2018.02.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 11/15/2022]
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41
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Khan AQ, Travers JB, Kemp MG. Roles of UVA radiation and DNA damage responses in melanoma pathogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:438-460. [PMID: 29466611 PMCID: PMC6031472 DOI: 10.1002/em.22176] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 05/10/2023]
Abstract
The growing incidence of melanoma is a serious public health issue that merits a thorough understanding of potential causative risk factors, which includes exposure to ultraviolet radiation (UVR). Though UVR has been classified as a complete carcinogen and has long been recognized for its ability to damage genomic DNA through both direct and indirect means, the precise mechanisms by which the UVA and UVB components of UVR contribute to the pathogenesis of melanoma have not been clearly defined. In this review, we therefore highlight recent studies that have addressed roles for UVA radiation in the generation of DNA damage and in modulating the subsequent cellular responses to DNA damage in melanocytes, which are the cell type that gives rise to melanoma. Recent research suggests that UVA not only contributes to the direct formation of DNA lesions but also impairs the removal of UV photoproducts from genomic DNA through oxidation and damage to DNA repair proteins. Moreover, the melanocyte microenvironment within the epidermis of the skin is also expected to impact melanomagenesis, and we therefore discuss several paracrine signaling pathways that have been shown to impact the DNA damage response in UV-irradiated melanocytes. Lastly, we examine how alterations to the immune microenvironment by UVA-associated DNA damage responses may contribute to melanoma development. Thus, there appear to be multiple avenues by which UVA may elevate the risk of melanoma. Protective strategies against excess exposure to UVA wavelengths of light therefore have the potential to decrease the incidence of melanoma. Environ. Mol. Mutagen. 59:438-460, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Aiman Q Khan
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
| | - Jeffrey B Travers
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
- Dayton Veterans Affairs Medical Center, Dayton, Ohio
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
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Wakaki T, Sakai K, Enomoto T, Kondo M, Masaoka S, Oisaki K, Kanai M. C(sp3
)−H Cyanation Promoted by Visible-Light Photoredox/Phosphate Hybrid Catalysis. Chemistry 2018; 24:8051-8055. [DOI: 10.1002/chem.201801746] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Takayuki Wakaki
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kentaro Sakai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takafumi Enomoto
- Institute for Molecular Science; National Institutes of Natural Sciences; 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
| | - Mio Kondo
- Institute for Molecular Science; National Institutes of Natural Sciences; 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
| | - Shigeyuki Masaoka
- Institute for Molecular Science; National Institutes of Natural Sciences; 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
| | - Kounosuke Oisaki
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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43
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Wauchope OR, Mitchener MM, Beavers WN, Galligan JJ, Camarillo JM, Sanders WD, Kingsley PJ, Shim HN, Blackwell T, Luong T, deCaestecker M, Fessel JP, Marnett LJ. Oxidative stress increases M1dG, a major peroxidation-derived DNA adduct, in mitochondrial DNA. Nucleic Acids Res 2018; 46:3458-3467. [PMID: 29438559 PMCID: PMC5909422 DOI: 10.1093/nar/gky089] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/29/2018] [Accepted: 02/03/2018] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) are formed in mitochondria during electron transport and energy generation. Elevated levels of ROS lead to increased amounts of mitochondrial DNA (mtDNA) damage. We report that levels of M1dG, a major endogenous peroxidation-derived DNA adduct, are 50-100-fold higher in mtDNA than in nuclear DNA in several different human cell lines. Treatment of cells with agents that either increase or decrease mitochondrial superoxide levels leads to increased or decreased levels of M1dG in mtDNA, respectively. Sequence analysis of adducted mtDNA suggests that M1dG residues are randomly distributed throughout the mitochondrial genome. Basal levels of M1dG in mtDNA from pulmonary microvascular endothelial cells (PMVECs) from transgenic bone morphogenetic protein receptor 2 mutant mice (BMPR2R899X) (four adducts per 106 dG) are twice as high as adduct levels in wild-type cells. A similar increase was observed in mtDNA from heterozygous null (BMPR2+/-) compared to wild-type PMVECs. Pulmonary arterial hypertension is observed in the presence of BMPR2 signaling disruptions, which are also associated with mitochondrial dysfunction and oxidant injury to endothelial tissue. Persistence of M1dG adducts in mtDNA could have implications for mutagenesis and mitochondrial gene expression, thereby contributing to the role of mitochondrial dysfunction in diseases.
