1
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Wang Y, Wei S. Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H +)GC motif. Phys Chem Chem Phys 2024; 26:5683-5692. [PMID: 38288746 DOI: 10.1039/d3cp05885a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
A comprehensive theoretical investigation was performed to illuminate the influence of hydrogen bonds (H-bonds) on the obscure reaction of a hydroxyl radical (HO˙) and guanine (G) by selecting the building block of parallel triplex DNA, C(H+)GC, as the model. By mapping the energy profiles for addition and hydrogen abstraction reactions, the favorable pathway is predicted. The results reveal that in the C(H+)GC context, barrierless hydrogen abstraction from N2 of G leading to a neutral radical G(N2-H)˙ appears to become significant, but electrophilic attack by HO˙ on C8 of G resulting in 8-oxoG is the most thermodynamically favorable course. This shows a strong structural dependence due to the context constrained by the H-bond, which is dramatically different from the situation in unencumbered G. More interestingly, it proves that the stability order of resulting adduct radicals is not altered by H-bonding, but the activity for possible sites of the hydroxylation reaction changes. The significant influence of the H-bond on elementary reactions involved in the reaction is emphasized in the C(H+)GC context but is not restricted to the H-abstraction reaction. It is greatly anticipated that the present study could provide thoughtful insights into the vague hydroxyl radical-induced oxidation chemistry.
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Affiliation(s)
- Yinghui Wang
- College of Science, Chang'an University, Xi'an 710064, China.
| | - Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang 712083, China.
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2
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Moscatello C, Di Marcantonio MC, Savino L, D’Amico E, Spacco G, Simeone P, Lanuti P, Muraro R, Mincione G, Cotellese R, Aceto GM. Emerging Role of Oxidative Stress on EGFR and OGG1-BER Cross-Regulation: Implications in Thyroid Physiopathology. Cells 2022; 11:cells11050822. [PMID: 35269445 PMCID: PMC8909339 DOI: 10.3390/cells11050822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/12/2022] Open
Abstract
Thyroid diseases have a complex and multifactorial aetiology. Despite the numerous studies on the signals referable to the malignant transition, the molecular mechanisms concerning the role of oxidative stress remain elusive. Based on its strong oxidative power, H2O2 could be responsible for the high level of oxidative DNA damage observed in cancerous thyroid tissue and hyperactivation of mitogen-activated protein kinase (MAPK) and PI3K/Akt, which mediate ErbB signaling. Increased levels of 8-oxoG DNA adducts have been detected in the early stages of thyroid cancer. These DNA lesions are efficiently recognized and removed by the base excision repair (BER) pathway initiated by 8-oxoG glycosylase1 (OGG1). This study investigated the relationships between the EGFR and OGG1-BER pathways and their mutual regulation following oxidative stress stimulus by H2O2 in human thyrocytes. We clarified the modulation of ErbB receptors and their downstream pathways (PI3K/Akt and MAPK/ERK) under oxidative stress (from H2O2) at the level of gene and protein expression, according to the mechanism defined in a human non-pathological cell system, Nthy-ori 3-1. Later, on the basis of the results obtained by gene expression cluster analysis in normal cells, we assessed the dysregulation of the relationships in a model of papillary thyroid cancer with RET/PTC rearrangement (TPC-1). Our observations demonstrated that a H2O2 stress may induce a physiological cross-regulation between ErbB and OGG1-BER pathways in normal thyroid cells (while this is dysregulated in the TPC-1 cells). Gene expression data also delineated that MUTYH gene could play a physiological role in crosstalk between ErbB and BER pathways and this function is instead lost in cancer cells. Overall, our data on OGG1 protein expression suggest that it was physiologically regulated in response to oxidative modulation of ErbB, and that these might be dysregulated in the signaling pathway involving AKT in the progression of thyroid malignancies with RET/PTC rearrangements.
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Affiliation(s)
- Carmelo Moscatello
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (C.M.); (E.D.); (G.S.); (R.C.)
| | - Maria Carmela Di Marcantonio
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio”, Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (M.C.D.M.); (L.S.); (R.M.); (G.M.)
| | - Luca Savino
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio”, Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (M.C.D.M.); (L.S.); (R.M.); (G.M.)
| | - Emira D’Amico
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (C.M.); (E.D.); (G.S.); (R.C.)
| | - Giordano Spacco
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (C.M.); (E.D.); (G.S.); (R.C.)
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (P.S.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.) at University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (P.S.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.) at University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy
| | - Raffaella Muraro
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio”, Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (M.C.D.M.); (L.S.); (R.M.); (G.M.)
| | - Gabriella Mincione
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio”, Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (M.C.D.M.); (L.S.); (R.M.); (G.M.)
| | - Roberto Cotellese
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (C.M.); (E.D.); (G.S.); (R.C.)
- Villa Serena Foundation for Research, 66013 Pescara, Italy
| | - Gitana Maria Aceto
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; (C.M.); (E.D.); (G.S.); (R.C.)
