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Tashiro R, Sugiyama H. Photoreaction of DNA Containing 5-Halouracil and its Products. Photochem Photobiol 2022; 98:532-545. [PMID: 34543451 PMCID: PMC9197447 DOI: 10.1111/php.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groove-binder/DNA and protein/DNA complexes using a 5-bromouracil-based electron transfer system is also described.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-Cyo, Suzuka, Mie, 513-8670, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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2
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Walton JC. Dissociations of free radicals to generate protons, electrophiles or nucleophiles: role in DNA strand breaks. Chem Soc Rev 2021; 50:7496-7512. [PMID: 34019058 DOI: 10.1039/d1cs00193k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The concept behind the research described in this article was that of marrying the 'soft' methods of radical generation with the effectiveness and flexibility of nucleophile/electrophile synthetic procedures. Classic studies with pulse radiolysis and laser flash photolysis had shown that free radicals could be more acidic than their closed shell counterparts. QM computations harmonised with this and helped to define which radical centres and which structural types were most effective. Radicals based on the sulfonic acid moiety and on the Meldrum's acid moiety (2,2-dimethyl-1,3-dioxane-4,6-dione) were found to be extreme examples in the superacid class. The ethyne unit could be used as a very effective spacer between the radical centre and the site of proton donation. The key factor in promoting acidity was understood to be the thermodynamic stabilisation of the conjugate anion-radicals released on deprotonation. Solvation played a key part in promoting this and theoretical microhydration studies provided notable support. A corollary was that heterolytic dissociations of free radicals to yield either electrophiles or nucleophiles were also enhanced relative to non-radical models. The most effective radical types for spontaneous releases of both these types of reagents were identified. Ethyne units were again effective as spacers. The enhancement of release of phosphate anions by adjacent radical centres was an important special case. Reactive oxygen species and also diradicals from endiyne antibiotics generate C4'-deoxyribose radicals from nucleotides. Radicals of these types spontaneously release phosphate and triphosphate and this is a contributor to DNA and RNA strand breaks.
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Affiliation(s)
- John C Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, UK.
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3
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Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
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4
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Mondal S, Mugesh G. Dehalogenation of Halogenated Nucleobases and Nucleosides by Organoselenium Compounds. Chemistry 2019; 25:1773-1780. [DOI: 10.1002/chem.201805112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Santanu Mondal
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
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5
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Zdrowowicz M, Wityk P, Michalska B, Rak J. 5-Bromo-2'-deoxycytidine-a potential DNA photosensitizer. Org Biomol Chem 2018; 14:9312-9321. [PMID: 27714178 DOI: 10.1039/c6ob01446a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A double-stranded oligonucleotide, 80 base pairs in length, was multiply labeled with 5-bromo-2'-deoxycytidine (BrdC) using polymerase chain reaction (PCR). The modified oligonucleotide was irradiated with 300 nm photons and its damage was assayed by employing DHPLC, LC-MS and denaturing polyacrylamide gel electrophoresis (PAGE). Two types of damage were demonstrated, namely, single strand breaks (SSBs) and intrastrand cross-links (ICLs); the ICLs were in the form of d(G^C) and d(C^C) dimers. The former species are probably formed due to photoinduced electron transfer between the photoexcited BrdC and the ground state 2'-deoxyguanosine (dG), whereas the latter is a result of a cycloaddition reaction. Since SSBs and ICLs are potentially lethal to the cell, BrdC could be considered as a nucleoside with possible clinical applications.
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Affiliation(s)
- Magdalena Zdrowowicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Paweł Wityk
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Barbara Michalska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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6
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Saha A, Kizaki S, Han JH, Yu Z, Sugiyama H. UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258. Bioorg Med Chem 2018; 26:37-40. [PMID: 29170027 DOI: 10.1016/j.bmc.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/15/2023]
Abstract
Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5'-AABrUBrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.
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Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Seiichiro Kizaki
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Ji Hoon Han
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Zutao Yu
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo, Kyoto 606-8502, Japan.