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Affiliation(s)
- Orrette R Wauchope
- A.B. Hancock, Jr., Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michelle M Mitchener
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William N Beavers
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James J Galligan
- A.B. Hancock, Jr., Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jeannie M Camarillo
- A.B. Hancock, Jr., Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William D Sanders
- A.B. Hancock, Jr., Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Philip J Kingsley
- A.B. Hancock, Jr., Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ha-Na Shim
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Thomas Blackwell
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Thong Luong
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mark deCaestecker
- Departments of Cell and Developmental Biology, Surgery and Medicine, USA
| | - Joshua P Fessel
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Lawrence J Marnett
- A.B. Hancock, Jr., Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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44
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Melatonin: A Versatile Protector against Oxidative DNA Damage. Molecules 2018; 23:molecules23030530. [PMID: 29495460 PMCID: PMC6017920 DOI: 10.3390/molecules23030530] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 12/15/2022] Open
Abstract
Oxidative damage to DNA has important implications for human health and has been identified as a key factor in the onset and development of numerous diseases. Thus, it is evident that preventing DNA from oxidative damage is crucial for humans and for any living organism. Melatonin is an astonishingly versatile molecule in this context. It can offer both direct and indirect protection against a wide variety of damaging agents and through multiple pathways, which may (or may not) take place simultaneously. They include direct antioxidative protection, which is mediated by melatonin's free radical scavenging activity, and also indirect ways of action. The latter include, at least: (i) inhibition of metal-induced DNA damage; (ii) protection against non-radical triggers of oxidative DNA damage; (iii) continuous protection after being metabolized; (iv) activation of antioxidative enzymes; (v) inhibition of pro-oxidative enzymes; and (vi) boosting of the DNA repair machinery. The rather unique capability of melatonin to exhibit multiple neutralizing actions against diverse threatening factors, together with its low toxicity and its ability to cross biological barriers, are all significant to its efficiency for preventing oxidative damage to DNA.
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45
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Gautam SD, Hardie ME, Murray V. The Sequence Preference of Gamma-Radiation-Induced Damage in End-Labeled DNA after Heat Treatment. Radiat Res 2017; 189:238-250. [PMID: 29286256 DOI: 10.1667/rr14886.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this work, we examined the DNA sequence preference of gamma-radiation-induced DNA damage in purified DNA sequences after heat treatment. DNA was fluorescently end-labeled and gamma-radiation-induced DNA cleavage was examined using capillary electrophoresis with laser-induced fluorescence detection. Our findings provide evidence that gamma-radiation-induced DNA damage to end-labeled DNA is nonrandom and has a sequence preference. The degree of cleavage was quantified at each nucleotide, and we observed that preferential cleavage occurred at C nucleotides with lesser cleavage at G nucleotides, while being very low at T nucleotides. The differences in percentage cleavage at individual nucleotides ranged up to sixfold. The DNA sequences surrounding the most intense radiation-induced DNA cleavage sites were examined and a consensus sequence 5'-AGGC*C (where C* is the cleavage site) was found. The highest intensity gamma-radiation-induced DNA cleavage sites were found at the dinucleotides, 5'-GG*, 5'-GC*, 5'-C*C and 5'-G*G and at the trinucleotides, 5'-GG*C, 5'-TC*A, 5'-GG*G and 5'-GC*C. These findings have implications for our understanding of ionizing radiation-induced DNA damage.