- Correspondence: ; Tel.: +39-0871-355-4115
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3
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Chen HY, Lin YF. DFT mechanistic study on the formation of 8-oxoguanine and spiroiminodihydantoin mediated by iron Fenton reactions. Dalton Trans 2021; 50:9842-9850. [PMID: 34190261 DOI: 10.1039/d1dt01508g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fenton reactions unavoidably take place in the human body and have been demonstrated to cause oxidative DNA damage. However, the molecular-level understanding of DNA damage mediated by Fenton reactions is limited. Herein, density functional theory (DFT) calculations were made to investigate the counterion effects on aqueous Fenton reactions and the detailed mechanisms of chemical modifications to guanine induced by Fenton reactions. Our calculations show that the activation energy of the Fenton reaction catalyzed by a pure aquo complex [FeII(H2O)6]2+ is too high to agree with experiments, whereas complexation with counteranions reduces the activation energy to a reasonable range. This result suggests that FeII-counteranion complexes are the real catalyst for fast aqueous Fenton reactions. In addition, we found that the Fenton oxidation mediated by FeII bonded to the N7 atom of guanine can result in the formation of 8-oxoguanine and spiroiminodihydantoin through multiple reaction pathways, including the electrophilic addition of ˙OH, H-abstraction by ˙OH, and oxygen atom transfer of oxoiron(iv) species. The activation of hydrogen peroxide by ferrous iron is the rate-determining step. The guanine N7-bound iron ion and the coordinated counteranion were found to play an important role in the Fenton oxidation of guanine.
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Affiliation(s)
- Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
| | - Yu-Fen Lin
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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4
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Moe MM, Tsai M, Liu J. Singlet Oxygen Oxidation of the Radical Cations of 8-Oxo-2'-deoxyguanosine and Its 9-Methyl Analogue: Dynamics, Potential Energy Surface, and Products Mediated by C5-O 2 -Addition. Chempluschem 2021; 86:1243-1254. [PMID: 34268890 DOI: 10.1002/cplu.202100238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Indexed: 01/24/2023]
Abstract
8-Oxo-2'-deoxyguanosine (OG) is the most common DNA lesion. Notably, OG becomes more susceptible to oxidative damage than the undamaged nucleoside, forming mutagenic products in vivo. Herein the reactions of singlet O2 with the radical cations of 8-oxo-2'-deoxyguanosine (OG.+ ) and 9-methyl-8-oxoguanine (9MOG.+ ) were investigated using ion-molecule scattering mass spectrometry, from which barrierless, exothermic O2 -addition products were detected for both reaction systems. Corroborated by static reaction potential energy surface constructed using multi-reference CASPT2 theory and molecular dynamics simulated in the presence of the reactants' kinetic and internal energies, the C5-terminal O2 -addition was pinpointed as the most probable reaction pathway. By elucidating the reaction mechanism, kinetics and dynamics, and reaction products and energetics, this work constitutes the first report unraveling the synergetic damage of OG by ionizing radiation and singlet O2 .
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY, 11101, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
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5
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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6
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Tolosa S, Sansón J, Hidalgo A. A procedure to understanding the C-G to A-T transversion. SMD simulations from guanine oxidation pathways assisted by one H2O2 molecule in the C-G basis pair. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Giorgio M, Dellino GI, Gambino V, Roda N, Pelicci PG. On the epigenetic role of guanosine oxidation. Redox Biol 2020; 29:101398. [PMID: 31926624 PMCID: PMC6926346 DOI: 10.1016/j.redox.2019.101398] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 01/14/2023] Open
Abstract
Chemical modifications of DNA and RNA regulate genome functions or trigger mutagenesis resulting in aging or cancer. Oxidations of macromolecules, including DNA, are common reactions in biological systems and often part of regulatory circuits rather than accidental events. DNA alterations are particularly relevant since the unique role of nuclear and mitochondrial genome is coding enduring and inheritable information. Therefore, an alteration in DNA may represent a relevant problem given its transmission to daughter cells. At the same time, the regulation of gene expression allows cells to continuously adapt to the environmental changes that occur throughout the life of the organism to ultimately maintain cellular homeostasis. Here we review the multiple ways that lead to DNA oxidation and the regulation of mechanisms activated by cells to repair this damage. Moreover, we present the recent evidence suggesting that DNA damage caused by physiological metabolism acts as epigenetic signal for regulation of gene expression. In particular, the predisposition of guanine to oxidation might reflect an adaptation to improve the genome plasticity to redox changes.