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7
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Westphal K, Makurat S, Rak J. The Sequence Dependence of Photoinduced Single Strand Break in 5-Bromo-2′-deoxyuridine Labeled DNA Supports That Electron Transfer Is Responsible for the Damage. J Phys Chem B 2017; 121:9169-9174. [DOI: 10.1021/acs.jpcb.7b07338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kinga Westphal
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Samanta Makurat
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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8
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Quantitative assay of photoinduced DNA strand breaks by real-time PCR. J Pharm Biomed Anal 2016; 128:480-484. [DOI: 10.1016/j.jpba.2016.06.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 12/28/2022]
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9
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Saha A, Kizaki S, De D, Endo M, Kim KK, Sugiyama H. Examining cooperative binding of Sox2 on DC5 regulatory element upon complex formation with Pax6 through excess electron transfer assay. Nucleic Acids Res 2016; 44:e125. [PMID: 27229137 PMCID: PMC5001601 DOI: 10.1093/nar/gkw478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/17/2016] [Indexed: 12/29/2022] Open
Abstract
Functional cooperativity among transcription factors on regulatory genetic elements is pivotal for milestone decision-making in various cellular processes including mammalian development. However, their molecular interaction during the cooperative binding cannot be precisely understood due to lack of efficient tools for the analyses of protein-DNA interaction in the transcription complex. Here, we demonstrate that photoinduced excess electron transfer assay can be used for analysing cooperativity of proteins in transcription complex using cooperative binding of Pax6 to Sox2 on the regulatory DNA element (DC5 enhancer) as an example. In this assay, (Br)U-labelled DC5 was introduced for the efficient detection of transferred electrons from Sox2 and Pax6 to the DNA, and guanine base in the complementary strand was replaced with hypoxanthine (I) to block intra-strand electron transfer at the Sox2-binding site. By examining DNA cleavage occurred as a result of the electron transfer process, from tryptophan residues of Sox2 and Pax6 to DNA after irradiation at 280 nm, we not only confirmed their binding to DNA but also observed their increased occupancy on DC5 with respect to that of Sox2 and Pax6 alone as a result of their cooperative interaction.
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Affiliation(s)
- Abhijit Saha
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Seiichiro Kizaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Debojyoti De
- Department of Molecular Cell Biology, Sungkyunkwan University, School of Medicine, Suwon 440-746, Korea
| | - Masayuki Endo
- Institute for Integrated Cell-Materials Sciences (iCeMS) Kyoto University, Yoshida-ushinomiyacho, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University, School of Medicine, Suwon 440-746, Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan Institute for Integrated Cell-Materials Sciences (iCeMS) Kyoto University, Yoshida-ushinomiyacho, Sakyo-Ku, Kyoto 606-8501, Japan
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10
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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11
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Rudra A, Hou D, Zhang Y, Coulter J, Zhou H, DeWeese TL, Greenberg MM. Bromopyridone Nucleotide Analogues, Anoxic Selective Radiosensitizing Agents That Are Incorporated in DNA by Polymerases. J Org Chem 2015; 80:10675-85. [PMID: 26509218 DOI: 10.1021/acs.joc.5b01833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ionizing radiation is frequently used to kill tumor cells. However, hypoxic solid tumor cells are more resistant to this treatment, providing the impetus to develop molecules that sensitize cells to ionizing radiation. 5-Bromo-2'-deoxyuridine (BrdU) has been investigated as a radiosensitizing agent in the lab and clinic for almost 5 decades. Recent reports that BrdU yields DNA interstrand cross-links (ICLs) in non-base-paired regions motivated us to develop radiosensitizing agents that generate cross-links in duplex DNA selectively under anoxic conditions. 4-Bromo- and 5-bromopyridone analogues of BrdU were synthesized and incorporated into oligonucleotides via solid-phase synthesis. Upon irradiation, these molecules yield DNA interstrand cross-links under anaerobic conditions. The respective nucleotide triphosphates are substrates for some DNA polymerases. ICLs are produced upon irradiation under anoxic conditions when the 4-bromopyridone is present in a PCR product. Because the nucleoside analogue is a poor phosphorylation substrate for human deoxycytidine kinase, a pro-nucleotide form of the 4-bromopyridone was used to incorporate this analogue into cellular DNA. Despite these efforts, the 4-bromopyridone nucleotide was not detected in cellular DNA. Although these molecules are improvements over previously reported nucleotide analogues designed to be hypoxic radiosensitizing agents, additional advances are needed to create molecules that function in cells.
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Affiliation(s)
- Arnab Rudra
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Dianjie Hou
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Yonggang Zhang
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine , 401 N. Broadway, Baltimore, Maryland 21231, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Jonathan Coulter
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine , 401 N. Broadway, Baltimore, Maryland 21231, United States
| | - Haoming Zhou
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine , 401 N. Broadway, Baltimore, Maryland 21231, United States
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine , 401 N. Broadway, Baltimore, Maryland 21231, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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12
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Rak J, Chomicz L, Wiczk J, Westphal K, Zdrowowicz M, Wityk P, Żyndul M, Makurat S, Golon Ł. Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation. J Phys Chem B 2015; 119:8227-38. [PMID: 26061614 DOI: 10.1021/acs.jpcb.5b03948] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hypoxia--a hallmark of solid tumors--makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet radiation. While incorporated into genomic DNA, modified nucleosides, 5-bromo-2'-deoxyuridine in particular, sensitize cells to both near-ultraviolet photons and γ rays. It is believed that, in both sensitization modes, the reactive nucleobase radical is formed as a primary product which swiftly stabilizes, leading to serious DNA damage, like strand breaks or cross-links. However, despite the apparent similarity, such radio- and photosensitization of DNA seems to be ruled by fundamentally different mechanisms. In this review, we demonstrate that the most important factors deciding on radiodamage to the labeled DNA are (i) the electron affinity (EA) of modified nucleoside (mNZ), (ii) the local surroundings of the label that significantly influences the EA of mNZ, and (iii) the strength of the chemical bond holding together the substituent and a nucleobase. On the other hand, we show that the UV damage to sensitized DNA is governed by long-range photoinduced electron transfer, the efficiency of which is controlled by local DNA sequences. A critical review of the literature mechanisms concerning both types of damage to the labeled biopolymer is presented. Ultimately, the perspectives of studies on DNA sensitization in the context of cancer therapy are discussed.
