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Zima V, Vlk M, Wan J, Cvačka J, Tureček F. Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry. J Phys Chem A 2023. [PMID: 37433135 DOI: 10.1021/acs.jpca.3c03179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.
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Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Mikuláš Vlk
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Jiahao Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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Izadi ME, Sabzyan H. Reactive Molecular Dynamics Simulation of the Structural Damages of the B-DNA Induced by the Oxidation/Nitration of Guanine. J Phys Chem B 2022; 126:10347-10359. [PMID: 36448964 DOI: 10.1021/acs.jpcb.2c05151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Reactive molecular dynamics simulations (RMD) have been carried out to investigate structural alterations of the dodecamer double-strand B-DNA due to the oxidation/nitration modifications introduced to its guanine bases, including 8-oxoguanine, 8-nitroguanine, and 5-guanidino-4-nitroimidazole, considering two distribution patterns. These modifications may arise in the case of cancer treatment using oxidative/nitrosative reactive nitrogen species as anticancer agents. Results show that these mutations affect structural characteristics of the B-DNA dodecamer in the order 8-nitroguanine > 5-guanidino-4-nitroimidazole ≫ 8-oxoguanine. For instance, the base-pair per turn for these modified B-DNA are changed respectively to 9.79, 10.88 and 10.58 from 10.51 in the native defect-free B-DNA, which is compatible with the experimental value of 10.10. In addition, these mutations allow more water molecules to diffuse into the dodecamer structure and consequently increase the possibility of the penetration of reactive and nonreactive species toward constituting nucleic base-pairs. The largest variation of the B-DNA structure is observed for the mutated B-DNA with 8-nitroguanine modifications applied to its separated CG base-pairs along the dodecamer chain. The structural changes introduced by these nitro-/oxo-modified guanine bases can be considered as a critical step in the damage of the DNA structure and alterations of its function.
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Affiliation(s)
| | - Hassan Sabzyan
- Department of Chemistry, University of Isfahan, Isfahan81746-873441, I. R. Iran
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Sánchez AG, Ibargoyen MN, Mastrogiovanni M, Radi R, Keszenman DJ, Peluffo RD. Fast and biphasic 8-nitroguanine production from guanine and peroxynitrite. Free Radic Biol Med 2022; 193:474-484. [PMID: 36332879 DOI: 10.1016/j.freeradbiomed.2022.10.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Guanine (Gua), among purines, is a preferred oxidation/nitration target because of its low one-electron redox potential. The reactive oxygen/nitrogen species peroxynitrite (ONOO-), produced in vivo by the reaction between nitric oxide (•NO) and superoxide radical (O2•‒), is responsible for several oxidative modifications in biomolecules, including nitration, nitrosation, oxidation, and peroxidation. In particular, the nitration of Gua, although detected, as well as its reaction kinetics have been seldom investigated. Thus, we studied the concentration- and temperature-dependent formation of 8-nitroguanine (8-NitroGua) in phosphate buffer (pH 7.40) using stopped-flow spectrophotometry. Traces showed a biexponential behavior, with best-fit rate constants: kfast = 4.4 s-1 and kslow = 0.41 s-1 (30 °C, 400 μM both Gua and ONOO-). kfast increased linearly with the concentration of both reactants whereas kslow was concentration-independent. Linear regression analysis of kfast as a function of Gua and ONOO- concentration yielded values of 2.5-6.3 × 103 M-1s-1 and 1.5-3.5 s-1 for the second-order (slope) and first-order (ordinate) rate constants, respectively (30 °C). Since ONOO- is a short-lived species, its decay kinetics was also taken into account for this analysis. The 8-NitroGua product was stable for at least 4 h, so no spontaneous denitration was observed. Stopped-flow assays using antioxidants and free-radical scavengers suggested a mixed direct/indirect reaction mechanism for 8-NitroGua formation. Gua nitration by ONOO- was also observed in the presence of physiologically relevant CO2 concentrations. The reaction product identity, its yield (∼4.2%, with 400 μM ONOO- and 200 μM Gua), and the reaction mechanism were unequivocally determined by HPLC-MS/MS experiments. In conclusion, 8-NitroGua production at physiologic pH reached significant levels in a few hundred milliseconds, suggesting that the process might be kinetically relevant in vivo and can likely cause permanent nitrative damage to DNA bases.
