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Olivier C, Luies L. Metabolic insights into HIV/TB co-infection: an untargeted urinary metabolomics approach. Metabolomics 2024; 20:78. [PMID: 39014031 PMCID: PMC11252185 DOI: 10.1007/s11306-024-02148-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024]
Abstract
INTRODUCTION Amid the global health crisis, HIV/TB co-infection presents significant challenges, amplifying the burden on patients and healthcare systems alike. Metabolomics offers an innovative window into the metabolic disruptions caused by co-infection, potentially improving diagnosis and treatment monitoring. AIM This study uses untargeted metabolomics to investigate the urinary metabolic signature of HIV/TB co-infection, enhancing understanding of the metabolic interplay between these infections. METHODS Urine samples from South African adults, categorised into four groups - healthy controls, TB-positive, HIV-positive, and HIV/TB co-infected - were analysed using GCxGC-TOFMS. Metabolites showing significant differences among groups were identified through Kruskal-Wallis and Wilcoxon rank sum tests. RESULTS Various metabolites (n = 23) were modulated across the spectrum of health and disease states represented in the cohorts. The metabolomic profiles reflect a pronounced disruption in biochemical pathways involved in energy production, amino acid metabolism, gut microbiome, and the immune response, suggesting a bidirectional exacerbation between HIV and TB. While both diseases independently perturb the host's metabolism, their co-infection leads to a unique metabolic phenotype, indicative of an intricate interplay rather than a simple additive effect. CONCLUSION Metabolic profiling revealed a unique metabolic landscape shaped by HIV/TB co-infection. The findings highlight the potential of urinary differential metabolites for co-infection, offering a non-invasive tool for enhancing diagnostic precision and tailoring therapeutic interventions. Future research should focus on expanding sample sizes and integrating longitudinal analyses to build upon these foundational insights, paving the way for metabolomic applications in combating these concurrent pandemics.
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Affiliation(s)
- Cara Olivier
- Focus Area Human Metabolomics, North-West University, Potchefstroom Campus, Private Bag X6001, Box 269, Potchefstroom, North West, 2520, South Africa
| | - Laneke Luies
- Focus Area Human Metabolomics, North-West University, Potchefstroom Campus, Private Bag X6001, Box 269, Potchefstroom, North West, 2520, South Africa.
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Das R, Karri R, Chalana A, Rai RK, Roy G. Uncovering the Role of Methylmercury on DNA Lesions at Cytotoxic Concentrations in Glutathione-Depleted Cells: Insights from Experimental and Computational Studies. Inorg Chem 2024; 63:10455-10465. [PMID: 38743433 DOI: 10.1021/acs.inorgchem.3c04579] [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: 05/16/2024]
Abstract
Organomercurials (RHg+), especially methylmercury (MeHg+) and ethylmercury (EtHg+), are considered to be more neurotoxic than the inorganic counterpart (Hg2+). They cause massive DNA damage in cells, especially in neurons, where cellular glutathione (GSH) levels are significantly low. However, the mechanism by which RHg+ exerts massive DNA damage at cytotoxic concentrations in brain cells remains obscure. In this study, we investigated the effect of RHg+ on the structural and electronic properties of nucleosides and its effects on DNA damage. The direct interaction of RHg+ with the nucleoside significantly weakens N-glycosidic bonds, decreases the C-H bond energy of sugar moieties, and increases the electrophilicity of the C8-center of purine bases. As a consequence, RHg+-conjugated DNA molecules are extremely labile and highly sensitive to any nucleophiles/radicals present in GSH-depleted cells and, thus, undergo enhanced oxidative and unusual alkylative DNA damage. We also report a functional model of organomercurial lyase, which showed excellent cytoprotective effect against RHg+-induced cytotoxicity; this reverses the activity of glutathione reductase inhibited by MeHgCl and ceases oxidative and alkylating DNA damage. This intriguing finding provides new mechanistic insight into the mode of action of organomercurials in GSH-depleted cells and their adverse effects on individuals with neurodegenerative disorders associated with oxidative stress.
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Affiliation(s)
- Ranajit Das
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Dadri, UP 201314, India
| | - Ramesh Karri
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Dadri, UP 201314, India
- Ruhvenile Biomedical OPC Pvt. Ltd., New Delhi 110070, Delhi, India
| | - Ashish Chalana
- Centre for Development of Biomaterials, Department of Chemistry & Biochemistry, Sharda University, Greater Noida, UP 201306, India
| | - Rakesh Kumar Rai
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati, AP 517619, India
| | - Gouriprasanna Roy
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati, AP 517619, India
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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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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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Thermogenic Adipose Redox Mechanisms: Potential Targets for Metabolic Disease Therapies. Antioxidants (Basel) 2023; 12:antiox12010196. [PMID: 36671058 PMCID: PMC9854447 DOI: 10.3390/antiox12010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Metabolic diseases, such as diabetes and non-alcoholic fatty liver disease (NAFLD), have several negative health outcomes on affected humans. Dysregulated energy metabolism is a key component underlying the pathophysiology of these conditions. Adipose tissue is a fundamental regulator of energy homeostasis that utilizes several redox reactions to carry out the metabolism. Brown and beige adipose tissues, in particular, perform highly oxidative reactions during non-shivering thermogenesis to dissipate energy as heat. The appropriate regulation of energy metabolism then requires coordinated antioxidant mechanisms to counterbalance the oxidation reactions. Indeed, non-shivering thermogenesis activation can cause striking changes in concentrations of both oxidants and antioxidants in order to adapt to various oxidative environments. Current therapeutic options for metabolic diseases either translate poorly from rodent models to humans (in part due to the challenges of creating a physiologically relevant rodent model) or tend to have numerous side effects, necessitating novel therapies. As increased brown adipose tissue activity results in enhanced energy expenditure and is associated with beneficial effects on metabolic health, such as decreased obesity, it has gathered great interest as a modulator of metabolic disease. One potential reason for the beneficial health effects may be that although non-shivering thermogenesis is enormously oxidative, it is also associated with decreased oxidant formation after its activation. However, targeting its redox mechanisms specifically to alter metabolic disease remains an underexplored area. Therefore, this review will discuss the role of adipose tissue in energy homeostasis, non-shivering thermogenesis in adults, and redox mechanisms that may serve as novel therapeutic targets of metabolic disease.