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Affiliation(s)
- Janusz Rak
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Lidia Chomicz
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Justyna Wiczk
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Kinga Westphal
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Magdalena Zdrowowicz
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paweł Wityk
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Michał Żyndul
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Samanta Makurat
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Łukasz Golon
- Faculty of Chemistry University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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13
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Saha A, Hashiya F, Kizaki S, Asamitsu S, Hashiya K, Bando T, Sugiyama H. A novel detection technique of polyamide binding sites by photo-induced electron transfer in BrU substituted DNA. Chem Commun (Camb) 2015; 51:14485-8. [DOI: 10.1039/c5cc05104e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate a highly sensitive detection technique of polyamide binding sites using the photochemistry of BrU labeled DNA.
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Affiliation(s)
- Abhijit Saha
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Fumitaka Hashiya
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Seiichiro Kizaki
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Sefan Asamitsu
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Kaori Hashiya
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Toshikazu Bando
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
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14
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Chomicz L, Petrovici A, Archbold I, Adhikary A, Kumar A, Sevilla MD, Rak J. An ESR and DFT study of hydration of the 2'-deoxyuridine-5-yl radical: a possible hydroxyl radical intermediate. Chem Commun (Camb) 2014; 50:14605-8. [PMID: 25306924 PMCID: PMC4213299 DOI: 10.1039/c4cc07089e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism of radiation-induced frank strand break formation in irradiated 5-bromo-2'-deoxyuridine (BrdU)-labelled DNA is still unclear despite the proven radiosensitizing properties of BrdU. Combination of ESR spectroscopy and quantum chemical modelling points to a simple reaction between the uridine-5-yl radical and water molecules that produces the genotoxic hydroxyl radical.
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Affiliation(s)
- Lidia Chomicz
- Department of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Alex Petrovici
- Department of Chemistry, Oakl and University, Rochester, Michigan 48309, USA
| | - Ian Archbold
- Department of Chemistry, Oakl and University, Rochester, Michigan 48309, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakl and University, Rochester, Michigan 48309, USA
| | - Anil Kumar
- Department of Chemistry, Oakl and University, Rochester, Michigan 48309, USA
| | - Michael D. Sevilla
- Department of Chemistry, Oakl and University, Rochester, Michigan 48309, USA
| | - Janusz Rak
- Department of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
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15
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Hashiya F, Saha A, Kizaki S, Li Y, Sugiyama H. Locating the uracil-5-yl radical formed upon photoirradiation of 5-bromouracil-substituted DNA. Nucleic Acids Res 2014; 42:13469-73. [PMID: 25398904 PMCID: PMC4267621 DOI: 10.1093/nar/gku1133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In a previous study, we found that 2-deoxyribonolactone is effectively generated in the specific 5-bromouracil (BrU)-substituted sequence 5′-(G/C)[A]n= 1,2BrUBrU-3′ and proposed that a formed uracil-5-yl radical mainly abstracts the C1′ hydrogen from the 5′-side of BrUBrU under 302-nm irradiation condition. In the present work, we performed photoirradiation of BrU-substituted DNA in the presence of a hydrogen donor, tetrahydrofuran, to quench the uracil-5-yl radical to uracil and then subjected the sample to uracil DNA glycosylase digestion. Slab gel sequence analysis indicated that uracil residues were formed at the hot-spot sequence of 5′-(G/C)[A]n= 1,2BrUBrU-3′ in 302-nm irradiation of BrU-substituted DNA. Furthermore, we found that the uracil residue was also formed at the reverse sequence 5′-BrUBrU[A]n= 1,2(G/C)-3′, which suggests that both 5′-(G/C)[A]n= 1,2BrUBrU-3′ and 5′-BrUBrU[A]n= 1,2(G/C)-3′ are hot-spot sequences for the formation of the uracil-5-yl radical.