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Affiliation(s)
- Ana G Sánchez
- Grupo de Biofisicoquímica, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay
| | - M Natalia Ibargoyen
- Grupo de Biofisicoquímica, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay
| | - Mauricio Mastrogiovanni
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800, Montevideo, Uruguay
| | - Rafael Radi
- Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800, Montevideo, Uruguay
| | - Deborah J Keszenman
- Grupo de Biofisicoquímica, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay
| | - R Daniel Peluffo
- Grupo de Biofisicoquímica, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Rivera 1350, 50000, Salto, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800, Montevideo, Uruguay; Department of Pharmacology, Physiology and Neuroscience, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, Newark, NJ, 07103, USA.
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Zhou W, Liu J. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules. Phys Chem Chem Phys 2021; 23:24464-24477. [PMID: 34698322 DOI: 10.1039/d1cp03884b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al., Phys. Chem. Chem. Phys., 2018, 20, 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands (i.e., 9MG˙+·(H2O)1-2) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙+ and are referred to as HAO6 and HAN7, respectively. The primary products of HAO6 and HAN7 reactions, including [9MG + HO6]+/[9MG + HN7]+ and ˙OH, react further to either form [8OH-9MG + HO6]˙+ and [8OH-9MG + HN7]˙+via C8-hydroxylation or form radical cations of 6-enol-guanine (6-enol-G˙+) and 7H-guanine (7HG˙+) via SN2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG+ by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + HN7]˙+ has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy.
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Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, 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. .,PhD 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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Zhang X, Jie J, Song D, Su H. Deprotonation of Guanine Radical Cation G •+ Mediated by the Protonated Water Cluster. J Phys Chem A 2020; 124:6076-6083. [PMID: 32585092 DOI: 10.1021/acs.jpca.0c03748] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H2O-PCM, 4H2O-PCM, 5H2O-PCM, and 7H2O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G•+.
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Affiliation(s)
- Xianwang Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100048, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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Hebert SP, Schlegel HB. Computational Investigation into the Oxidation of Guanine to Form Imidazolone (Iz) and Related Degradation Products. Chem Res Toxicol 2020; 33:1010-1027. [PMID: 32119534 DOI: 10.1021/acs.chemrestox.0c00039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Imidazolone (Iz) is one of the many products resulting from oxidative damage to DNA. Three pathways for the formation of Iz and related degradation products have been studied by density functional theory using the ωB97XD functional with the 6-31+G(d,p) basis set and SMD implicit water solvation plus a small number of explicit water molecules positioned to help stabilize charged species and facilitate reaction steps. The first pathway starts with guanine radical and the addition of superoxide at C5. Endoperoxide formation was calculated to have slightly lower barriers than diol formation. The next steps are pyrimidine ring opening and decarboxylation. Ring migration then proceeds via an acyclic intermediate rather than a bicyclic intermediate and is followed by formamide loss to yield Iz. The second pathway starts with 8oxoG and proceeds via C5 superoxide addition and diol formation to a relatively stable intermediate, oxidized guanidinohydantoin (Ghox). The barriers for hydroxide ion addition to Ghox are much lower than for water addition and should yield more Iz and parabanic acid at higher pH. The third pathway starts with 8-hydroxy guanine radical formed by hydroxyl radical addition to C8 of guanine or water addition to C8 of guanine radical. Superoxide addition at C5 is followed by diol formation, ring opening and decarboxylation similar to pathways 1 and 2, subsequently leading to Iz formation. The calculated pathways are in good agreement with experimental observations.