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Affiliation(s)
- Marco Giorgio
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Valentina Gambino
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Niccolo' Roda
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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8
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Reaction of HSSS. radical with guanine and formation of 8-thioguanine: a computational study. Struct Chem 2019. [DOI: 10.1007/s11224-019-01465-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Behera B, Das P, Jena NR. Accurate Base Pair Energies of Artificially Expanded Genetic Information Systems (AEGIS): Clues for Their Mutagenic Characteristics. J Phys Chem B 2019; 123:6728-6739. [PMID: 31290661 DOI: 10.1021/acs.jpcb.9b04653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, several artificial nucleobases, such as B, S, J, V, X, K, P, and Z, have been proposed to help in the expansion of the genetic information system and diagnosis of diseases. Among these bases, P and Z were identified to form stable DNA and to participate in the replication. However, the stabilities of P:Z and other artificial base pairs are not fully understood. The abilities of these unnatural nucleobases in mispairing with themselves and with natural bases are also not known. Here, the ωB97X-D dispersion-corrected density functional theoretical and complete basis set (CBS-QB3) methods are used to obtain accurate structural and energetic data related to base pair interactions involving these unnatural nucleobases. The roles of protonation and deprotonation of certain artificial bases in inducing mutations are also studied. It is found that each artificial purine has a complementary artificial pyrimidine, the base pair interactions between which are similar to those of the natural Watson-Crick base pairs. Hence, these base pairs will function naturally and would not impart mutagenicity. Among these base pairs, the J:V complex is found to be the most stable and promising artificial base pair. Remarkably, the noncomplementary artificial nucleobases are found to form stable mispairs, which may generate mutagenic products in DNA. Similarly, the misinsertions of natural bases opposite artificial bases are also found to be mutagenic. The mechanisms of these mutations are explained in detail. These results are in agreement with earlier biochemical studies. It is thus expected that this study would aid in the advancement of the synthetic biology to design more robust artificial nucleotides.
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Affiliation(s)
- B Behera
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
| | - P Das
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
| | - N R Jena
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
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10
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Jena NR. Manganese‐Coordinated Tyrosine Bio Materials for the Sensing of Reactive Oxygen Species. ChemistrySelect 2019. [DOI: 10.1002/slct.201900966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nihar Ranjan Jena
- Discipline of Natural SciencesIndian Institute of Information Technology, Design and Manufacturing, Khamaria Jabalpur- 482005 India
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11
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Thapa B, Hebert SP, Munk BH, Burrows CJ, Schlegel HB. Computational Study of the Formation of C8, C5, and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical Anion. J Phys Chem A 2019; 123:5150-5163. [DOI: 10.1021/acs.jpca.9b03598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Sebastien P. Hebert
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara H. Munk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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12
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An P, Wang Y, Li S, Zhou L. Repair of Oxidizing Hydroxyl Adduct Radicals of DNA Bases by Hydroxyl‐
trans
‐Stilbenes via Single Electron Transfer. ChemistrySelect 2019. [DOI: 10.1002/slct.201803802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ping An
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 P.R.China
| | - Yuyue Wang
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 P.R.China
| | - Shujin Li
- College of ChemistryChemical Engineering and Materials ScienceSoochow University Suzhou 215123 P.R.China
| | - Liping Zhou
- College of PhysicsOptoelectronics and EnergySoochow University Suzhou 215006 P.R.China
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13
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Hebert SP, Schlegel HB. Computational Study of the pH-Dependent Competition between Carbonate and Thymine Addition to the Guanine Radical. Chem Res Toxicol 2019; 32:195-210. [PMID: 30592213 DOI: 10.1021/acs.chemrestox.8b00302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
When oligonucleotides are oxidized by carbonate radical, thymine and carbonate can add to guanine radical, yielding either a guanine-thymine cross-link product (G∧T) or 8-oxo-7,8-dehydroguanine (8oxoG) and its further oxidation products such as spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). The ratio of thymine addition to carbonate addition depends strongly on the pH. Details of the mechanism have been explored by density functional calculations using the ωB97XD/6-31+G(d,p) level of theory with the SMD implicit solvation method, augmented with a few explicit waters. Free energies of intermediates and transition states in aqueous solution have been calculated along the pathways for addition of thymine, CO32-/HCO3- and carbonate radical to guanine radical. The pH dependence was examined by using appropriate explicit proton donors/acceptors as computational models for buffers at pH 2.5, 7, and 10. Deprotonation of thymine is required for nucleophilic addition at C8 of guanine radical, and thus is favored at higher pH. The barrier for carbonate radical addition is lower than for bicarbonate or carbonate dianion addition; however, for low concentrations of carbonate radical, the reaction may proceed by addition of bicarbonate/carbonate dianion to guanine radical. Thymine and bicarbonate/carbonate dianion addition are followed by oxidation by O2, loss of a proton from C8 and decarboxylation of the carbonate adduct. At pH 2.5, guanine radical cation can be formed by oxidization with sulfate radical. Water addition to guanine radical cation is the preferred path for forming 8oxoG at pH 2.5.