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Affiliation(s)
- Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Abhijit Saha
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Seiichiro Kizaki
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yue Li
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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16
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Hou D, Greenberg MM. DNA interstrand cross-linking upon irradiation of aryl halide C-nucleotides. J Org Chem 2014; 79:1877-84. [PMID: 24559326 DOI: 10.1021/jo4028227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
γ-Radiolysis kills cells by damaging DNA via radical processes. Many of the radical pathways are O2 dependent, which results in a reduction in the cytotoxicity of ionizing radiation in hypoxic tumor cells. Consequently, there is a need for chemical agents that increase DNA damage by ionizing radiation under O2-deficient conditions. Modified nucleotides that are incorporated in DNA and produce highly reactive σ-radicals are useful as radiosensitizing agents. Aryl halide C-nucleotides (4-6) were incorporated into oligonucleotides by solid-phase synthesis. Duplex DNA containing 4-6 forms interstrand cross-links upon γ-radiolysis under anaerobic conditions or UV irradiation. Deep Vent (exo(-)) DNA polymerase accepted the nucleotide triphosphate of C-nucleotide 6 as a substrate and preferentially incorporated it opposite pyrimidines, but no further extension was detected. Incorporation of 6 in extended products by Deep Vent (exo(-)) during PCR or by Sequenase during copying of single stranded DNA plasmid was undetectable. Aryl halide nucleotide analogues that produce DNA interstrand cross-links under anaerobic conditions upon irradiation are potentially useful as radiosensitizing agents, but further research is needed to identify molecules that are incorporated by DNA polymerases and do not block further polymerization for this approach to be useful in cells.
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Affiliation(s)
- Dianjie Hou
- Department of Chemistry Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218, United States
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17
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Storoniak P, Rak J, Polska K, Blancafort L. Local Excitation of the 5-Bromouracil Chromophore in DNA. Computational and UV Spectroscopic Studies. J Phys Chem B 2011; 115:4532-7. [DOI: 10.1021/jp201028a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Piotr Storoniak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Janusz Rak
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Katarzyna Polska
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Lluís Blancafort
- Institute of Computational Chemistry, Department of Chemistry, University of Girona, Campus de Montilivi, 17071 Girona, Spain
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Tashiro R, Ohtsuki A, Sugiyama H. The distance between donor and acceptor affects the proportion of C1' and C2' oxidation products of DNA in a BrU-containing excess electron transfer system. J Am Chem Soc 2011; 132:14361-3. [PMID: 20873822 DOI: 10.1021/ja106184w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have investigated the products of (Br)U in excess electron transfer and have demonstrated that in DNA the proportion of products changes with the distance between the donor and acceptor. On the basis of a labeling experiment using H(2)(18)O, we have shown that hole migration from Py(•+) formed after charge separation is involved in the reaction.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
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19
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Wong RS, Sczepanski JT, Greenberg MM. Excision of a lyase-resistant oxidized abasic lesion from DNA. Chem Res Toxicol 2010; 23:766-70. [PMID: 20232790 DOI: 10.1021/tx9003984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The C2'-oxidized abasic lesion (C2-AP) is produced in DNA that is subjected to oxidative stress. The lesion disrupts replication and gives rise to mutations that are dependent upon the identity of the upstream nucleotide. Ape1 incises C2-AP, but the 5'-phosphorylated fragment is not a substrate for the lyase activity of DNA polymerase beta. Excision of the lesion is achieved by strand displacement synthesis in the presence of flap endonuclease during which C2-AP and the 3'-adjacent nucleotide are replaced. The oxidized abasic lesion is also a substrate for the bacterial UvrABC nucleotide excision repair system. These data suggest that the redundant nature of DNA repair systems provides a means for removing a lesion that resists excision by short patch base excision repair.
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Affiliation(s)
- Remus S Wong
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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21
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Schyman P, Eriksson LA, Laaksonen A. Hydrogen Abstraction from Deoxyribose by a Neighboring 3′-Uracil Peroxyl Radical. J Phys Chem B 2009; 113:6574-8. [DOI: 10.1021/jp9007569] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patric Schyman
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden, and Örebro Life Science Center, School of Science and Technology, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden, and Örebro Life Science Center, School of Science and Technology, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
| | - Aatto Laaksonen
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden, and Örebro Life Science Center, School of Science and Technology, Örebro University, Fakultetsgatan 1, 701 82 Örebro, Sweden