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Discovery and validation of bladder cancer related excreted nucleosides biomarkers by dilution approach in cell culture supernatant and urine using UHPLC-MS/MS. J Proteomics 2023; 270:104737. [PMID: 36174950 DOI: 10.1016/j.jprot.2022.104737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 02/01/2023]
Abstract
The exploration of nucleoside changes in human biofluids has profound potential for cancer diagnosis. Herein, we developed a rapid methodology to quantify 17 nucleosides by UHPLC-MS/MS. Five pairs of isomers were successfully separated within 8 min. The ME was mostly eliminated by sample dilution folds of 1000 for urine and 40 for CCS. The optimized method was firstly applied to screen potential nucleoside biomarkers in CCS by comprising bladder cancer cell lines (5637 and T24) and normal human bladder cell line SV-HUC-1 together with student's t-test and OPLS-DA. Nucleosides with significant differences in the supernatant of urine samples were also uncovered comparing BCa with the non-tumor group, as well as a comparison of BCa recurrence group with the non-recurrence group. By intersecting the differential nucleosides in CCS and urine supernatant, and then further confirmed using validation sets, the combination of m3C and m1A with AUC of 0.775 was considered as a potential biomarker for bladder cancer diagnosis. A panel of m3C, m1A, m1G, and m22G was defined as potential biomarkers for bladder cancer prognosis with an AUC of 0.819. Above all, this method provided a new perspective for diagnosis and recurrence monitoring of bladder cancer. SIGNIFICANCE: The exploration of nucleoside changes in body fluids has profound potential for the diagnosis and elucidation of the pathogenesis of cancer. In this study, we developed a rapid methodology for the simultaneous quantitative determination of 17 nucleosides in the supernatant of cells and urine samples using UHPLC-MS/MS to discover and validate bladder cancer related excreted nucleoside biomarkers. The results of this paper provide a new strategy for diagnosis and postoperative recurrence monitoring of bladder cancer and provide theoretical support for the exploration of its pathogenesis.
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Bennett R, Cohen RD, Wang H, Pereira T, Haverick MA, Loughney JW, Barbacci DC, Pristatsky P, Bowman AM, Losacco GL, Richardson DD, Mangion I, Regalado EL. Selective Plate-Based Assay for Trace EDTA Analysis via Boron Trifluoride-methanol Derivatization UHPLC-QqQ-MS/MS Enabling Biologic and Vaccine Processes. Anal Chem 2021; 94:1678-1685. [PMID: 34928586 DOI: 10.1021/acs.analchem.1c04224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The employment of ethylenediaminetetraacetic acid (EDTA) across several fields in chemistry and biology has required the creation of a high number of quantitative assays. Nonetheless, the determination of trace EDTA, especially in biologics and vaccines, remains challenging. Herein, we introduce an automated high-throughput approach based on EDTA esterification in 96-well plates using boron trifluoride-methanol combined with rapid analysis by ultra-high-performance liquid chromatography-triple quadrupole tandem mass spectrometry (UHPLC-QqQ-MS/MS). Derivatization of EDTA to its methyl ester (Me-EDTA) serves to significantly improve chromatographic performance (retention, peak shape, and selectivity), while also delivering a tremendous enhancement of sensitivity in the positive ion mode electrospray ionization (ESI+). This procedure, in contrast to previous EDTA methods based on complexation with metal ions, is not affected by high concentration of other metals, buffers, and related salts abundantly present in biopharmaceutical processes (e.g., iron, copper, citrate, etc.). Validation of this assay for the determination of ng·mL-1 level EDTA in monoclonal antibody and vaccine products demonstrated excellent performance (repeatability, precision, and linear range) with high recovery from small sample volumes while also providing an advantageous automation-friendly workflow for high-throughput analysis.
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Affiliation(s)
- Raffeal Bennett
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - Ryan D Cohen
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Heather Wang
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tony Pereira
- Transporters & In Vitro Technologies, PPDM, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark A Haverick
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - John W Loughney
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - Damon C Barbacci
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - Pavlo Pristatsky
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - Amy M Bowman
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - Gioacchino Luca Losacco
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Douglas D Richardson
- Analytical Research & Development, Merck & Co. Inc., West Point, Pennsylvania 19486, United States
| | - Ian Mangion
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Erik L Regalado
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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Halliwell B, Adhikary A, Dingfelder M, Dizdaroglu M. Hydroxyl radical is a significant player in oxidative DNA damage in vivo. Chem Soc Rev 2021; 50:8355-8360. [PMID: 34128512 PMCID: PMC8328964 DOI: 10.1039/d1cs00044f] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent publications have suggested that oxidative DNA damage mediated by hydroxyl radical (˙OH) is unimportant in vivo, and that carbonate anion radical (CO3˙-) plays the key role. We examine these claims and summarize the evidence that ˙OH does play a key role as an important member of the reactive oxygen species (ROS) in vivo.
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Affiliation(s)
- Barry Halliwell
- Department of Biochemistry, National University of Singapore, Centre for Life Sciences, #05-01A, 28 Medical Drive, 117456, Singapore.
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9
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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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Bortňák D, Pecher D, Végh D, Breza M, Mikuš P, Milata V. Mass spectrometrical and quantum-chemical study of pentafluorophenylhydrazones. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4540. [PMID: 33247509 DOI: 10.1002/jms.4540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/02/2020] [Accepted: 04/30/2020] [Indexed: 06/12/2023]
Abstract
Twenty-one pentafluorphenylhydrazones have been analyzed by means of tandem mass spectrometry (ESI MS/MS) conditions to compare their fragmentations with those ones obtained from quantum-chemical calculations of the hydrazone moiety depending on the substitution from the aldehyde site. The hydrazone N-N bond is disrupted under such conditions, and these results are in accordance with the facts that an electron-rich particle, such as an anion and or radical in a solution, can cause this disruption and simultaneous defluorination in para-position of the hydrazone part of the molecule.