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Affiliation(s)
- Sebastien P Hebert
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
| | - H Bernhard Schlegel
- Department of Chemistry , Wayne State University , Detroit , Michigan 48202 , United States
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14
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Peroxisomes and cancer: The role of a metabolic specialist in a disease of aberrant metabolism. Biochim Biophys Acta Rev Cancer 2018; 1870:103-121. [PMID: 30012421 DOI: 10.1016/j.bbcan.2018.07.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 01/02/2023]
Abstract
Cancer is irrevocably linked to aberrant metabolic processes. While once considered a vestigial organelle, we now know that peroxisomes play a central role in the metabolism of reactive oxygen species, bile acids, ether phospholipids (e.g. plasmalogens), very-long chain, and branched-chain fatty acids. Immune system evasion is a hallmark of cancer, and peroxisomes have an emerging role in the regulation of cellular immune responses. Investigations of individual peroxisome proteins and metabolites support their pro-tumorigenic functions. However, a significant knowledge gap remains regarding how individual functions of proteins and metabolites of the peroxisome orchestrate its potential role as a pro-tumorigenic organelle. This review highlights new advances in our understanding of biogenesis, enzymatic functions, and autophagic degradation of peroxisomes (pexophagy), and provides evidence linking these activities to tumorigenesis. Finally, we propose avenues that may be exploited to target peroxisome-related processes as a mode of combatting cancer.
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15
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Mechanisms of scavenging superoxide, hydroxyl, nitrogen dioxide and methoxy radicals by allicin: catalytic role of superoxide dismutase in scavenging superoxide radical. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1509-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Jena NR, Patel C, Sahoo SC, Mishra PC. Cysteine‐metal Porous Frameworks as Biosensing Elements for the Adsorption of Reactive Oxygen Species. ChemistrySelect 2018. [DOI: 10.1002/slct.201800537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- N. R. Jena
- Discipline of Natural SciencesIndian Institute of Information Technology, Design and Manufacturing, Khamaria Jabalpur-482005 India
| | - C. Patel
- Discipline of Natural SciencesIndian Institute of Information Technology, Design and Manufacturing, Khamaria Jabalpur-482005 India
| | - Subash Ch. Sahoo
- Department of ChemistryPanjab University Chandigarh-160014 India
| | - P. C. Mishra
- Department of PhysicsBanaras Hindu University Varanasi-221005 India
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17
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A theoretical characterization of reactions of HOOO radical with guanine: formation of 8-oxoguanine. Struct Chem 2018. [DOI: 10.1007/s11224-018-1095-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Bhattacharjee K, Shukla PK. Does 8-Nitroguanine Form 8-Oxoguanine? An Insight from Its Reaction with •OH Radical. J Phys Chem B 2018; 122:1852-1861. [PMID: 29360382 DOI: 10.1021/acs.jpcb.7b12192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
8-Nitroguanine (8-nitroG) formed due to nitration of guanine base of DNA plays an important role in mutagenesis and carcinogenesis. In the present contribution, state-of-the-art quantum chemical calculations using M06-2X density functional and domain-based local pair natural orbital-coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) methods have been carried out to investigate the mechanism of reaction of •OH radical with 8-nitroG leading to the formation of 8-oxoguanine (8-oxoG) (one of the most mutagenic and carcinogenic derivatives of guanine) in gas phase and aqueous media. Calculations of barrier energies and rate constants involved in the addition reactions of •OH radical at different sites of 8-nitroguanine show that C8 and C2 sites are the most and least reactive sites, respectively. Relative stability and Boltzmann populations of adducts show that the adduct formed at the C8 site occurs predominantly in equilibrium. Our calculations reveal that 8-nitroG is very reactive toward •OH radical and is converted readily into 8-oxoG when attacked by •OH radicals, in agreement with available experimental observations.
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Affiliation(s)
| | - P K Shukla
- Department of Physics, Assam University , Silchar 788011, India
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Liu P, Wang Q, Niu M, Wang D. Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution. Sci Rep 2017; 7:7798. [PMID: 28798372 PMCID: PMC5552687 DOI: 10.1038/s41598-017-08219-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.