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22
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Tashiro R, Sugiyama H. Photochemistry of 5-Bromouracil- or 5-Iodouracil-containing DNA: Probe for DNA Structure and Charge Transfer Along DNA. J SYN ORG CHEM JPN 2009. [DOI: 10.5059/yukigoseikyokaishi.67.1261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ryu Tashiro
- Faculty of Phamaceutical Sciences, Suzuka University of Medical Science
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Sciences, Kyoto University
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23
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Wenska G, Taras-Goslinska K, Filipiak P, Hug GL, Marciniak B. Photochemical reactions of 4-thiouridine disulfide and 4-benzylthiouridine—the involvement of the 4-pyrimidinylthiyl radical. Photochem Photobiol Sci 2008; 7:250-6. [DOI: 10.1039/b713218b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Watanabe T, Tashiro R, Sugiyama H. Photoreaction at 5'-(G/C)AA(Br)UT-3' sequence in duplex DNA: efficient generation of uracil-5-yl radical by charge transfer. J Am Chem Soc 2007; 129:8163-8. [PMID: 17564445 DOI: 10.1021/ja0692736] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoreactivities of 5-halouracil-containing DNA have widely been used for analysis of protein-DNA interactions and have recently been used for probing charge-transfer processes along DNA. Despite such practical usefulness, the detailed mechanisms of the photochemistry of 5-halouracil-containing DNA are not well understood. We recently discovered that photoirradiation of BrU-substituted DNA efficiently produced 2'-deoxyribonolactone at 5'-(G/C)AABrUBrU-3' and 5'-(G/C)ABrUBrU-3' sequences in duplex DNA. Using synthetic oligonucleotides, we found that similar photoreactivities were maintained at the 5'-(G/C)AABrUT-3' sequence, providing ribonolactone as a major product with concomitant release of adenine base. In this paper, the photoreactivities of various oligonucleotides possessing the 5'-BrUT-3' sequence were examined to elucidate the essential factors of this photoreaction. HPLC product analysis indicated that the yield of 2'-deoxyribonolactone largely depends on the ionization potential of the purine derivatives located 5'-upstream of 5'-BrUT-3', as well as the electron-donating ability of their pairing cytosine derivatives. Oligonucleotides that possess G in the complementary strand provided the ribonolactone with almost the same efficiency. These results clearly suggest that the photoinduced charge transfer from the G-5' upstream of 5'-BrUT-3' sequence, in the same strand and the complementary strand, initiates the reaction. To examine the role of intervening A/T base pair(s) between the G/C and the 5'-BrUT-3' sequence, the photoreactivities of a series of oligonucleotides with different numbers of intervening A/T base pairs were examined. The results revealed that the hotspot sequence consists of the electron-donating G/C base pair, the 5'-BrUT-3' sequence as an acceptor, and an appropriate number of A/T base pairs as a bridge for the charge-transfer process.
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Affiliation(s)
- Takayoshi Watanabe
- Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda, Tokyo, Japan
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25
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Abstract
The various conformations of DNA--the A, B, and Z forms, the protein-induced DNA kink, and the G-quartet form--are thought to play important biological roles in processes such as DNA replication, gene expression and regulation, and the repair of DNA damage. The investigation of local DNA conformational changes associated with biological events is therefore essential for understanding the function of DNA. In this Minireview, we discuss the use of photochemical dehalogenation of 5-halouracil-containing DNA to probe the structure of DNA. Hydrogen abstraction by the resultant uracil-5-yl radicals is atom-specific and highly dependent on the structure of the DNA, suggesting that this photochemical approach could be applied as a probe of DNA conformations in living cells.
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Affiliation(s)
- Yan Xu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
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Sugiyama H. Chemical Biology that Controls DNA Structure and Function: Lessons in Organic Chemistry from Nature. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.823] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Abstract
The various conformations of DNA are thought to have important biological roles. Investigation of the local DNA conformational changes associated with biological events is therefore essential to an understanding of the functions of DNA. We have reported the photoreactivities of 5-halouracil in the five characteristic local DNA structures: the A, B and Z forms, protein-induced DNA kinks and the G-quadruplex form. These studies demonstrate the detailed relationships between the local DNA structures and the photochemical products of photoinduced hydrogen abstraction by the resulting uracil-5-yl radicals, and show that this photochemical method can be used to detect DNA structures. Here, we describe in detail procedures that have been developed in our laboratory for probing DNA conformations by product analysis of photoirradiated 5-halouracil-containing DNA. The protocol includes the preparation of 5-halouracil-containing DNA and the characterization of the photoproducts, and it can be completed in 2 weeks.