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Affiliation(s)
- Dušan Bortňák
- Department of Organic Chemistry, Slovak Technical University, Radlinského 9, Bratislava, SK-812 37, Slovakia
| | - Daniel Pecher
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, Bratislava, SK-832 32, Slovakia
| | - Daniel Végh
- Department of Organic Chemistry, Slovak Technical University, Radlinského 9, Bratislava, SK-812 37, Slovakia
| | - Martin Breza
- Department of Physical Chemistry, Faculty of Chemical and Food Technology, Slovak Technical University, Radlinského 9, Bratislava, SK-812 37, Slovakia
| | - Peter Mikuš
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, Bratislava, SK-832 32, Slovakia
| | - Viktor Milata
- Department of Organic Chemistry, Slovak Technical University, Radlinského 9, Bratislava, SK-812 37, Slovakia
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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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Razskazovskiy Y, Tegomoh M, Roginskaya M. Association with Polyamines and Polypeptides Increases the Relative Yield of 2-Deoxyribonolactone Lesions in Radiation-Damaged DNA. Radiat Res 2019; 192:324-330. [DOI: 10.1667/rr15396.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Modeste Tegomoh
- Departments of Chemistry, East Tennessee State University, Johnson City, Tennessee 37614
| | - Marina Roginskaya
- Departments of Chemistry, East Tennessee State University, Johnson City, Tennessee 37614
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Lee CL, Mowery YM, Daniel AR, Zhang D, Sibley AB, Delaney JR, Wisdom AJ, Qin X, Wang X, Caraballo I, Gresham J, Luo L, Van Mater D, Owzar K, Kirsch DG. Mutational landscape in genetically engineered, carcinogen-induced, and radiation-induced mouse sarcoma. JCI Insight 2019; 4:128698. [PMID: 31112524 DOI: 10.1172/jci.insight.128698] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cancer development is influenced by hereditary mutations, somatic mutations due to random errors in DNA replication, or external factors. It remains unclear how distinct cell-intrinsic and -extrinsic factors impact oncogenesis within the same tissue type. We investigated murine soft tissue sarcomas generated by oncogenic alterations (KrasG12D activation and p53 deletion), carcinogens (3-methylcholanthrene [MCA] or ionizing radiation), and in a novel model combining both factors (MCA plus p53 deletion). Whole-exome sequencing demonstrated distinct mutational signatures in individual sarcoma cohorts. MCA-induced sarcomas exhibited high mutational burden and predominantly G-to-T transversions, while radiation-induced sarcomas exhibited low mutational burden and a distinct genetic signature characterized by C-to-T transitions. The indel to substitution ratio and amount of gene copy number variations were high for radiation-induced sarcomas. MCA-induced tumors generated on a p53-deficient background showed the highest genomic instability. MCA-induced sarcomas harbored mutations in putative cancer-driver genes that regulate MAPK signaling (Kras and Nf1) and the Hippo pathway (Fat1 and Fat4). In contrast, radiation-induced sarcomas and KrasG12Dp53-/- sarcomas did not harbor recurrent oncogenic mutations, rather they exhibited amplifications of specific oncogenes: Kras and Myc in KrasG12Dp53-/- sarcomas, and Met and Yap1 for radiation-induced sarcomas. These results reveal that different initiating events drive oncogenesis through distinct mechanisms.
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5',8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance. Cells 2019; 8:cells8060513. [PMID: 31141888 PMCID: PMC6628319 DOI: 10.3390/cells8060513] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/18/2019] [Accepted: 05/22/2019] [Indexed: 12/14/2022] Open
Abstract
Purine 5′,8-cyclo-2′-deoxynucleosides (cPu) are tandem-type lesions observed among the DNA purine modifications and identified in mammalian cellular DNA in vivo. These lesions can be present in two diasteroisomeric forms, 5′R and 5′S, for each 2′-deoxyadenosine and 2′-deoxyguanosine moiety. They are generated exclusively by hydroxyl radical attack to 2′-deoxyribose units generating C5′ radicals, followed by cyclization with the C8 position of the purine base. This review describes the main recent achievements in the preparation of the cPu molecular library for analytical and DNA synthesis applications for the studies of the enzymatic recognition and repair mechanisms, their impact on transcription and genetic instability, quantitative determination of the levels of lesions in various types of cells and animal model systems, and relationships between the levels of lesions and human health, disease, and aging, as well as the defining of the detection limits and quantification protocols.
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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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16
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Grokhovsky SL. Use of β Radiation to Localize the Binding Sites of Mercury Ions and Platinum-Containing Ligand in DNA. Mol Biol 2018. [DOI: 10.1134/s0026893318050072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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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: 210] [Impact Index Per Article: 30.0] [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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18
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Xie J, Wang Y, Liu W, Yin X, Chen L, Zou Y, Diwu J, Chai Z, Albrecht-Schmitt TE, Liu G, Wang S. Highly Sensitive Detection of Ionizing Radiations by a Photoluminescent Uranyl Organic Framework. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700919] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jian Xie
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Yaxing Wang
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Wei Liu
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Xuemiao Yin
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Lanhua Chen
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Youming Zou
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Juan Diwu
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Zhifang Chai
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Thomas E. Albrecht-Schmitt
- Department of Chemistry and Biochemistry, F; lorida State University; 95 Chieftain Way Tallahassee FL 32306 USA
| | - Guokui Liu
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne IL 60439 USA
| | - Shuao Wang
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
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19
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Xie J, Wang Y, Liu W, Yin X, Chen L, Zou Y, Diwu J, Chai Z, Albrecht-Schmitt TE, Liu G, Wang S. Highly Sensitive Detection of Ionizing Radiations by a Photoluminescent Uranyl Organic Framework. Angew Chem Int Ed Engl 2017; 56:7500-7504. [DOI: 10.1002/anie.201700919] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/05/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Jian Xie
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Yaxing Wang
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Wei Liu
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Xuemiao Yin
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Lanhua Chen
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Youming Zou
- High Magnetic Field Laboratory; Chinese Academy of Sciences; Hefei Anhui 230031 China
| | - Juan Diwu
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Zhifang Chai
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
| | - Thomas E. Albrecht-Schmitt
- Department of Chemistry and Biochemistry, F; lorida State University; 95 Chieftain Way Tallahassee FL 32306 USA
| | - Guokui Liu
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne IL 60439 USA
| | - Shuao Wang
- School for Radiological and interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; 199 Ren'ai Road Suzhou 215123 China
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20
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Quiñones JL, Demple B. When DNA repair goes wrong: BER-generated DNA-protein crosslinks to oxidative lesions. DNA Repair (Amst) 2016; 44:103-109. [PMID: 27264558 PMCID: PMC6420214 DOI: 10.1016/j.dnarep.2016.05.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Free radicals generate an array of DNA lesions affecting all parts of the molecule. The damage to deoxyribose receives less attention than base damage, even though the former accounts for ∼20% of the total. Oxidative deoxyribose fragments (e.g., 3'-phosphoglycolate esters) are removed by the Ape1 AP endonuclease and other enzymes in mammalian cells to enable DNA repair synthesis. Oxidized abasic sites are initially incised by Ape1, thus recruiting these lesions into base excision repair (BER) pathways. Lesions such as 2-deoxypentos-4-ulose can be removed by conventional (single-nucleotide) BER, which proceeds through a covalent Schiff base intermediate with DNA polymerase β (Polβ) that is resolved by hydrolysis. In contrast, the lesion 2-deoxyribonolactone (dL) must be processed by multinucleotide ("long-patch") BER: attempted repair via the single-nucleotide pathway leads to a dead-end, covalent complex with Polβ cross- linked to the DNA by an amide bond. We recently detected these stable DNA-protein crosslinks (DPC) between Polβ and dL in intact cells. The features of the DPC formation in vivo are exactly in keeping with the mechanistic properties seen in vitro: Polβ-DPC are formed by oxidative agents in line with their ability to form the dL lesion; they are not formed by non-oxidative agents; DPC formation absolutely requires the active-site lysine-72 that attacks the 5'-deoxyribose; and DPC formation depends on Ape1 to incise the dL lesion first. The Polβ-DPC are rapidly processed in vivo, the signal disappearing with a half-life of 15-30min in both mouse and human cells. This removal is blocked by inhibiting the proteasome, which leads to the accumulation of ubiquitin associated with the Polβ-DPC. While other proteins (e.g., topoisomerases) also form DPC under these conditions, 60-70% of the trapped ubiquitin depends on Polβ. The mechanism of ubiquitin targeting to Polβ-DPC, the subsequent processing of the expected 5'-peptidyl-dL, and the biological consequences of unrepaired DPC are important to assess. Many other lyase enzymes that attack dL can also be trapped in DPC, so the processing mechanisms may apply quite broadly.