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Affiliation(s)
- Peng Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qiong Wang
- College of Chemistry, Shandong Normal University, Jinan, 250014, China
| | - Meixing Niu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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Smyk B, Mędza G, Kasparek A, Pyrka M, Gryczynski I, Maciejczyk M. Spectroscopic Properties and Conformational Analysis of Methyl Ester of Sinapic Acid in Various Environments. J Phys Chem B 2017; 121:7299-7310. [DOI: 10.1021/acs.jpcb.7b05508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- B. Smyk
- Department
of Physics and Biophysics, University of Warmia and Mazury, Oczapowskiego
4, 10-719 Olsztyn, Poland
| | - G. Mędza
- Department
of Physics and Biophysics, University of Warmia and Mazury, Oczapowskiego
4, 10-719 Olsztyn, Poland
| | - A. Kasparek
- Department
of Physics and Biophysics, University of Warmia and Mazury, Oczapowskiego
4, 10-719 Olsztyn, Poland
| | - M. Pyrka
- Department
of Physics and Biophysics, University of Warmia and Mazury, Oczapowskiego
4, 10-719 Olsztyn, Poland
| | - I. Gryczynski
- Department
of Cell Biology and Immunology, Center for Fluorescence Technologies
and Nanomedicine, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - M. Maciejczyk
- Department
of Physics and Biophysics, University of Warmia and Mazury, Oczapowskiego
4, 10-719 Olsztyn, Poland
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21
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Theoretical study of the reaction of chitosan monomer with 2,3-epoxypropyl-trimethyl quaternary ammonium chloride catalyzed by an imidazolium-based ionic liquid. Carbohydr Polym 2016; 146:46-51. [DOI: 10.1016/j.carbpol.2016.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/28/2016] [Accepted: 03/15/2016] [Indexed: 11/23/2022]
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22
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TIWARI MANISHK, MISHRA PC. Anti-oxidant activity of 6-gingerol as a hydroxyl radical scavenger by hydrogen atom transfer, radical addition and electron transfer mechanisms. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1128-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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23
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Park J, Park JW, Oh H, Maria FS, Kang J, Tian X. Gene-Specific Assessment of Guanine Oxidation as an Epigenetic Modulator for Cardiac Specification of Mouse Embryonic Stem Cells. PLoS One 2016; 11:e0155792. [PMID: 27249188 PMCID: PMC4889044 DOI: 10.1371/journal.pone.0155792] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/03/2016] [Indexed: 12/11/2022] Open
Abstract
Epigenetics have essential roles in development and human diseases. Compared to the complex histone modifications, epigenetic changes on mammalian DNA are as simple as methylation on cytosine. Guanine, however, can be oxidized as an epigenetic change which can undergo base-pair transversion, causing a genetic difference. Accumulating evidence indicates that reactive oxygen species (ROS) are important signaling molecules for embryonic stem cell (ESC) differentiation, possibly through transient changes on genomic DNA such as 7,8-dihydro-8-oxoguanine (8-oxoG). Technical limitations on detecting such DNA modifications, however, restrict the investigation of the role of 8-oxoG in ESC differentiation. Here, we developed a Hoogsteen base pairing-mediated PCR-sequencing assay to detect 8-oxoG lesions that can subsequently cause G to T transversions during PCR. We then used this assay to assess the epigenetic and transient 8-oxoG formation in the Tbx5 gene of R1 mouse ESCs subjected to oxidative stress by removing 2-mercaptoethanol (2ME) from the culture media. To our surprise, significantly higher numbers of 8-oxoG-mediated G∙C to C∙G transversion, not G∙C to T∙A, were detected at 7th and 9th base position from the transcription start site of exon 1 of Tbx5 in ESCs in the (-)2ME than (+)2ME group (p < 0.05). This was consistent with the decrease in the amount of amplifiable of DNA harboring the 8-oxoG lesions at the Tbx5 promoter region in the oxidative stressed ESCs. The ESCs responded to oxidative stress, possibly through the epigenetic effects of guanine oxidation with decreased proliferation (p < 0.05) and increased formation of beating embryoid bodies (EBs; p < 0.001). Additionally, the epigenetic changes of guanine induced up-regulation of Ogg1 and PolB, two base excision repairing genes for 8-oxoG, in ESCs treated with (-)2ME (p < 0.01). Together, we developed a gene-specific and direct quantification assay for guanine oxidation. Using oxidative stressed mouse ESCs, we validated this assay and assessed the epigenetic effects of 8-oxoG by studying expression of DNA repair genes, ESC proliferation, and EB formation.
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Affiliation(s)
- Joonghoon Park
- Center for Regenerative Biology and Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, United States of America
| | - Jong Woo Park
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, 440746, Republic of Korea
| | - Hawmok Oh
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, 440746, Republic of Korea
| | - Fernanda S Maria
- Center for Regenerative Biology and Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, United States of America
- Department of Animal Reproduction, College of Veterinary Medicine, University of Sao Paulo, Sao Paulo, 05508, Brazil
| | - Jaeku Kang
- Department of Pharmacology, College of Medicine, Konyang University, Daejeon, 302718, Republic of Korea
| | - Xiuchun Tian
- Center for Regenerative Biology and Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, United States of America
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Jena NR, Bansal M, Mishra PC. Conformational stabilities of iminoallantoin and its base pairs in DNA: implications for mutagenicity. Phys Chem Chem Phys 2016; 18:12774-83. [DOI: 10.1039/c6cp02212j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Under acidic conditions, insertion of G opposite Ia may lead to G to C mutations in DNA.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology
- Design and Manufacturing
- Jabalpur-482005
- India
| | - Manju Bansal
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - P. C. Mishra
- Department of Physics
- Banaras Hindu University
- Varanasi-221005
- India
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25
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Jena NR, Mishra PC. Normal and reverse base pairing of Iz and Oz lesions in DNA: structural implications for mutagenesis. RSC Adv 2016. [DOI: 10.1039/c6ra14031a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
During replication, incorporation of G opposite Oz lesion is mainly responsible for G to C mutations in DNA.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology
- Design and Manufacturing
- Jabalpur-482005
- India
| | - P. C. Mishra
- Department of Physics
- Banaras Hindu University
- Varanasi-221005
- India
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26
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Tiwari MK, Mishra PC. Catalytic role of iron-superoxide dismutase in hydrogen abstraction by super oxide radical anion from ascorbic acid. RSC Adv 2016. [DOI: 10.1039/c6ra11455e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The catalytic role of iron-superoxide dismutase (Fe-SOD) in the working of ascorbic acid (AA) as a superoxide radical anion scavenger has been studied by employing a model developed recently for the active site of the enzyme.
