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Denisov SA, Ward S, Shcherbakov V, Stark AD, Kaczmarek R, Radzikowska-Cieciura E, Debnath D, Jacobs T, Kumar A, Sevilla MD, Pernot P, Dembinski R, Mostafavi M, Adhikary A. Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group. J Phys Chem B 2022; 126:430-442. [PMID: 34990129 PMCID: PMC8776618 DOI: 10.1021/acs.jpcb.1c09068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O-)═S)). ESR investigations show that DMTP(O-)═S reacts with Cl2•- to form the σ2σ*1 adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O-)═S to produce [-P-S[Formula: see text]S-P-]-. -P-S[Formula: see text]Cl in G-P(O-)═S undergoes hole transfer to Gua, forming the cation radical (G•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O-)═S forms the thiyl radical (-P-S•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]-. Gua in G-P(O-)═S is oxidized unimolecularly by the -P-S• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.
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Affiliation(s)
- Sergey A. Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Alexander D. Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Ewa Radzikowska-Cieciura
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Michael D. Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Roman Dembinski
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA,Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
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Huwaidi A, Kumari B, Robert G, Guérin B, Sanche L, Wagner JR. Profiling DNA Damage Induced by the Irradiation of DNA with Gold Nanoparticles. J Phys Chem Lett 2021; 12:9947-9954. [PMID: 34617774 DOI: 10.1021/acs.jpclett.1c02598] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The presence of gold nanoparticles (AuNPs) greatly enhances the formation of DNA damage when exposed to therapeutic X-rays. Three types of DNA damage are assessed in irradiated DNA by enzymatic digestion coupled to liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. The major type of damage is release of the four nonmodified nucleobases, with a bias toward the release of cytosine and thymine. The second most important pathway involves the formation of several common reduction and oxidation products of DNA. Lastly, eight unique modifications of the 2-deoxyribose moiety are formed, which includes the 2',3'- and 2',5'-dideoxynucleosides (ddNs) of the four canonical nucleosides. The yield of ddNs decreases in the following order: ddG > ddA > ddC > ddT. From the yield and distribution of products, most of the damage is considered to arise from the generation of Auger/low-energy electrons (LEEs) and their reaction with DNA.
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Affiliation(s)
- Alaa Huwaidi
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Bhavini Kumari
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Gabriel Robert
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Brigitte Guérin
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
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Kaczmarek R, Ward S, Debnath D, Jacobs T, Stark AD, Korczyński D, Kumar A, Sevilla MD, Denisov SA, Shcherbakov V, Pernot P, Mostafavi M, Dembinski R, Adhikary A. One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate. Chemistry 2020; 26:9495-9505. [PMID: 32059063 PMCID: PMC7416487 DOI: 10.1002/chem.202000247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/09/2020] [Indexed: 12/26/2022]
Abstract
The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S- )=S was calculated to be slightly lower than that of guanine in 5'-dGMP. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S- . 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S- . 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S- . 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.
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Affiliation(s)
- Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Alexander D Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Sergey A Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Roman Dembinski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
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Ma J, Denisov SA, Adhikary A, Mostafavi M. Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides. Int J Mol Sci 2019; 20:ijms20194963. [PMID: 31597345 PMCID: PMC6801490 DOI: 10.3390/ijms20194963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 12/18/2022] Open
Abstract
Among the radicals (hydroxyl radical (•OH), hydrogen atom (H•), and solvated electron (esol−)) that are generated via water radiolysis, •OH has been shown to be the main transient species responsible for radiation damage to DNA via the indirect effect. Reactions of these radicals with DNA-model systems (bases, nucleosides, nucleotides, polynucleotides of defined sequences, single stranded (ss) and double stranded (ds) highly polymeric DNA, nucleohistones) were extensively investigated. The timescale of the reactions of these radicals with DNA-models range from nanoseconds (ns) to microseconds (µs) at ambient temperature and are controlled by diffusion or activation. However, those studies carried out in dilute solutions that model radiation damage to DNA via indirect action do not turn out to be valid in dense biological medium, where solute and water molecules are in close contact (e.g., in cellular environment). In that case, the initial species formed from water radiolysis are two radicals that are ultrashort-lived and charged: the water cation radical (H2O•+) and prethermalized electron. These species are captured by target biomolecules (e.g., DNA, proteins, etc.) in competition with their inherent pathways of proton transfer and relaxation occurring in less than 1 picosecond. In addition, the direct-type effects of radiation, i.e., ionization of macromolecule plus excitations proximate to ionizations, become important. The holes (i.e., unpaired spin or cation radical sites) created by ionization undergo fast spin transfer across DNA subunits. The exploration of the above-mentioned ultrafast processes is crucial to elucidate our understanding of the mechanisms that are involved in causing DNA damage via direct-type effects of radiation. Only recently, investigations of these ultrafast processes have been attempted by studying concentrated solutions of nucleosides/tides under ambient conditions. Recent advancements of laser-driven picosecond electron accelerators have provided an opportunity to address some long-term puzzling questions in the context of direct-type and indirect effects of DNA damage. In this review, we have presented key findings that are important to elucidate mechanisms of complex processes including excess electron-mediated bond breakage and hole transfer, occurring at the single nucleoside/tide level.