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Affiliation(s)
- Jason Luis Quiñones
- Stony Brook University School of Medicine, Department of Pharmacological Sciences, Stony Brook, NY, 11794, USA
| | - Bruce Demple
- Stony Brook University School of Medicine, Department of Pharmacological Sciences, Stony Brook, NY, 11794, USA.
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21
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Roginskaya M, Mohseni R, Ampadu-Boateng D, Razskazovskiy Y. DNA damage by the sulfate radical anion: hydrogen abstraction from the sugar moiety versus one-electron oxidation of guanine. Free Radic Res 2016; 50:756-66. [DOI: 10.3109/10715762.2016.1166488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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23
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Roginskaya M, Moore TJ, Ampadu-Boateng D, Razskazovskiy Y. Efficacy and site specificity of hydrogen abstraction from DNA 2-deoxyribose by carbonate radicals. Free Radic Res 2015; 49:1431-7. [PMID: 26271311 DOI: 10.3109/10715762.2015.1081187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The carbonate radical anion CO(3)(•-) is a potent reactive oxygen species (ROS) produced in vivo through enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO(2) with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO(3)(•-) is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO(3)(•-) with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO(3)(•-) on the sugar-phosphate backbone in vitro were analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4' > C1' > C5' for both CO(3)(•-) and the hydroxyl radical, though the relative contribution of the C1' damage induced by CO(3)(•-) is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1' by CO3(•-) prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO(3)(•-) primarily as a one-electron oxidant with fairly low reactivity toward the sugar-phosphate backbone.
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Affiliation(s)
- M Roginskaya
- a Department of Chemistry , East Tennessee State University , Johnson City , USA
| | - T J Moore
- a Department of Chemistry , East Tennessee State University , Johnson City , USA
| | - D Ampadu-Boateng
- a Department of Chemistry , East Tennessee State University , Johnson City , USA
| | - Y Razskazovskiy
- b Department of Physics and Astronomy , East Tennessee State University , Johnson City , USA
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24
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Lartia R, Constant JF. Synthetic access to the chemical diversity of DNA and RNA 5′-aldehyde lesions. J Org Chem 2015; 80:705-10. [PMID: 25372153 DOI: 10.1021/jo502170e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen atom abstraction from the C5′-position of nucleotides in DNA results in direct strand scission by generating alkali-labile fragments from the oxidized nucleotide. The major damage consists in a terminus containing a 5′-aldehyde as part of an otherwise undamaged nucleotide. Moreover it is considered as a polymorphic DNA strand break lesion since it can be borne by any of the four nucleosides encountered in DNA. Here we propose an expeditious synthesis of oligonucleotides (ON) ending with this 5′-aldehyde group (5′-AODN). This straightforward and cheap strategy relies on Pfitzner–Moffatt oxidation performed on solid support followed by a transient protection of the resulting aldehyde function. This method is irrespective of the 5′-terminal nucleobase and most interestingly can be directly extended to RNA to produce the corresponding 5′-AORN. We also report preliminary results on recognition of 5′-AODN by base excision repair (BER) enzymes.
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25
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Enzyme mechanism-based, oxidative DNA-protein cross-links formed with DNA polymerase β in vivo. Proc Natl Acad Sci U S A 2015; 112:8602-7. [PMID: 26124145 DOI: 10.1073/pnas.1501101112] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Free radical attack on the C1' position of DNA deoxyribose generates the oxidized abasic (AP) site 2-deoxyribonolactone (dL). Upon encountering dL, AP lyase enzymes such as DNA polymerase β (Polβ) form dead-end, covalent intermediates in vitro during attempted DNA repair. However, the conditions that lead to the in vivo formation of such DNA-protein cross-links (DPC), and their impact on cellular functions, have remained unknown. We adapted an immuno-slot blot approach to detect oxidative Polβ-DPC in vivo. Treatment of mammalian cells with genotoxic oxidants that generate dL in DNA led to the formation of Polβ-DPC in vivo. In a dose-dependent fashion, Polβ-DPC were detected in MDA-MB-231 human cells treated with the antitumor drug tirapazamine (TPZ; much more Polβ-DPC under 1% O2 than under 21% O2) and even more robustly with the "chemical nuclease" 1,10-copper-ortho-phenanthroline, Cu(OP)2. Mouse embryonic fibroblasts challenged with TPZ or Cu(OP)2 also incurred Polβ-DPC. Nonoxidative agents did not generate Polβ-DPC. The cross-linking in vivo was clearly a result of the base excision DNA repair pathway: oxidative Polβ-DPC depended on the Ape1 AP endonuclease, which generates the Polβ lyase substrate, and they required the essential lysine-72 in the Polβ lyase active site. Oxidative Polβ-DPC had an unexpectedly short half-life (∼ 30 min) in both human and mouse cells, and their removal was dependent on the proteasome. Proteasome inhibition under Cu(OP)2 treatment was significantly more cytotoxic to cells expressing wild-type Polβ than to cells with the lyase-defective form. That observation underscores the genotoxic potential of oxidative Polβ-DPC and the biological pressure to repair them.