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Affiliation(s)
- Yan Xu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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28
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Greenberg MM. Elucidating DNA damage and repair processes by independently generating reactive and metastable intermediates. Org Biomol Chem 2006; 5:18-30. [PMID: 17164902 DOI: 10.1039/b612729k] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA damage is a double-edged sword. The modifications produced in the biopolymer are associated with aging, and give rise to a variety of diseases, including cancer. DNA is also the target of anti-tumor agents and the most generally used nonsurgical treatment of cancer, ionizing radiation. Agents that damage DNA produce a variety of radicals. Elucidating the chemistry of individual DNA radicals is challenging due to the availability of multiple reactive pathways and complexities inherent with carrying out mechanistic studies on a heterogeneous polymer. The ability to independently generate radicals and their metastable products at defined sites in DNA has greatly facilitated understanding this biologically important chemistry.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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29
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Kawashima E, Terui Y, Kodama R, Yokozeki K. Highly diastereoselective chemoenzymatic synthesis of (2′R)- and (2′S)-2′-deoxy[2′-2H]guanosines. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.02.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Xu Y, Sugiyama H. Die photochemische Untersuchung verschiedener DNA-Strukturen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200501962] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Ali MM, Hazra TK, Hong D, Kow YW. Action of human endonucleases III and VIII upon DNA-containing tandem dihydrouracil. DNA Repair (Amst) 2005; 4:679-86. [PMID: 15907775 DOI: 10.1016/j.dnarep.2005.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 03/01/2005] [Accepted: 03/02/2005] [Indexed: 02/08/2023]
Abstract
We have shown previously that endonuclease III from Escherichia coli, its yeast homolog Ntg1p and E. coli endonuclease VIII recognize single dihydrouracil (DHU) lesions efficiently. However, these enzymes have limited capacities for completely removing DHU, when the lesion is present on duplex DNA as a tandem lesion. A duplex 30-mer (duplex1920) containing tandem DHU lesions at positions 19 and 20 from the 5' terminus was used as a substrate for human endonuclease III (hNTH) and endonuclease VIII (NEIL1). Two cleavage products, 18beta and 19beta were formed, when duplex1920 was treated with hNTH. The 18beta corresponded to the expected beta-elimination product generated from duplex1920, when the 5'-DHU of the tandem DHU was processed by hNTH. Similarly, 19beta is the beta-elimination product generated, when the 3'-DHU of the tandem DHU was processed by hNTH; 19beta thus still contained a DHU lesion at the 3' terminus. When these hNTH reaction products were further treated with human APE1, a single new product that corresponded to an 18mer was observed. These data suggested that human APE1 can help to process the 3' terminals following the action of hNTH on DHU lesions. Similarly, when duplex1920 was treated with NEIL1, two cleavage products, 18p and 19p were observed. The 18p and 19p corresponded to the expected beta,delta-elimination products derived from NEIL1 induced cleavage at the 5'-DHU and 3'-DHU of the tandem DHU, respectively. The 3'-phosphoryl group present in 18p can be readily removed by T4 polynucleotide kinase (PNK) to yield an 18mer that is suitable for repair synthesis. However, 19p required the participation of both PNK and APE1 to generate the 18mer. Together, we suggest that the processing of DNA-containing tandem DHU lesions, initiated by hNTH and NEIL1 can be channeled into two sub-pathways, the PNK-independent, APE1-dependent and the PNK, APE1-dependent pathways, respectively.
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Affiliation(s)
- Mohsin M Ali
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
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32
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Tashiro R, Sugiyama H. Unique charge transfer properties of the four-base pi-stacks in Z-DNA. J Am Chem Soc 2004; 125:15282-3. [PMID: 14664559 DOI: 10.1021/ja0380291] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To investigate the photoreactions of BrU in Z-DNA, the photoirradiation of 5'-d(C1G2C3G4BrU5G6C7G8)-3'/5'-d(C9mG10C11A12C13mG14C15G16)-3'(ODN 1-2) was investigated. In accord with previous observations, B-form ODN 1-2 with the 5'-GBrU sequence showed very weak photoreactivity. However, Z-form ODN 1-2 in 2 M NaCl underwent photoreaction to afford 5'-d(CGC)rGd(UGCG)-3' together with the formation of imidazolone (Iz) contained 5'-d(CIzCACmGCG)-3'. The results clearly indicate that structural changes caused by the B-Z transition dramatically increased the photoreactivity of ODN 1-2. Inspection of the molecular structure of Z-DNA suggests that there is unique four-base pi-stacks at the G4-BrU5-C11-mG10 in ODN 1-2. These results suggest that the intriguing possibility that the mG10 in a complementary strand located at the end of the four-base pi-stacks may act as an electron donor. To test the hypothesis of interstrand charge transfer from mG10 to BrU5 within the four-base pi-stacks in Z-DNA, ODN 1-3 samples in which the putative donor G10 residue was replaced with 8-methoxyguanine (moG) were prepared, since moG is known to trap cation radicals to yield Iz moieties in DNA. Photoirradiation of ODN 1-3 efficiently produced 5'-d(CGC)rGd(UGCG)-3' together with formation of 5'-d(CIzCACmGCG)-3'. These results clearly indicate that the interstrand charge transfer from mG10 to BrU5 initiates the photoreaction. In clear contrast, other replacements of G with moG did not enhance the photoreactivity. The present study revealed the presence of unique four-base pi-stacks in Z-DNA and photoirradition of BrU in Z-DNA causes efficient electron transfer from G within this cluster.