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Affiliation(s)
- Manish K. Tiwari
- Department of Physics
- Institute of Science
- Banaras Hindu University
- Varanasi – 221 005
- India
| | - Phool C. Mishra
- Department of Physics
- Institute of Science
- Banaras Hindu University
- Varanasi – 221 005
- India
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Uranga J, Mujika JI, Matxain JM. ·OH Oxidation Toward S- and OH-Containing Amino Acids. J Phys Chem B 2015; 119:15430-42. [DOI: 10.1021/acs.jpcb.5b09825] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jon Uranga
- Kimika Fakultatea,
Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International
Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Jon I. Mujika
- Kimika Fakultatea,
Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International
Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Jon M. Matxain
- Kimika Fakultatea,
Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International
Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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28
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29
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Prasad AK, Mishra P. Mechanism of Action of Sulforaphane as a Superoxide Radical Anion and Hydrogen Peroxide Scavenger by Double Hydrogen Transfer: A Model for Iron Superoxide Dismutase. J Phys Chem B 2015; 119:7825-36. [DOI: 10.1021/acs.jpcb.5b01496] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ajit Kumar Prasad
- Department
of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - P.C. Mishra
- Department
of Physics, Banaras Hindu University, Varanasi 221 005, India
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30
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Li M, Diao L, Liao X, Kou L, Lu W. DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Minjie Li
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Ling Diao
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xiaofei Liao
- School of Information Science and Technology; Donghua University; Shanghai 201620 China
| | - Li Kou
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Wencong Lu
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
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31
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Cerón-Carrasco JP, Requena A, Zúñiga J, Jacquemin D. Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair. Front Chem 2015; 3:13. [PMID: 25798437 PMCID: PMC4351615 DOI: 10.3389/fchem.2015.00013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/16/2015] [Indexed: 12/04/2022] Open
Abstract
We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.
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Affiliation(s)
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia Murcia, Spain
| | - Denis Jacquemin
- Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR Centre National de la Recherche Scientifique, Université de Nantes Nantes, France ; Institut Universitaire de France Paris, France
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32
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Grüber R, Dumont É. DFT investigation of the formation of linear aminols as the first step toward the induction of oxidatively generated interstrand cross-link DNA lesions. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1631-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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33
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Chaban GM, Wang D, Huo WM. Ab Initio Study of Guanine Damage by Hydroxyl Radical. J Phys Chem A 2015; 119:377-82. [DOI: 10.1021/jp508771g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Galina M. Chaban
- NASA Ames Research Center, Mail Stop 258-1, P.O.
Box 1, Moffett Field, California 94035-0001, United States
| | - Dunyou Wang
- Shandong Normal University, 88
E. Wenhua Road, Jinan, Shangdong 250014, P. R. China
| | - Winifred M. Huo
- NASA Ames Research Center, Mail Stop 258-1, Moffett
Field, California 94035-0001, United States
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Jena NR, Gaur V, Mishra PC. The R- and S-diastereoisomeric effects on the guanidinohydantoin-induced mutations in DNA. Phys Chem Chem Phys 2015; 17:18111-20. [DOI: 10.1039/c5cp02636a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although, Gh (Gh1 or Gh2) in DNA would induce mainly G to C mutations, other mutations cannot be ignored.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology
- Design and Manufacturing
- Jabalpur-482005
- India
| | - Vivek Gaur
- Discipline of Mechanical Engineering
- Indian Institute of Information Technology
- Design and Manufacturing
- Jabalpur-482005
- India
| | - P. C. Mishra
- NASI Senior Scientist
- Department of Physics
- Banaras Hindu University
- Varanasi-221005
- India
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Jena NR, Mark AE, Mishra PC. Does Tautomerization of FapyG Influence Its Mutagenicity? Chemphyschem 2014; 15:1779-84. [DOI: 10.1002/cphc.201400045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/10/2014] [Indexed: 01/28/2023]
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36
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Formation of spiroiminodihydantoin due to the reaction between 8-oxoguanine and carbonate radical anion: A quantum computational study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Kumar A, Sevilla MD. π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study. J Phys Chem B 2013; 117:11623-32. [PMID: 24000793 DOI: 10.1021/jp407897n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form π- or σ-radicals. While most DNA base systems form π-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauraci1, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive σ-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of π- and σ-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of π- and σ-radicals in Cs symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that σ- and π-radical states in one-electron-oxidized bases of thymine, T(N3-H)(•), and uracil, U(N3-H)(•), are very close in energy; i.e., the π-radical is only ca. 4 kcal/mol more stable than the σ-radical. For the one-electron-oxidized radicals of cytosine, C(•+), C(N4-H)(•), adenine, A(•+), A(N6-H)(•), and guanine, G(•+), G(N2-H)(•), G(N1-H)(•), the π-radicals are ca. 16-41 kcal/mol more stable than their corresponding σ-radicals. Inclusion of solvent (PCM) is found to stabilize the π- over σ-radical of each of the systems. U(N3-H)(•) with three discrete water molecules in the gas phase is found to form a three-electron σ bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the π-radical remains most stable.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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38