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Affiliation(s)
- Jun Ma
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215000, China.
| | - Sergey A Denisov
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, 91405 Orsay, CEDEX, France.
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309, USA.
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, 91405 Orsay, CEDEX, France.
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Black PJ, Miller AS, Hayes JJ. Radioresistance of GGG sequences to prompt strand break formation from direct-type radiation damage. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2016; 55:411-422. [PMID: 27349757 PMCID: PMC5093048 DOI: 10.1007/s00411-016-0660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 06/19/2016] [Indexed: 06/06/2023]
Abstract
As humans, we are constantly exposed to ionizing radiation from natural, man-made and cosmic sources which can damage DNA, leading to deleterious effects including cancer incidence. In this work, we introduce a method to monitor strand breaks resulting from damage due to the direct effect of ionizing radiation and provide evidence for sequence-dependent effects leading to strand breaks. To analyze only DNA strand breaks caused by radiation damage due to the direct effect of ionizing radiation, we combined an established technique to generate dehydrated DNA samples with a technique to analyze single-strand breaks on short oligonucleotide sequences via denaturing gel electrophoresis. We find that direct damage primarily results in a reduced number of strand breaks in guanine triplet regions (GGG) when compared to isolated guanine (G) bases with identical flanking base context. In addition, we observe strand break behavior possibly indicative of protection of guanine bases when flanked by pyrimidines and sensitization of guanine to strand break when flanked by adenine (A) bases in both isolated G and GGG cases. These observations provide insight into the strand break behavior in GGG regions damaged via the direct effect of ionizing radiation. In addition, this could be indicative of DNA sequences that are naturally more susceptible to strand break due to the direct effect of ionizing radiation.
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Affiliation(s)
- Paul J Black
- Department of Radiation Oncology, Columbia University, New York, NY, 10027, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, 14642, USA
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Close DM, Nelson WH, Bernhard WA. DNA damage by the direct effect of ionizing radiation: products produced by two sequential one-electron oxidations. J Phys Chem A 2013; 117:12608-15. [PMID: 24131335 DOI: 10.1021/jp4084844] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It has long been assumed that the population of radicals trapped in irradiated DNA (that is, the radicals escaping recombination) would quantitatively account for the lesions observed in DNA. Recent results indicate that this is not the case. The yield of DNA lesions exceed the yield of trappable radicals. To account for a portion of this shortfall, it is thought that some of the initially formed 2'-deoxyribose radicals undergo a second oxidation by nearby base cation radicals to form 2'-carbocations. The carbocations react to give strand breaks and free base release. Schemes are presented to account for the major oxidation products observed including 8-oxoGua, 8-oxoAde, 5-OHMeUra, and free base release. Theoretical calculations were performed to ascertain the likelihood of the second oxidation step in these reaction pathways actually occurring, and to account for base sequence dependence and various levels of hydration.