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Affiliation(s)
- Ryu Tashiro
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda, Tokyo 101-0062, Japan
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33
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Oyoshi T, Kawai K, Sugiyama H. Efficient C2'alpha-hydroxylation of deoxyribose in protein-induced Z-form DNA. J Am Chem Soc 2003; 125:1526-31. [PMID: 12568612 DOI: 10.1021/ja028388g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA local conformations are thought to play an important biological role in processes such as gene expression by altering DNA-protein interactions. Although left-handed Z-form DNA is one of the best-characterized and significant local structures of DNA, having been extensively investigated for more than two decades, the biological relevance of Z-form DNA remains unclear. This is presumably due to the lack of a versatile detection method in a living cell. Previously, we demonstrated that the incorporation of a methyl group at the guanine C8 position (m(8)G) dramatically stabilizes the Z-form of short oligonucleotides in a variety of sequences. To develop a photochemical method to detect Z-form DNA, we examined the photoreaction of 5-iodouracil-containing Z-form d(CGCG(I)UGCG)(ODN 1)/d(Cm(8)GCAm(8)GCG)(ODN 2) in 2 M NaCl and found stereospecific C2'alpha-hydroxylation occurred at G(4) to provide d(CGCrGUGCG), 5. Recently, Rich and co-workers [Schwartz et al. Science 1999, 284, 1841. Schwartz et al. Nat. Struct. Biol. 2001, 8, 761] found that an ubiquitous RNA editing enzyme, adenosine deaminase 1 (ADAR1), and tumor-associated protein DML-1 specifically bind to Z-form DNA. In the present study, we investigate the photoreactivity of octanucleotide ODN 1-2 in Z-form induced by Zalpha, which is the NH(2)-terminal domain of ADAR1 responsible for tight binding of ADAR1. Detailed product analysis revealed that the C2'alpha-hydroxylated products 5 and 6 produced significantly higher yields in Z-form ODN 1-2 induced by Zalpha compared with that in 2 M NaCl. Upon treatment with ribonuclease T1, 5 and 6 were quantitatively hydrolyzed at the 3'-phosphodiester bond of the rG residue to provide d(UGCG) as a common hydrolyzed fragment on the 3' side. Quantitative analysis demonstrated that the amount of photochemically formed 5 and 6 from ODN 1-2 directly correlated with the proportion of Z-form induced by Zalpha or NaCl. These results suggest that this photochemical and enzymatic procedure can be used as a specific probe for the existence of local Z-form structure in cellular DNA.
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Affiliation(s)
- Takanori Oyoshi
- Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda, Tokyo 101-0062, Japan
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Wojcik A, von Sonntag C, Obe G. Application of the biotin-dUTP chromosome labelling technique to study the role of 5-bromo-2'-deoxyuridine in the formation of UV-induced sister chromatid exchanges in CHO cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2003; 69:139-44. [PMID: 12633986 DOI: 10.1016/s1011-1344(02)00415-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The role of 5-bromo-2'-deoxyuridine (BrdU) in the formation of sister chromatid exchanges (SCEs) in cells exposed to UV radiation was studied. Cells were unifilarily labelled (labelling of one strand of chromosomal DNA) with BrdU or biotin-16-2'-deoxyuridine (biotin-dU) and irradiated in G(1) phase of the cell cycle either with 254 nm, which is absorbed by all nucleobases including bromouracil (BrU) or with 313 nm radiation, which is predominantly absorbed by the BrU moiety. Elevated SCE frequencies were observed in cells irradiated at 254 nm (1.2 and 3.0 J m(-2)) which were pre-labelled with BrdU or biotin-dU. Following irradiation at 313 nm (38 and 96 J m(-2)) a statistically elevated SCE frequency was observed in cells pre-labelled with BrdU but not with biotin-dU. In cells pre-labelled with BrdU, UV-radiation at 254 nm was 50-80 times more effective in inducing SCEs than that at 313 nm. This result can be accounted for by the fact that in BrdU-DNA the cross-section for uracilyl radical and bromine atom formation is approximately 100-fold higher at 254 nm than that at 313 nm. Upon irradiation at 254 nm, BrdU had a strong sensitising effect on SCE induction: the SCE frequencies observed in cells pre-labelled with BrdU are approximately 6 times higher than in cells pre-labelled with biotin-dU. From this it follows that BrdU-induced damage is responsible for more than 80% of the SCEs formed in UV irradiated cells unifilarily labelled with BrdU. Based on photochemical considerations and the fact that chemical agents which form DNA interstrand cross-links are among the most potent inducers of SCEs, we propose that an interstrand cross-link may be the major lesion leading to SCEs in BrdU-labelled cells.
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Affiliation(s)
- Andrzej Wojcik
- Institute of Nuclear Chemistry and Technology, 03-195 Warszawa, Poland.
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Oyoshi T, Wang AHJ, Sugiyama H. Photoreactivity of 5-iodouracil-containing DNA-Sso7d complex in solution: the protein-induced DNA kink causes intrastrand hydrogen abstraction from the 5-methyl of thymine at the 5' side. J Am Chem Soc 2002; 124:2086-7. [PMID: 11878941 DOI: 10.1021/ja016968s] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoirradiation of 5-iodouracil-containing DNA, d(GTAAT(I)UAC)(2) with Sso7d protein, possessing significant kink in DNA in the crystal structure induces an unprecedented intrastrand H abstraction at the methyl group of T(5), together with selective photooxidations at Met29 of Sso7d. The reactivity of the deoxyuridin-5-yl radical can be explained by the crystal structure of the d(GTAATTAC)(2)-Sso7d complex, suggesting that the interaction of DNA-Sso7d in solution is substantially similar to its crystal structure.