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Affiliation(s)
- Shweta D Gautam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Megan E Hardie
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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46
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Bedi MF, Li W, Gutwald T, Bryant-Friedrich AC. Synthesis of damaged DNA containing the oxidative lesion 3'-oxothymidine. Bioorg Med Chem 2017; 25:5598-5602. [PMID: 28927804 DOI: 10.1016/j.bmc.2017.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/16/2022]
Abstract
Oxidative events that take place during regular oxygen metabolism can lead to the formation of organic or inorganic radicals. The interaction of these radicals with macromolecules in the organism and with DNA in particular is suspected to lead to apoptosis, DNA lesions and cell damage. Independent generation of DNA lesions resulting from oxidative damage is used to promote the study of their effects on biological systems. An efficient synthesis of oligodeoxyribonucleotides (ODNs) containing the oxidative damage lesion 3'-oxothymidine has been accomplished via incorporation of C3'-hydroxymethyl thymidine as its corresponding 5'-phosphoramidite. Through oxidative cleavage using sodium periodate in aqueous solution, the lesion of interest is easily generated. Due to its inherent instability it cannot be directly isolated, but must be generated in situ. 3'-Oxothymidine is a demonstrated damage product formed upon generation of the C3'-thymidinyl radical in ODN.
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Affiliation(s)
- Mel F Bedi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801 W. Bancroft St., Toledo, OH, United States
| | - Weiye Li
- Department of Medicinal Chemistry and Pharmacognosy, The University of Illinois Chicago, 1601 Parkview Ave. Rm A301, Rockford, IL 61107, United States
| | - Taylor Gutwald
- Chicago College of Pharmacy, Midwestern University, Chicago, 555 31st Street, Downers Grove, IL 60515, United States
| | - Amanda C Bryant-Friedrich
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, 2801 W. Bancroft St., Toledo, OH, United States.
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47
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Wang P, Amato NJ, Wang Y. Cytotoxic and Mutagenic Properties of C3'-Epimeric Lesions of 2'-Deoxyribonucleosides in Escherichia coli Cells. Biochemistry 2017. [PMID: 28650656 DOI: 10.1021/acs.biochem.7b00146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactive oxygen species (ROS), resulting from endogenous metabolism and/or environmental exposure, can induce damage to the 2-deoxyribose moiety in DNA. Specifically, a hydrogen atom from each of the five carbon atoms in 2-deoxyribose can be abstracted by hydroxyl radical, and improper chemical repair of the ensuing radicals formed at the C1', C3', and C4' positions can lead to the stereochemical inversion at these sites to yield epimeric 2-deoxyribose lesions. Although ROS-induced single-nucleobase lesions have been well studied, the biological consequences of the C3'-epimeric lesions of 2'-deoxynucleosides, i.e., 2'-deoxyxylonucleosides (dxN), have not been comprehensively investigated. Herein, we assessed the impact of dxN lesions on the efficiency and fidelity of DNA replication in Escherichia coli cells by conducting a competitive replication and adduct bypass assay with single-stranded M13 phage containing a site-specifically incorporated dxN. Our results revealed that, of the four dxN lesions, only dxG constituted a strong impediment to DNA replication, and intriguingly, dxT and dxC conferred replication bypass efficiencies higher than those of the unmodified counterparts. In addition, the three SOS-induced DNA polymerases (Pol II, Pol IV, and Pol V) did not play any appreciable role in bypassing these lesions. Among the four dxNs, only dxA directed a moderate frequency of dCMP misincorporation. These results provided important insights into the impact of the C3'-epimeric lesions on DNA replication in E. coli cells.
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Affiliation(s)
- Pengcheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Nicholas J Amato
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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48
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Cadet J, Davies KJA, Medeiros MH, Di Mascio P, Wagner JR. Formation and repair of oxidatively generated damage in cellular DNA. Free Radic Biol Med 2017; 107:13-34. [PMID: 28057600 PMCID: PMC5457722 DOI: 10.1016/j.freeradbiomed.2016.12.049] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/27/2016] [Accepted: 12/31/2016] [Indexed: 12/18/2022]
Abstract
In this review article, emphasis is placed on the critical survey of available data concerning modified nucleobase and 2-deoxyribose products that have been identified in cellular DNA following exposure to a wide variety of oxidizing species and agents including, hydroxyl radical, one-electron oxidants, singlet oxygen, hypochlorous acid and ten-eleven translocation enzymes. In addition, information is provided about the generation of secondary oxidation products of 8-oxo-7,8-dihydroguanine and nucleobase addition products with reactive aldehydes arising from the decomposition of lipid peroxides. It is worth noting that the different classes of oxidatively generated DNA damage that consist of single lesions, intra- and interstrand cross-links were unambiguously assigned and quantitatively detected on the basis of accurate measurements involving in most cases high performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. The reported data clearly show that the frequency of DNA lesions generated upon severe oxidizing conditions, including exposure to ionizing radiation is low, at best a few modifications per 106 normal bases. Application of accurate analytical measurement methods has also allowed the determination of repair kinetics of several well-defined lesions in cellular DNA that however concerns so far only a restricted number of cases.