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Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University , Johnson City, Tennessee 37614, United States
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Black PJ, Bernhard WA. Excess electron trapping in duplex DNA: long range transfer via stacked adenines. J Phys Chem B 2012; 116:13211-8. [PMID: 23067129 DOI: 10.1021/jp307851g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An understanding of charge transfer (CT) in DNA lies at the root of assessing the risks and benefits of exposure to ionizing radiation. Energy deposition by high-energy photons and fast-charged particles creates holes and excess electrons (EEs) in DNA, and the subsequent reactions determine the complexity of DNA damage and ultimately the risk of disease. Further interest in CT comes from the possibility that hole transfer, excess electron transfer (EET), or both in DNA might be used to develop nanoscale circuits. To study EET in DNA, EPR spectroscopy was used to determine the distribution of EE trapping by oligodeoxynucleotides irradiated and observed at 4 K. Our results indicate that stretches of consecutive adenine bases on the same strand serve as an ideal conduit for intrastrand EET in duplex DNA at 4 K. Specifically, we show that A is an efficient trap for EE at 4 K if, and only if, the A strand of the duplex does not contain one of the other three bases. If there is a T, C, or G on the A strand, then trapping occurs at T or C instead of A. This holds true for stretches up to 32 A's. Whereas T competes effectively against A for the EE, it does not compete effectively against C. Long stretches of T pass the majority of EE to C. Our results show that AT stretches channel EE to cytosine, an end point with significance to both radiation damage and the photochemical repair of pyrimidine dimers.
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Affiliation(s)
- Paul J Black
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA.
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Peoples AR, Lee J, Weinfeld M, Milligan JR, Bernhard WA. Yields of damage to C4' deoxyribose and to pyrimidines in pUC18 by the direct effect of ionizing radiation. Nucleic Acids Res 2012; 40:6060-9. [PMID: 22467205 PMCID: PMC3401456 DOI: 10.1093/nar/gks271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Our mechanistic understanding of damage formation in DNA by the direct effect relies heavily on what is known of free radical intermediates studied by EPR spectroscopy. Bridging this information to stable product formation requires methods with comparable sensitivities, a criterion met by the 32P-post-labeling assay developed by Weinfeld and Soderlind, [Weinfeld,M. and Soderlind,K.-J.M. (1991) 32P-Postlabeling detection of radiation-induced DNA damage: identification and estimation of thymine glycols and phosphoglycolate termini. Biochemistry, 30, 1091–1097] which when applied to the indirect effect, detected phosphoglycolate (pg) and thymine glycol (Tg). Here we applied this assay to the direct effect, measuring product yields in pUC18 films with hydration levels (Γ) of 2.5, 16 or 23 waters per nucleotide and X-irradiated at either 4 K or room temperature (RT). The yields of pg [G(pg)] for Γ ∼ 2.5 were 2.8 ± 0.2 nmol/J (RT) and 0.2 ± 0.3 nmol/J (4 K), which is evidence that the C4′ radical contributes little to the total deoxyribose damage via the direct effect. The yield of detectable base damage [G(B*)] at Γ ∼ 2.5 was found to be 30.2 ± 1.0 nmol/J (RT) and 12.9 ± 0.7 nmol/J (4 K). While the base damage called B*, could be due to either oxidation or reduction, we argue that two reduction products, 5,6-dihydrouracil and 5,6-dihydrothymine, are the most likely candidates.
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Affiliation(s)
- Anita R Peoples
- Department of Biochemistry and Biophysics, University of Rochester, Medical Center, Rochester, NY 14642, USA
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Lee M, Urata SM, Aguilera JA, Perry CC, Milligan JR. Modeling the Influence of Histone Proteins on the Sensitivity of DNA to Ionizing Radiation. Radiat Res 2012; 177:152-63. [DOI: 10.1667/rr2812.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Galano A, Alvarez-Idaboy JR. On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium. Phys Chem Chem Phys 2012; 14:12476-84. [DOI: 10.1039/c2cp40799j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Konigsfeld KM, Lee M, Urata SM, Aguilera JA, Milligan JR. Free terminal amines in DNA-binding peptides alter the product distribution from guanine radicals produced by single electron oxidation. Int J Radiat Biol 2011; 88:230-8. [PMID: 22124251 DOI: 10.3109/09553002.2012.643853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE Electron deficient guanine radical species are major intermediates produced in DNA by the direct effect of ionizing irradiation. There is evidence that they react with amine groups in closely bound ligands to form covalent crosslinks. Crosslink formation is very poorly characterized in terms of quantitative rate and yield data. We sought to address this issue by using oligo-arginine ligands to model the close association of DNA and its binding proteins in chromatin. MATERIALS AND METHODS Guanine radicals were prepared in plasmid DNA by single electron oxidation. The product distribution derived from them was assayed by strand break formation after four different post-irradiation incubations. RESULTS We compared the yields of DNA damage produced in the presence of four ligands in which neither, one, or both of the amino and carboxylate termini were blocked with amides. Free carboxylate groups were unreactive. Significantly higher yields of heat labile sites were observed when the amino terminus was unblocked. The rate of the reaction was characterized by diluting the unblocked amino group with its amide blocked derivative. CONCLUSION These observations provide a means to develop quantitative estimates for the yields in which these labile sites are formed in chromatin by exposure to ionizing irradiation.