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Affiliation(s)
- Takanori Oyoshi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda, Tokyo 101-0062, Japan
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36
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Fujimoto K, Ikeda Y, Ishihara S, Saito I. Deoxyribonolactone formation in photoirradiation of 5-bromouracil-containing oligonucleotides by direct C1′ hydrogen abstraction. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00231-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chen T, Cook GP, Koppisch AT, Greenberg MM. Investigation of the Origin of the Sequence Selectivity for the 5-Halo-2‘-deoxyuridine Sensitization of DNA to Damage by UV-Irradiation. J Am Chem Soc 2000. [DOI: 10.1021/ja994357i] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tongqian Chen
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Gary P. Cook
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Andrew T. Koppisch
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Marc M. Greenberg
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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Cook GP, Chen T, Koppisch AT, Greenberg MM. The effects of secondary structure and O2 on the formation of direct strand breaks upon UV irradiation of 5-bromodeoxyuridine-containing oligonucleotides. CHEMISTRY & BIOLOGY 1999; 6:451-9. [PMID: 10381405 DOI: 10.1016/s1074-5521(99)80063-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND 5-Bromodeoxyuridine is a radiosensitizing agent that is currently being evaluated in clinical trials as an adjuvant in the treatment of a variety of cancers. gamma-Radiolysis and UV irradiation of oligonucleotides containing 5-bromodeoxyuridine result in the formation of direct strand breaks at the 5'-adjacent nucleotide by oxidation of the respective deoxyribose. We investigated the effects of DNA secondary structure and O2 on the induction of direct strand breaks in 5-bromodeoxyuridine-containing oligonucleotides. RESULTS The efficiency of direct strand break formation in duplex DNA is dependent upon O2 and results in fragments containing 3'-phosphate and the labile 3'-ketodeoxyadenosine termini. The ratio of the 3'-termini is also dependent upon O2 and structure. Deuterium product isotope effects and tritium-transfer studies indicate that hydrogen-atom abstraction from the C1'- and C2'-positions occurs in an O2- and structure-dependent manner. CONCLUSIONS The reaction mechanisms by which DNA containing 5-bromodeoxyuridine is sensitized to damage by UV irradiation are dependent upon whether the substrate is hybridized and upon the presence or absence of O2. Oxygen reduces the efficiency of direct strand break formation in duplex DNA, but does not affect the overall strand damage. It is proposed that the sigma radical abstracts hydrogen atoms from the C1'- and C2'-positions of the 5'-adjacent deoxyribose moiety, whereas the nucleobase peroxyl radical selectively abstracts the C1'-hydrogen atom from this site. This is the second example of DNA damage amplification by a nucleobase peroxyl radical, and might be indicative of a general reaction pattern for this family of reactive intermediates.
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Affiliation(s)
- G P Cook
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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39
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Kawai K, Saito I, Kawashima E, Ishido Y, Sugiyama H. Intrastrand 2′β hydrogen abstraction of 5′-adjacent deoxyguanosine by deoxyuridin-5-yl in Z-form DNA. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)00254-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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40
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Kawai K, Saito I, Sugiyama H. Conformation-Dependent Photochemistry of 5-Halouracil-Containing DNA: Stereospecific 2‘α-Hydroxylation of Deoxyribose in Z-form DNA. J Am Chem Soc 1999. [DOI: 10.1021/ja9827200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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42
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Pogozelski WK, Tullius TD. Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety. Chem Rev 1998; 98:1089-1108. [PMID: 11848926 DOI: 10.1021/cr960437i] [Citation(s) in RCA: 841] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wendy Knapp Pogozelski
- Department of Chemistry, State University of New York at Geneseo, Geneseo, New York 14454, and Department of Chemistry, Boston University, Boston, Massachusetts 02215
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Fujimoto K, Sugiyama H, Saito I. Sequence dependent photoreduction of 5-bromouracil-contaning oligonucleotides via electron transfer. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00079-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Beckwith ALJ, Crich D, Duggan PJ, Yao Q. Chemistry of beta-(Acyloxy)alkyl and beta-(Phosphatoxy)alkyl Radicals and Related Species: Radical and Radical Ionic Migrations and Fragmentations of Carbonminus signOxygen Bonds. Chem Rev 1997; 97:3273-3312. [PMID: 11851491 DOI: 10.1021/cr950207o] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Athelstan L. J. Beckwith
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia, Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, and Department of Chemistry, Monash University, Clayton, Victoria 3168, Australia
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Sugiyama H, Fujimoto K, Saito I. Preferential C1′ Hydrogen Abstraction by a Uracilyl Radical in a DNA-RNA Hybrid. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)10108-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Cook GP, Greenberg MM. A Novel Mechanism for the Formation of Direct Strand Breaks upon Anaerobic Photolysis of Duplex DNA Containing 5-Bromodeoxyuridine. J Am Chem Soc 1996. [DOI: 10.1021/ja960652g] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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