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Affiliation(s)
- Jean Cadet
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4.
| | - Kelvin J A Davies
- Leonard Davis School of Gerontology of the Ethel Percy Andrus Gerontology Center, The University of Southern California, Los Angeles, CA 90089-0191, United States; Division of Molecular & Computational Biology, Department of Biological Sciences of the Dornsife College of Letters, Arts, and Sciences, The University of Southern California, Los Angeles, CA 90089-0191, United States
| | - Marisa Hg Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508 000 São Paulo, SP, Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, CEP 05508 000 São Paulo, SP, Brazil
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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49
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Fleming AM, Burrows CJ. Formation and processing of DNA damage substrates for the hNEIL enzymes. Free Radic Biol Med 2017; 107:35-52. [PMID: 27880870 PMCID: PMC5438787 DOI: 10.1016/j.freeradbiomed.2016.11.030] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022]
Abstract
Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed. The major G base oxidation products are 8-oxo-7,8-dihydroguanine (OG), 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), spiroiminodihydantoin (Sp), and 5-guanidinohydantoin (Gh). The yields of these products show dependency on the oxidant and the reaction context that includes nucleoside, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and G-quadruplex DNA (G4-DNA) structures. Upon formation of these products in cells, they are recognized by the DNA glycosylases in the base excision repair (BER) pathway. This review focuses on initiation of BER by the mammalian Nei-like1-3 (NEIL1-3) glycosylases for removal of 2Ih, Sp, and Gh. The unique ability of the human NEILs to initiate removal of the hydantoins in ssDNA, bulge-DNA, bubble-DNA, dsDNA, and G4-DNA is outlined. Additionally, when Gh exists in a G4 DNA found in a gene promoter, NEIL-mediated repair is modulated by the plasticity of the G4-DNA structure provided by additional G-runs flanking the sequence. On the basis of these observations and cellular studies from the literature, the interplay between DNA oxidation and BER to alter gene expression is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, United States.
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50
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Vilanova B, Fernández D, Casasnovas R, Pomar AM, Alvarez-Idaboy JR, Hernández-Haro N, Grand A, Adrover M, Donoso J, Frau J, Muñoz F, Ortega-Castro J. Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor. Int J Biol Macromol 2017; 98:664-675. [PMID: 28192135 DOI: 10.1016/j.ijbiomac.2017.01.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 01/08/2023]
Abstract
DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal-guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal-guanine adducts can cause structural changes in an oligonucleotide model. A thermodynamic study of other glycating agents including methylglyoxal, acrolein, crotonaldehyde, 4-hydroxynonenal and 3-deoxyglucosone revealed that, at neutral pH, cyclic adducts were more stable than open adducts; at basic pH, however, the open adducts of 3-deoxyglucosone, methylglyoxal and glyoxal were more stable than their cyclic counterparts. This result can be ascribed to the ability of the adducts to cross-link DNA. The new insights may contribute to improve our understanding of the connection between glycation and DNA cross-linking.
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Affiliation(s)
- B Vilanova
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain.
| | - D Fernández
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - R Casasnovas
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - A M Pomar
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J R Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | | | - A Grand
- Univ. Greboble Alpes, INAC-SCIB, F-38000 Grenoble, France; CEA, INAC-SyMMES, F-38000 Grenoble, France; Universidad Autónoma de Chile, Carlos Antúnez 1920, 7500566, Providencia, Santiago de, Chile
| | - M Adrover
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J Donoso
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J Frau
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - F Muñoz
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
| | - J Ortega-Castro
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain; Instituto de Investigación Sanitaria de Palma (IdISPA), 07010 Palma de Mallorca, Spain
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