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26
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Terzidis MA, Ferreri C, Chatgilialoglu C. Radiation-induced formation of purine lesions in single and double stranded DNA: revised quantification. Front Chem 2015; 3:18. [PMID: 25853120 PMCID: PMC4367438 DOI: 10.3389/fchem.2015.00018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 02/25/2015] [Indexed: 12/13/2022] Open
Abstract
The formation of oxidative lesions arising from double stranded DNA damage is of major significance to chemical biology from the perspective of application to human health. The quantification of purine lesions arising from γ-radiation-induced hydroxyl radicals (HO(•)) has been the subject of numerous studies, with discrepancies on the measured 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG) lesions reported by different groups. Here we applied an ameliorative protocol for the analysis of DNA damage with quantitative determination of these lesions via isotope dilution liquid chromatography coupled with tandem mass spectrometry. Tandem-type purine lesions were quantified along with 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG) and 7,8-dihydro-8-oxo-2'-deoxyadenosine (8-oxo-dA) in single and double stranded DNA, generated during DNA exposure to diffusible HO(•) radicals in the absence or presence of physiological levels of oxygen. The cdA and cdG lesions in absence of oxygen were found ~2 times higher in single than double stranded DNA, with 5'R being ~6.5 and ~1.5 times more predominant than 5'S in cdG and cdA, respectively. Interestingly, in the presence of 5% molecular oxygen the R/S ratios are retained with substantially decreased yields for cdA and cdG, whereas 8-oxo-dA and 8-oxo-dG remain nearly constant. The overall lesion formation follows the order: 8-oxo-dG >> 8-oxo-dA > 5'R-cdG > 5'R-cdA > 5'S-cdA > 5'S-cdG. By this method, there was a conclusive evaluation of radiation-induced DNA purine lesions.
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Affiliation(s)
- Michael A Terzidis
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche Bologna, Italy
| | - Carla Ferreri
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche Bologna, Italy ; Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research "Demokritos" Athens, Greece
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27
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Liu C, Zhang F, Munske G, Zhang H, Xian M. Isotope dilution mass spectrometry for the quantification of sulfane sulfurs. Free Radic Biol Med 2014; 76:200-7. [PMID: 25152234 PMCID: PMC4254298 DOI: 10.1016/j.freeradbiomed.2014.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/29/2014] [Accepted: 08/12/2014] [Indexed: 02/03/2023]
Abstract
Sulfane sulfurs are one type of important reactive sulfur species. These molecules have unique reactivity that allows them to attach reversibly to other sulfur atoms and exhibit regulatory effects in diverse biological systems. Recent studies have suggested that sulfane sulfurs are involved in signal transduction processes regulated by hydrogen sulfide (H2S). Accurate and reliable measurements of sulfane sulfurs in biological samples are thus needed to reveal their production and mechanisms of actions. Herein we report a convenient and accurate method for the determination of sulfane sulfur concentrations. The method employs a triphenylphosphine derivative (P2) to capture sulfane sulfurs as a stable phosphine sulfide product, PS2. The concentration of PS2 was then determined by isotope dilution mass spectrometry, using a (13)C3-labeled phosphine sulfide, PS1, as the internal standard. The specificity and efficiency of the method were proven by model reactions. It was also applied to the measurement of sulfane sulfurs in mouse tissues including brain, kidney, lung, liver, heart, spleen, and blood.
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Affiliation(s)
- Chunrong Liu
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; Research Institute of Science and Technology, Central China Normal University, Wuhan 430079, China
| | - Faya Zhang
- Department of Pharmaceutical Sciences, Washington State University, Pullman, WA 99164, USA
| | - Gerhard Munske
- Center for Reproductive Biology, Molecular Biology and Genomics Core, Washington State University, Pullman, WA 99164, USA
| | - Hui Zhang
- Department of Pharmaceutical Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA.
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28
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Liu J, Chan W. Quantification of Thiazolidine-4-carboxylic Acid in Toxicant-Exposed Cells by Isotope-Dilution Liquid Chromatography–Mass Spectrometry Reveals an Intrinsic Antagonistic Response to Oxidative Stress-Induced Toxicity. Chem Res Toxicol 2014; 28:394-400. [DOI: 10.1021/tx500342w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jingjing Liu
- Environmental Science Programs and ‡Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Wan Chan
- Environmental Science Programs and ‡Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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29
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Gavina JMA, Yao C, Feng YL. Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants. Talanta 2014; 130:475-94. [PMID: 25159438 DOI: 10.1016/j.talanta.2014.06.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 02/08/2023]
Abstract
DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.
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Affiliation(s)
- Jennilee M A Gavina
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Chunhe Yao
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9.
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30
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Bajacan JEV, Hong IS, Penning TM, Penning TW, Greenberg MM. Quantitative detection of 8-Oxo-7,8-dihydro-2'-deoxyguanosine using chemical tagging and qPCR. Chem Res Toxicol 2014; 27:1227-35. [PMID: 24932862 PMCID: PMC4106692 DOI: 10.1021/tx500120p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
8-Oxo-7,8-dihydro-2′-deoxyguanosine
(8-oxodGuo) is a commonly
formed DNA lesion that is useful as a biomarker for oxidative stress.
Although methods for selective quantification of 8-oxodGuo exist,
there is room for additional methods that are sensitive and utilize
instrumentation that is widely available. We previously took advantage
of the reported reactivity of 8-oxodGuo to develop a method for detecting
the lesion by selectively covalently tagging it with a molecule equipped
with a biotin label that can be used subsequently with a reporting
method (XueL., and GreenbergM. M. (2007) J. Am. Chem. Soc.129, 701017497789). We now report a method that can
detect as little as 14 amol of 8-oxodGuo by tagging DNA with a reagent
containing a disulfide that reduces background due to nonspecific
binding. The reagent also contains biotin that enables capturing target
DNA on streptavidin-coated magnetic beads. The captured DNA is quantified
using quantitative PCR. The method is validated by comparing the amount
of 8-oxodGuo detected as a function of Fe2+/H2O2/ascorbate-dose to that reported previously using mass
spectrometry.
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Affiliation(s)
- John Ernest Vallarta Bajacan
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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31
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Cadet J, Wagner JR. Oxidatively generated base damage to cellular DNA by hydroxyl radical and one-electron oxidants: similarities and differences. Arch Biochem Biophys 2014; 557:47-54. [PMID: 24820329 DOI: 10.1016/j.abb.2014.05.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 01/05/2023]
Abstract
Hydroxyl radical (OH) and one-electron oxidants that may be endogenously formed through oxidative metabolism, phagocytosis, inflammation and pathological conditions constitute the main sources of oxidatively generated damage to cellular DNA. It is worth mentioning that exposure of cells to exogenous physical agents (UV light, high intensity UV laser, ionizing radiation) and chemicals may also induce oxidatively generated damage to DNA. Emphasis is placed in this short review article on the mechanistic aspects of OH and one-electron oxidant-mediated formation of single and more complex damage (tandem lesions, intra- and interstrand cross-links, DNA-protein cross-links) in cellular DNA arising from one radical hit. This concerns DNA modifications that have been accurately measured using suitable analytical methods such as high performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Evidence is provided that OH and one-electron oxidants after generating neutral radicals and base radical cations respectively may partly induce common degradation pathways. In addition, selective oxidative reactions giving rise to specific degradation products of OH and one-electron oxidation reactions that can be used as representative biomarkers of these oxidants have been identified.
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Affiliation(s)
- Jean Cadet
- Institut Nanosciences et Cryogénie, CEA/Grenoble, F-38054 Grenoble Cedex 9, France; Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada.