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Prasad AK, Mishra PC. Study of scavenging action of zingerone towards the OH radical: formation of vanillin and ferulic acid. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ajit Kumar Prasad
- Department of Physics; Banaras Hindu University; Varanasi 221 005 India
| | - P. C. Mishra
- Department of Physics; Banaras Hindu University; Varanasi 221 005 India
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Jena NR, Mishra PC. Is FapyG Mutagenic?: Evidence from the DFT Study. Chemphyschem 2013; 14:3263-70. [DOI: 10.1002/cphc.201300535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/10/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Nihar Ranjan Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Khamaria, Jabalpur‐482005 (India)
- Current address School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072 (Australia)
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40
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Modeling the activity of glutathione as a hydroxyl radical scavenger considering its neutral non-zwitterionic form. J Mol Model 2012; 19:767-77. [DOI: 10.1007/s00894-012-1601-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/20/2012] [Indexed: 01/02/2023]
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41
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Yadav A, Mishra P. Carbonate radical anion as an efficient reactive oxygen species: Its reaction with guanyl radical and formation of 8-oxoguanine. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Kumar A, Pottiboyina V, Sevilla MD. One-electron oxidation of neutral sugar radicals of 2'-deoxyguanosine and 2'-deoxythymidine: a density functional theory (DFT) study. J Phys Chem B 2012; 116:9409-16. [PMID: 22793263 DOI: 10.1021/jp3059068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One electron oxidation of neutral sugar radicals has recently been suggested to lead to important intermediates in the DNA damage process culminating in DNA strand breaks. In this work, we investigate sugar radicals in a DNA model system to understand the energetics of sugar radical formation and oxidation. The geometries of neutral sugar radicals C(1')(•), C(2')(•), C(3')(•), C(4')(•), and C(5')(•) of 2'-deoxyguanosine (dG) and 2'-deoxythymidine (dT) were optimized in the gas phase and in solution using the B3LYP and ωB97x functionals and 6-31++G(d) basis set. Their corresponding cations (C(1')(+), C(2')(+), C(3')(+), C(4')(+), and C(5')(+)) were generated by removing an electron (one-electron oxidation) from the neutral sugar radicals, and their geometries were also optimized using the same methods and basis set. The calculation predicts the relative stabilities of the neutral sugar radicals in the order C(1')(•) > C(4')(•) > C(5')(•) > C(3')(•) > C(2')(•), respectively. Of the neutral sugar radicals, C(1')(•) has the lowest vertical ionization potential (IP(vert)), ca. 6.33 eV in the gas phase and 4.71 eV in solution. C(2')(•) has the highest IP(vert), ca. 8.02 eV, in the gas phase, and the resultant C(2') cation is predicted to undergo a barrierless hydride transfer from the C(1') site to produce the C(1') cation. One electron oxidation of C(2')(•) in dG is predicted to result in a low lying triplet state consisting of G(+•) and C(2')(•). The 5',8-cyclo-2'-deoxyguanosin-7-yl radical formed by intramolecular bonding between C(5')(•) and C(8) of guanine transfers spin density from C(5') site to guanine, and this structure has IP(vert) 6.25 and 5.48 eV in the gas phase and in solution.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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Jena NR, Mishra PC. Formation of ring-opened and rearranged products of guanine: mechanisms and biological significance. Free Radic Biol Med 2012; 53:81-94. [PMID: 22583701 DOI: 10.1016/j.freeradbiomed.2012.04.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 03/30/2012] [Accepted: 04/06/2012] [Indexed: 11/16/2022]
Abstract
DNA damage by endogenous and exogenous agents is a serious concern, as the damaged products can affect genome integrity severely. Damage to DNA may arise from various factors such as DNA base modifications, strand break, inter- and intrastrand crosslinks, and DNA-protein crosslinks. Among these factors, DNA base modification is a common and important form of DNA damage that has been implicated in mutagenesis, carcinogenesis, and many other pathological conditions. Among the four DNA bases, guanine (G) has the smallest oxidation potential, because of which it is frequently modified by reactive species, giving rise to a plethora of lethal lesions. Similarly, 8-oxo-7,8-dihydroguanine (8-oxoG), an oxidatively damaged guanine lesion, also undergoes various degradation reactions giving rise to several mutagenic species. The various products formed from reactions of G or 8-oxoG with different reactive species are mainly 2,6-diamino-4-oxo-5-formamidopyrimidine, 2,5-diamino-4H-imidazolone, 2,2,4-triamino-5-(2H)-oxazolone, 5-guanidino-4-nitroimidazole, guanidinohydantoin, spiroiminodihydantoin, cyanuric acid, parabanic acid, oxaluric acid, and urea, among others. These products are formed from either ring opening or ring opening and subsequent rearrangement. The main aim of this review is to provide a comprehensive overview of various possible reactions and the mechanisms involved, after which these ring-opened and rearranged products of guanine would be formed in DNA. The biological significance of oxidatively damaged products of G is also discussed.