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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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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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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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Matter B, Seiler CL, Murphy K, Ming X, Zhao J, Lindgren B, Jones R, Tretyakova N. Mapping three guanine oxidation products along DNA following exposure to three types of reactive oxygen species. Free Radic Biol Med 2018; 121:180-189. [PMID: 29702150 PMCID: PMC6858621 DOI: 10.1016/j.freeradbiomed.2018.04.561] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 12/18/2022]
Abstract
Reactive oxygen and nitrogen species generated during respiration, inflammation, and immune response can damage cellular DNA, contributing to aging, cancer, and neurodegeneration. The ability of oxidized DNA bases to interfere with DNA replication and transcription is strongly influenced by their chemical structures and locations within the genome. In the present work, we examined the influence of local DNA sequence context, DNA secondary structure, and oxidant identity on the efficiency and the chemistry of guanine oxidation in the context of the Kras protooncogene. A novel isotope labeling strategy developed in our laboratory was used to accurately map the formation of 2,2-diamino-4-[(2-deoxy-β-D-erythropentofuranosyl)amino]- 5(2 H)-oxazolone (Z), 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG), and 8-nitroguanine (8-NO2-G) lesions along DNA duplexes following photooxidation in the presence of riboflavin, treatment with nitrosoperoxycarbonate, and oxidation in the presence of hydroxyl radicals. Riboflavin-mediated photooxidation preferentially induced OG lesions at 5' guanines within GG repeats, while treatment with nitrosoperoxycarbonate targeted 3'-guanines within GG and AG dinucleotides. Little sequence selectivity was observed following hydroxyl radical-mediated oxidation. However, Z and 8-NO2-G adducts were overproduced at duplex ends, irrespective of oxidant identity. Overall, our results indicate that the patterns of Z, OG, and 8-NO2-G adduct formation in the genome are distinct and are influenced by oxidant identity and the secondary structure of DNA.
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Affiliation(s)
- Brock Matter
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L Seiler
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kristopher Murphy
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xun Ming
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jianwei Zhao
- Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Bruce Lindgren
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Roger Jones
- Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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Chen L, Wu N, Sun B, Su H, Ai S. Colorimetric detection of peroxynitrite-induced DNA damage using gold nanoparticles, and on the scavenging effects of antioxidants. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-0958-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Kumar N, Shukla P, Mishra P. Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Agnihotri N, Mishra PC. Formation of 8-Nitroguanine Due to Reaction between Guanyl Radical and Nitrogen Dioxide: Catalytic Role of Hydration. J Phys Chem B 2010; 114:7391-404. [DOI: 10.1021/jp9122437] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neha Agnihotri
- 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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14
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Quantum chemical investigation of nitrotyrosine (3-nitro-l-tyrosine) and 8-nitroguanine. Amino Acids 2009; 38:319-27. [DOI: 10.1007/s00726-009-0253-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 02/02/2009] [Indexed: 12/31/2022]
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15
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Agnihotri N, Mishra PC. Mutagenic Product Formation Due to Reaction of Guanine Radical Cation with Nitrogen Dioxide. J Phys Chem B 2009; 113:3129-38. [DOI: 10.1021/jp805942y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Neha Agnihotri
- 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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Shukla PK, Mishra PC. Reactions of NO2Cl with Imidazole: A Model Study for the Corresponding Reactions of Guanine. J Phys Chem B 2008; 112:7925-36. [DOI: 10.1021/jp801093r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- P. K. Shukla
- Department of Physics, Banaras Hindu University, Varanasi-221005, India
| | - P. C. Mishra
- Department of Physics, Banaras Hindu University, Varanasi-221005, India
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17
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Modeling the reaction mechanisms for redox regulation of protein tyrosine phosphatase 1B activity. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0343-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Jena NR, Kushwaha PS, Mishra PC. Reaction of hypochlorous acid with imidazole: Formation of 2-chloro- and 2-oxoimidazoles. J Comput Chem 2007; 29:98-107. [PMID: 17508410 DOI: 10.1002/jcc.20768] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Reaction of hypochlorous acid (HOCl) with imidazole (Im) taken as a model for the 5-membered ring of guanine, leading to the products 2-chloro- and 2-oxo-imidazoles was investigated at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels of density functional theory. For all cases, single point energy calculations were performed at the MP2/AUG-cc-pVDZ level of theory using the geometries optimised at the B3LYP/AUG-cc-pVDZ level. Intrinsic reaction coordinate calculations were performed to ensure genuineness of all the calculated transition states. Effect of aqueous media was investigated by solvating all the species involved in the reactions using the polarizable continuum model. It is found that 2-chloroimidazole (2-ClIm) can be formed following three different reaction schemes while 2-oxoimidazole (2-oxoIm) can be formed following two different reaction schemes. The calculated barrier energies show that formation of 2-oxoIm would be less favored than that of 2-ClIm, which explains the experimental observations on relative yields of 8-chlorodeoxyguanosine and 8-oxodeoxyguanosine.
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Affiliation(s)
- N R Jena
- Department of Physics, Banaras Hindu University, Varanasi, India
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