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Affiliation(s)
- Katie M Konigsfeld
- Department of Radiology, University of California at San Diego, La Jolla, California 92093-0610, USA
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Phadatare SD, Sharma KKK, Rao BSM, Naumov S, Sharma GK. Spectral Characterization of Guanine C4-OH Adduct: A Radiation and Quantum Chemical Study. J Phys Chem B 2011; 115:13650-8. [DOI: 10.1021/jp203899j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suvarna D. Phadatare
- National Centre for Free Radical Research (NCFRR), Department of Chemistry, University of Pune, 411007, Maharashtra, India
| | - Kiran Kumar K. Sharma
- School of Chemical Sciences, Department of Physical Chemistry, North Maharashtra University, Jalgaon, 425001, Maharashtra, India
| | - B. S. M. Rao
- National Centre for Free Radical Research (NCFRR), Department of Chemistry, University of Pune, 411007, Maharashtra, India
- Department of Chemistry, Indian Institute Science Education and Research (IISER), Pune 411021, India
| | - S. Naumov
- Leibniz-Institut für Oberflächenmodifizierung e. V. (IOM), Permoserstr. 15, D-04318 Leipzig, Germany
| | - Geeta K. Sharma
- National Centre for Free Radical Research (NCFRR), Department of Chemistry, University of Pune, 411007, Maharashtra, India
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Sharma KKK, Swarts SG, Bernhard WA. Mechanisms of direct radiation damage to DNA: the effect of base sequence on base end products. J Phys Chem B 2011; 115:4843-55. [PMID: 21473599 DOI: 10.1021/jp200902h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
It has been generally assumed that product formation in DNA damaged by ionizing radiation is relatively independent of base sequence, i.e., that the yield of a given product depends primarily on the chemical properties of each DNA constituent and not on its base sequence context. We examined this assumption by comparing direct-type end products produced in films of d(CTCTCGAGAG)(2) with those produced in films of d(GCACGCGTGC)(2). Here we report the product yields in d(CTCTCGAGAG)(2) hydrated to Γ = 2.5 and 15, where Γ is the hydration level given in moles of H(2)O/mole of nucleotide. Of the 17 products monitored by GC/MS, seven exhibited statistically significant yields: 8-oxoGua, 8-oxoAde, 5-OHMeUra, 5,6-diHUra, 5,6-diHThy, 5-OHCyt, and 5-OHUra. These yields at Γ = 2.5 are compared with the yields from our previously reported study of d(GCACGCGTGC)(2) (after projecting the yields to a CG/AT ratio of 1). The ratio of projected yields, d(CTCTCGAGAG)(2) divided by d(GCACGCGTGC)(2), are 1.3 ± 0.9, 1.8 ± 0.3, 1.6 ± 0.6, 11.4 ± 4.7, 0.2 ± 0.1, >28, and 0.8 ± 1.1, respectively. Considering just d(CTCTCGAGAG)(2), the ratios of yields at Γ = 2.5 divided by yields at Γ = 15 are 0.7 ± 0.2, 0.5 ± 0.1, 2.3 ± 4.0, 3.4 ± 1.2, 3.5 ± 3.3, 1.2 ± 0.2, and 0.4 ± 0.2, respectively. The effects of sequence and hydration on base product yields are explained by a working model emphasizing the difference between two distinctly different types of reaction: (i) radical reactions that progress to nonradical intermediates and product prior to dissolution and (ii) reactions that stem from radicals trapped in the solid state at room temperature that go on to yield nonradical product after sample dissolution. Based on these findings, insights into rates of hole and excess electron-transfer relative to rates of proton transfer are discussed.
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Affiliation(s)
- Kiran K K Sharma
- School of Chemical Sciences, North Maharashtra University, Jalgaon, Maharashtra, India
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