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Tiwari AK, Kumar DA, Sweeya PS, Chauhan HA, Lavanya V, Sireesha K, Pavithra K, Zehra A. Vegetables' juice influences polyol pathway by multiple mechanisms in favour of reducing development of oxidative stress and resultant diabetic complications. Pharmacogn Mag 2014; 10:S383-91. [PMID: 24991118 PMCID: PMC4078340 DOI: 10.4103/0973-1296.133290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/14/2013] [Accepted: 05/28/2014] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Hyperglycemia induced generation of free radicals and consequent development of oxidative stress by polyol pathway is one of the crucial mechanisms stirring up development of diabetic complications. We evaluated influence of ten vegetables' juice on polyol pathway along with their antioxidant and antioxidative stress potentials. MATERIALS AND METHODS Aldose reductase activity was determined utilising goat lens and human erythrocytes. In goat lens, utilization of nicotinamine adenine dinucleotide phosphate (NADPH) and aldose reductase inhibition was assayed. In human erythrocytes, sorbitol formation was measured as an index of aldose reductase activity under normoglycemic and hyperglycemic conditions. Ability of juices in inhibiting oxidative damage to deoxyribose sugar and calf thymus DNA and inhibitory activity against hydrogen peroxide induced hemolysis of erythrocytes was also analysed. Phytochemical contents like total polyphenol, total flavonoid and total protein were measured to find their influence on biological activities. RESULTS Vegetables' juice displayed varying degrees of inhibitory potentials in mitigating NADPH dependent catalytic activity of aldose reductase in goat lens, accumulation of sorbitol in human erythrocytes under different glucose concentrations; Fenton-reaction induced oxidative damage to deoxyribose sugar, and calf thymus DNA. Substantial variations in vegetables phytochemicals content were also noticed in this study. CONCLUSIONS Vegetables' juice possesses potent activities in influencing polyol pathway by various mechanisms in favour of reducing development of oxidative stress independent of their inherent antioxidative properties. Juice of ivy gourd followed by green cucumber and ridge gourd were among the most potent for they displayed strong activities on various parameters analysed in this study. These vegetables' juice may become part of mechanism-based complementary antioxidant therapy to prevent development of diabetic complications.
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Affiliation(s)
- Ashok K. Tiwari
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - D. Anand Kumar
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - Pisupati S. Sweeya
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - H. Anusha Chauhan
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - V. Lavanya
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - K. Sireesha
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - K. Pavithra
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
| | - Amtul Zehra
- Medicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Andhra Pradesh, India
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Ming X, Matter B, Song M, Veliath E, Shanley R, Jones R, Tretyakova N. Mapping structurally defined guanine oxidation products along DNA duplexes: influence of local sequence context and endogenous cytosine methylation. J Am Chem Soc 2014; 136:4223-35. [PMID: 24571128 PMCID: PMC3985951 DOI: 10.1021/ja411636j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Indexed: 02/07/2023]
Abstract
DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2,4-triamino-2H-oxal-5-one (Z) and 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) in double stranded DNA. While both lesions are overproduced within endogenously methylated (Me)CG dinucleotides and at 5' Gs in runs of several guanines, the formation of Z (but not OG) is strongly preferred at solvent-exposed guanine nucleobases at duplex ends. Targeted oxidation of (Me)CG sequences may be caused by a lowered ionization potential of guanine bases paired with (Me)C and the preferential intercalation of riboflavin photosensitizer adjacent to (Me)C:G base pairs. Importantly, some of the most frequently oxidized positions coincide with the known p53 lung cancer mutational "hotspots" at codons 245 (GGC), 248 (CGG), and 158 (CGC) respectively, supporting a possible role of oxidative degradation of DNA in the initiation of lung cancer.
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Affiliation(s)
- Xun Ming
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brock Matter
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew Song
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elizabeth Veliath
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Ryan Shanley
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Roger Jones
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Cunniffe S, O'Neill P, Greenberg MM, Lomax ME. Reduced repair capacity of a DNA clustered damage site comprised of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 2-deoxyribonolactone results in an increased mutagenic potential of these lesions. Mutat Res 2014; 762:32-9. [PMID: 24631220 PMCID: PMC3990186 DOI: 10.1016/j.mrfmmm.2014.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/28/2014] [Accepted: 02/18/2014] [Indexed: 12/03/2022]
Abstract
A dL lesion is not repaired as effectively as an AP site. The repair of a cluster with dL and 8-oxodGuo lesions is compromised. Delayed repair of the cluster leads to an increase in mutation frequency.
A signature of ionizing radiation is the induction of DNA clustered damaged sites. Non-double strand break (DSB) clustered damage has been shown to compromise the base excision repair pathway, extending the lifetimes of the lesions within the cluster, compared to isolated lesions. This increases the likelihood the lesions persist to replication and thus increasing the mutagenic potential of the lesions within the cluster. Lesions formed by ionizing radiation include 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) and 2-deoxyribonolactone (dL). dL poses an additional challenge to the cell as it is not repaired by the short-patch base excision repair pathway. Here we show recalcitrant dL repair is reflected in mutations observed when DNA containing it and a proximal 8-oxodGuo is replicated in Escherichia coli. 8-oxodGuo in close proximity to dL on the opposing DNA strand results in an enhanced frequency of mutation of the lesions within the cluster and a 20 base sequence flanking the clustered damage site in an E. coli based plasmid assay. In vitro repair of a dL lesion is reduced when compared to the repair of an abasic (AP) site and a tetrahydrofuran (THF), and this is due mainly to a reduction in the activity of polymerase β, leading to retarded FEN1 and ligase 1 activities. This study has given insights in to the biological effects of clusters containing dL.
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Affiliation(s)
- Siobhan Cunniffe
- CRUK-MRC Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Peter O'Neill
- CRUK-MRC Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Marc M Greenberg
- Johns Hopkins University, Department of Chemistry, 3400 N. Charles St. , Baltimore, MD 21218, USA
| | - Martine E Lomax
- CRUK-MRC Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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Raposo M, Coelho M, Gomes PJ, Vieira P, Ribeiro PA, Mason NJ, Hunniford CA, McCullough RW. DNA damage induced by carbon ions (C³⁺) beam accessed by independent component analysis of infrared spectra. Int J Radiat Biol 2014; 90:344-50. [PMID: 24517474 DOI: 10.3109/09553002.2014.892650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To understand the degradation processes and role of secondary species on deoxyribonucleic acid (DNA)-damaged fragments as a result of irradiation with energetic ions. MATERIALS AND METHODS Damage caused to DNA thin films as a result of exposure to 4 keV carbon ions beam was accessed by analyzing the infrared spectra, obtained in situ for different irradiation times, with both bi-dimensional (2D) correlation spectroscopy and independent component analysis (ICA). RESULTS Results indicated that deoxyribose, phosphate and base groups of the DNA molecule were being damaged and new reaction products as oxime and furfural groups are being formed. CONCLUSIONS Damage on DNA bases is consistent with the formation of oxime products which react with DNA deoxyribose products forming furfural groups and confirming that DNA damage is caused by direct and indirect processes.