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Affiliation(s)
- N R Jena
- Department of Physics, Indian Institute of Information Technology, Design and Manufacturing, Khamaria, Jabalpur 482005, India.
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Kumar A, Pottiboyina V, Sevilla MD. Hydroxyl radical (OH•) reaction with guanine in an aqueous environment: a DFT study. J Phys Chem B 2011; 115:15129-37. [PMID: 22050033 PMCID: PMC3240735 DOI: 10.1021/jp208841q] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The reaction of hydroxyl radical (OH(•)) with DNA accounts for about half of radiation-induced DNA damage in living systems. Previous literature reports point out that the reaction of OH(•) with DNA proceeds mainly through the addition of OH(•) to the C═C bonds of the DNA bases. However, recently it has been reported that the principal reaction of OH(•) with dGuo (deoxyguanosine) is the direct hydrogen atom abstraction from its exocyclic amine group rather than addition of OH(•) to the C═C bonds. In the present work, these two reaction pathways of OH(•) attack on guanine (G) in the presence of water molecules (aqueous environment) are investigated using the density functional theory (DFT) B3LYP method with 6-31G* and 6-31++G** basis sets. The calculations show that the initial addition of the OH(•) at C(4)═C(5) double bond of guanine is barrier free and the adduct radical (G-OH(•)) has only a small activation barrier of ca. 1-6 kcal/mol leading to the formation of a metastable ion-pair intermediate (G(•+)---OH(-)). The formation of ion-pair is a result of the highly oxidizing nature of the OH(•) in aqueous media. The resulting ion-pair (G(•+)---OH(-)) deprotonates to form H(2)O and neutral G radicals favoring G(N(1)-H)(•) with an activation barrier of ca. 5 kcal/mol. The overall process from the G(C(4))-OH(•) (adduct) to G(N(1)-H)(•) and water is found to be exothermic in nature by more than 13 kcal/mol. (G-OH(•)), (G(•+)---OH(-)), and G(N(1)-H)(•) were further characterized by the CAM-B3LYP calculations of their UV-vis spectra and good agreement between theory and experiment is achieved. Our calculations for the direct hydrogen abstraction pathway from N(1) and N(2) sites of guanine by the OH(•) show that this is also a competitive route to produce G(N(2)-H)(•), G(N(1)-H)(•) and H(2)O.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
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Agnihotri N, Mishra PC. Scavenging mechanism of curcumin toward the hydroxyl radical: a theoretical study of reactions producing ferulic acid and vanillin. J Phys Chem A 2011; 115:14221-32. [PMID: 22035040 DOI: 10.1021/jp209318f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Curcumin is known to be an antioxidant, as it can scavenge free radicals from biological media. A sequence of H-abstraction and addition reactions involving up to eight OH radicals and curcumin or its degradation products leading to the formation of two other antioxidants, namely, ferulic acid and vanillin, was studied. Single electron transfer from curcumin to an OH radical was also studied. All relevant extrema on the potential energy surfaces were located by optimizing geometries of the reactant and product complexes, as well as those of the transition states, at the BHandHLYP/6-31G(d,p) level of density functional theory in the gas phase. Single-point energy calculations were also performed in the gas phase at the BHandHLYP/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Solvent effects in aqueous media were treated by performing single-point energy calculations at all of the above-mentioned levels of theory employing the polarizable continuum model and the geometries optimized at the BHandHLYP/6-31G(d,p) level in the gas phase. A few reaction steps were also studied by geometry optimization in aqueous media, and the thus-obtained Gibbs free energy barriers were similar to those obtained by corresponding single-point energy calculations. Our calculations show that the hydrogen atom of the OH group attached to the phenol moiety of curcumin would be most efficiently abstracted by an OH radical, in agreement with experimental observations. Further, our study shows that OH addition would be most favored at the C10 site of the heptadiene chain. It was found that curcumin can serve as an effective antioxidant.
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Affiliation(s)
- Neha Agnihotri
- Department of Physics, Banaras Hindu University, Varanasi, India
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Ash S, De SP, Beg H, Misra A. Excited state intramolecular proton transfer in 3-hydroxychromone: a DFT-based computational study. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.577073] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Shukla P, Ganapathy V, Mishra P. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Theoretical study of hydrogen peroxide interacting with DNA base and DNA base pair in terms of ab initio method and ABEEMσπ/MM fluctuating charge potential model. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Jena NR, Bansal M. Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair. Phys Biol 2011; 8:046007. [PMID: 21666294 DOI: 10.1088/1478-3975/8/4/046007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg128 into the DNA double helix and its interaction with the O6MG:C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.
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Affiliation(s)
- N R Jena
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India.
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