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Affiliation(s)
- Maria Raposo
- CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa , Caparica , Portugal
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Roginskaya M, Mohseni R, Moore TJ, Bernhard WA, Razskazovskiy Y. Identification of the C4′-Oxidized Abasic Site as the Most Abundant 2-Deoxyribose Lesion in Radiation-Damaged DNA Using a Novel HPLC-Based Approach. Radiat Res 2014; 181:131-7. [DOI: 10.1667/rr12993.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Marina Roginskaya
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee
| | - Reza Mohseni
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee
| | - Terence J. Moore
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee
| | - William A. Bernhard
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Yuriy Razskazovskiy
- Department of Physics and Astronomy, East Tennessee State University, Johnson City, Tennessee
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37
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Judah L, Marin R, Stroup D, Wesdemiotis C, Bose RN. DNA damage by oxo- and peroxo-chromium(v) complexes: insight into the mutation and carcinogenesis mechanisms. Toxicol Res (Camb) 2014. [DOI: 10.1039/c3tx50061f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Malyarchuk S, Castore R, Shi R, Harrison L. Artemis is required to improve the accuracy of repair of double-strand breaks with 5'-blocked termini generated from non-DSB-clustered lesions. Mutagenesis 2013; 28:357-66. [PMID: 23448902 DOI: 10.1093/mutage/get009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clustered DNA lesions are defined as ≥2 damage events within 20 bp. Oxidised bases, abasic (AP) sites, single-strand breaks and double-strand breaks (DSBs) exist in radiation-induced clusters, and these lesions are more difficult to repair and can be more mutagenic than single lesions. Understanding clustered lesion repair is therefore important for the design of complementary treatments to enhance radiotherapy. Non-DSB-clustered lesions consisting of opposing AP sites can be converted to DSBs by base excision repair, and non-homologous end-joining (NHEJ) plays a role in repairing these DSBs. Artemis is an endonuclease that removes blocking groups from DSB termini during NHEJ. Hence, we hypothesised that Artemis plays a role in the processing of DSBs or complex DSBs generated from non-DSB-clustered lesions. We examined the repair of clusters containing two or three lesions in wild-type (WT) or Artemis-deficient (ART(-/-)) mouse fibroblasts using a reporter plasmid. Each cluster contained two opposing tetrahydrofurans (an AP site analogue), which AP endonuclease can convert to a DSB with blocked 5' termini. Loss of Artemis did not decrease plasmid survival, but did result in more mutagenic repair with plasmids containing larger deletions. This increase in deletions did not occur with ClaI-linearised plasmid. Since Mre11 has been implicated in deletional NHEJ, we used small interfering RNA to reduce Mre11 in WT and ART(-/-) cells, but decreasing Mre11 did not change the size of deletions in the repair products. This work implicates Artemis in limiting the deletions introduced during repair of 5'-blocked termini DSBs generated from non-DSB-clustered lesions. Decreasing repair accuracy without decreasing repair capacity could result in mutated cells surviving irradiation. Inhibiting Artemis in normal cells could promote carcinogenesis, while in tumour cells enhanced mutagenic repair following irradiation could promote tumour recurrence.
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Affiliation(s)
- Svitlana Malyarchuk
- Department of Molecular and Cellular Physiology, Louisiana Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA
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39
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Li J, Leung EMK, Choi MMF, Chan W. Combination of pentafluorophenylhydrazine derivatization and isotope dilution LC-MS/MS techniques for the quantification of apurinic/apyrimidinic sites in cellular DNA. Anal Bioanal Chem 2013; 405:4059-66. [PMID: 23423125 DOI: 10.1007/s00216-013-6823-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 01/09/2023]
Abstract
Apurinic/apyrimidinic (AP) sites are common DNA lesions arising from spontaneous hydrolysis of the N-glycosidic bond and base-excision repair mechanisms of the modified bases. Due to the strong association of AP site formation with physically/chemically induced DNA damage, quantifying AP sites provides important information for risk assessment of exposure to genotoxins and oxidative stress. However, rigorous quantification of AP sites in DNA has been hampered by technical problems relating to the sensitivity and selectivity of existing analytical methods. We have developed a new isotope dilution liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) method for the rigorous quantification of AP sites in genomic DNA. The method entails enzymatic digestion of AP site-containing DNA by endo- and exonucleases, derivatization with pentafluorophenylhydrazine (PFPH), addition of an isotopically labeled PFPH derivative as internal standard, and quantification by LC-MS/MS. The combination of PFPH derivatization with LC-MS/MS analysis on a triple quadrupole mass spectrometer allows for sensitive and selective quantification of AP sites in DNA at a detection limit of 6.5 fmol, corresponding to 4 AP sites/10(9) nt in 5 μg of DNA, which is at least ten times more sensitive than existing analytical methods. The protocol was validated by AP site-containing oligonucleotides and applied in quantifying methyl methanesulfonate-induced formation of AP sites in cellular DNA.
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Affiliation(s)
- Jie Li
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, SAR, China
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40
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Abstract
The carcinogenicity of cadmium, arsenic, and chromium(VI) compounds has been recognized for some decades. However, the underlying molecular mechanisms seem to be complex and are not completely understood at present. Although, with the exception of chromium(VI), direct DNA damage seems to be of minor importance, interactions with DNA repair processes, tumor suppressor functions, and signal transduction pathways have been described in diverse biological systems. In addition to the induction of damage to cellular macromolecules by reactive oxygen species, the interference with cellular redox regulation by reaction with redox-sensitive protein domains or amino acids may provide one plausible mechanism involved in metal carcinogenicity. Consequences are the distortion of zinc-binding structures and the activation or inactivation of redox-regulated signal transduction pathways, provoking metal-induced genomic instability. Nevertheless, the relevance of the respective mechanisms depends on the actual metal or metal species under consideration and more research is needed to further strengthen this hypothesis.
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Affiliation(s)
- Andrea Hartwig
- Institute of Applied Biosciences, Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.
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41
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Madugundu GS, Park Y, Sanche L, Wagner JR. Radiation-induced formation of 2',3'-dideoxyribonucleosides in DNA: a potential signature of low-energy electrons. J Am Chem Soc 2012; 134:17366-8. [PMID: 23057636 DOI: 10.1021/ja306810w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have identified a series of modifications of the 2'-deoxyribose moiety of DNA arising from the exposure of isolated and cellular DNA to ionizing radiation. The modifications consist of 2',3'-dideoxyribonucleoside derivatives of T, C, A, and G, as identified by enzymatic digestion and LC-MS/MS. Under dry conditions, the yield of these products was 6- to 44-fold lower than the yield of 8-oxo-7,8-dihydroguanine. We propose that 2',3'-dideoxyribonucleosides are generated from the reaction of low-energy electrons with DNA, leading to cleavage of the C3'-O bond and formation of the corresponding C3'-deoxyribose radical.
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Affiliation(s)
- Guru S Madugundu
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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Adhikary A, Becker D, Palmer BJ, Heizer AN, Sevilla MD. Direct formation of the C5'-radical in the sugar-phosphate backbone of DNA by high-energy radiation. J Phys Chem B 2012; 116:5900-6. [PMID: 22553971 DOI: 10.1021/jp3023919] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA strand scission and cross-linking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5' (C5'(•)) is one of the most abundant (ca. 30%) sugar radicals formed by γ- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of γ-irradiated dimethyl phosphate were carried out. CH(3)OP(O(2)(-))OCH(2)(•) is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. The formation of CH(3)OP(O(2)(-))OCH(2)(•) is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5'(•) found in DNA and of CH(3)OP(O(2)(-))OCH(2)(•) do not show an observable β-phosphorus hyperfine coupling (HFC). Furthermore, C5'(•) found in DNA does not show a significant C4'-H β-proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorus HFC in CH(3)OP(O(2)(-))OCH(2)(•) shows that in its minimum energy conformation, CH(3)OP(O(2)(-))OCH(2)(•), has a negligible β-phosphorus HFC. On the basis of these results, the formation of radiation-induced C5'(•) is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone, and the rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5'(•) in irradiated DNA is found to be in a conformation that does not exhibit β-proton or β-phosphorus HFCs.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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Cadet J, Douki T, Ravanat JL, Wagner JR. Measurement of oxidatively generated base damage to nucleic acids in cells: facts and artifacts. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12566-012-0029-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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44
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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45
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Solivio MJ, Nemera DB, Sallans L, Merino EJ. Biologically relevant oxidants cause bound proteins to readily oxidatively cross-link at Guanine. Chem Res Toxicol 2012; 25:326-36. [PMID: 22216745 DOI: 10.1021/tx200376e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidative DNA-protein cross-links have received less attention than other types of DNA damage and remain as one of the least understood types of oxidative lesion. A model system using ribonuclease A and a 27-nucleotide DNA was used to determine the propensity of oxidative cross-linking to occur in the presence of oxidants. Cross-link formation was examined using four different oxidation systems that generate singlet oxygen, superoxide, and metal-based Fenton reactions. It is shown that oxidative cross-linking occurs in yields ranging from 14% to a maximal yield of 61% in all oxidative systems when equivalent concentrations of DNA and protein are present. Because singlet oxygen is the most efficient oxidation system in generating DNA-protein cross-links, it was chosen for further analyses. Cross-linking occurred with single-stranded DNA binding protein and not with bovine serum albumin. Addition of salt lowered nonspecific binding affinity and lowered cross-link yield by up to 59%. The yield of cross-linking increased with increased ratios of protein compared with DNA. Cross-linking was highly dependent on the number of guanines in a DNA sequence. Loss of guanine content on the 27-nucleotide DNA led to nearly complete loss in cross-linking, while primer extension studies showed cross-links to predominantly occur at guanine base on a 100-nucleotide DNA. The chemical species generated were examined using two peptides derived from the ribonuclease A sequence, N-acetyl-AAAKF and N-acetyl-AYKTT, which were cross-linked to 2'-deoxyguanosine. The cross-link products were spiroiminodihydantoin, guanidinohydantoin, and tyrosyl-based adducts. Formation of tyrosine-based adducts may be competitive with the more well-studied lysine-based cross-links. We conclude that oxidative cross-links may be present at high levels in cells since the propensity to oxidatively cross-link is high and so much of the genomic DNA is coated with protein.
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Affiliation(s)
- Morwena J Solivio
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
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Konigsfeld KM, Lee M, Urata SM, Aguilera JA, Milligan JR. Free terminal amines in DNA-binding peptides alter the product distribution from guanine radicals produced by single electron oxidation. Int J Radiat Biol 2011; 88:230-8. [PMID: 22124251 DOI: 10.3109/09553002.2012.643853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE Electron deficient guanine radical species are major intermediates produced in DNA by the direct effect of ionizing irradiation. There is evidence that they react with amine groups in closely bound ligands to form covalent crosslinks. Crosslink formation is very poorly characterized in terms of quantitative rate and yield data. We sought to address this issue by using oligo-arginine ligands to model the close association of DNA and its binding proteins in chromatin. MATERIALS AND METHODS Guanine radicals were prepared in plasmid DNA by single electron oxidation. The product distribution derived from them was assayed by strand break formation after four different post-irradiation incubations. RESULTS We compared the yields of DNA damage produced in the presence of four ligands in which neither, one, or both of the amino and carboxylate termini were blocked with amides. Free carboxylate groups were unreactive. Significantly higher yields of heat labile sites were observed when the amino terminus was unblocked. The rate of the reaction was characterized by diluting the unblocked amino group with its amide blocked derivative. CONCLUSION These observations provide a means to develop quantitative estimates for the yields in which these labile sites are formed in chromatin by exposure to ionizing irradiation.
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Affiliation(s)
- Katie M Konigsfeld
- Department of Radiology, University of California at San Diego, La Jolla, California 92093-0610, USA
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47
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Chatgilialoglu C, D’Angelantonio M, Kciuk G, Bobrowski K. New Insights into the Reaction Paths of Hydroxyl Radicals with 2′-Deoxyguanosine. Chem Res Toxicol 2011; 24:2200-6. [DOI: 10.1021/tx2003245] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Mila D’Angelantonio
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Gabriel Kciuk
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Krzysztof Bobrowski
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
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Ma J, Ma W, Chen C, Ji H, Zhao J. An Efficient Anthraquinone-Resin Hybrid Co-Catalyst for Fenton-Like Reactions: Acceleration of the Iron Cycle Using a Quinone Cycle under Visible-Light Irradiation. Chem Asian J 2011; 6:2264-8. [DOI: 10.1002/asia.201100347] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Indexed: 11/08/2022]
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49
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Kryston TB, Georgiev AB, Pissis P, Georgakilas AG. Role of oxidative stress and DNA damage in human carcinogenesis. Mutat Res 2011; 711:193-201. [DOI: 10.1016/j.mrfmmm.2010.12.016] [Citation(s) in RCA: 644] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/22/2010] [Accepted: 12/31/2010] [Indexed: 04/08/2023]
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