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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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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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Zdrowowicz M, Michalska B, Zylicz-Stachula A, Rak J. Photoinduced single strand breaks and intrastrand cross-links in an oligonucleotide labeled with 5-bromouracil. J Phys Chem B 2014; 118:5009-16. [PMID: 24766391 DOI: 10.1021/jp500192z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Bromouracil (BrU) is photoreactive toward near UVB photons and can be introduced into genomic DNA during its biosynthesis in cells. However, PCR seems to be a simpler approach, which can be used to obtain labeled DNA similar to that synthesized within the cell. In the current work, PCR has been employed and optimized in order to substitute all thymines (besides those present in starters) with BrU in the dsDNA fragment of 80 base pairs (bp) in length. The modified oligonucleotide was irradiated with 300 nm photons in a buffered aqueous solution (pH = 7) and digested with a cocktail of enzymes specific to the phosphodiester bond cleavage. Initially, the extent of damage in the intact photolyte was measured with DHPLC. Then, the digested reaction mixture was subjected to HPLC and MS analyses and, in addition to the formation of 5-bromo-2'-deoxuyridine, which proves the occurrence of single strand breaks (SSBs) due to irradiation, U∧U and U∧C dimers were found, whose molecular structure was confirmed by MS/MS analysis. Although the abundance of such tandem lesions is lower than that of the SSB type, they pose a potent threat to genome integrity. Thus, our findings shed new light on the photosensitizing properties of BrU toward DNA.
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Affiliation(s)
- Magdalena Zdrowowicz
- Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-308 Gdańsk, Poland
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Wiczk J, Miloch J, Rak J. DHPLC and MS studies of a photoinduced intrastrand cross-link in DNA labeled with 5-bromo-2'-deoxyuridine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 130:86-92. [PMID: 24300995 DOI: 10.1016/j.jphotobiol.2013.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/29/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
Abstract
It is well known that the replacement of thymidine with 5-bromo-2'-deoxyuridine (BrdU) in DNA sensitizes it to UVB light. Irradiation of a biopolymer substituted in such a way leads to manifold kinds of DNA damage, such as intrastrand cross-links, single- and double-strand breaks or alkali-labile sites that were studied in the past with a broad spectrum of analytical methods. Here, we demonstrate that completely denaturing high-performance liquid chromatography (DHPLC), underestimated so far in DNA damage studies, could act as an inexpensive, and high-resolution substitute for the commonly employed gel electrophoresis. We report on the DHPLC/mass spectrometry (MS) analyses of photolytes obtained with the UV irradiation of aqueous solutions containing 40 base pairs of a long, double-stranded oligonucleotide labeled with BrdU in one of its strands. The UV-product was detected by HPLC at a temperature of 70°C. Subsequent MS analysis with electrospray ionization (ESI-MS) of the photolyte, enzymatic digestion of the irradiated material and HPLC and MS analysis (LC-MS) of the digest demonstrated unequivocally that an intrastrand covalent dimer, involving adenine and uracil, is formed in the irradiated system.
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Affiliation(s)
- Justyna Wiczk
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Justyna Miloch
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Janusz Rak
- Department of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
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Lepczyńska J, Komodziński K, Milecki J, Kierzek R, Gdaniec Z, Franzen S, Skalski B. Photoaddition of 5-bromouracil to uracil in oligonucleotides leading to 5,5'-bipyrimidine-type adducts: mechanism of the photoreaction. J Org Chem 2012. [PMID: 23186224 DOI: 10.1021/jo3021067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Bromouracil ((Br)U) modified di- and hexanucleotides having (Br)U flanked on the 5' or the 3' side by uracil (U) have been synthesized, and their photochemical reactivity was examined under the conditions of irradiation with near UV light. The results indicate that the primary photochemical process in all of these compounds involves the formation of an intermediate cyclobutane phodoadduct composed of (Br)U and U, which undergoes further photochemically and thermally induced transformations to 5,5'-bipyrimidine type adducts.
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Affiliation(s)
- Jolanta Lepczyńska
- Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
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Ito T, Hamaguchi Y, Tanabe K, Yamada H, Nishimoto SI. Transporting Excess Electrons along Potential Energy Gradients Provided by 2′-Deoxyuridine Derivatives in DNA. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ito T, Hamaguchi Y, Tanabe K, Yamada H, Nishimoto SI. Transporting Excess Electrons along Potential Energy Gradients Provided by 2′-Deoxyuridine Derivatives in DNA. Angew Chem Int Ed Engl 2012; 51:7558-61. [DOI: 10.1002/anie.201202141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Indexed: 01/08/2023]
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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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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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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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Ito T, Kondo A, Terada S, Nishimoto SI. Photoinduced reductive repair of thymine glycol: implications for excess electron transfer through DNA containing modified bases. J Am Chem Soc 2007; 128:10934-42. [PMID: 16910690 DOI: 10.1021/ja061304+] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced reduction of thymine glycol in oligodeoxynucleotides was investigated using either a reduced form of flavin adenine dinucleotide (FADH(-)) as an intermolecular electron donor or covalently linked phenothiazine (PTZ) as an intramolecular electron donor. Intermolecular electron donation from photoexcited flavin (FADH(-)) to free thymidine glycol generated thymidine in high yield, along with a small amount of 6-hydroxy-5,6-dihydrothymidine. In the case of photoreduction of 4-mer long single-stranded oligodeoxynucleotides containing thymine glycol by *FADH(-), the restoration yield of thymine was varied depending on the sequence of oligodeoxynucleotides. Time-resolved spectroscopic study on the photoreduction by laser-excited N,N-dimethylaniline (DMA) suggested elimination of a hydroxyl ion from the radical anion of thymidine glycol with a rate constant of approximately 10(4) s(-1) generates 6-hydroxy-5,6-dihydrothymidine (6-HOT(*)) as a key intermediate, followed by further reduction of 6-HOT(*) to thymidine or 6-hydroxy-5,6-dihydrothymdine (6-HOT). On the other hand, an excess electron injected into double-stranded DNA containing thymine glycol was not trapped at the lesion but was further transported along the duplex. Considering redox properties of the nucleobases and PTZ, competitive excess electron trapping at pyrimidine bases (thymine, T and cytosine, C) which leads to protonation of the radical anion (T(-)(*), C(-)(*)) or rapid back electron transfer to the radical cation of PTZ (PTZ(+)(*)), is presumably faster than elimination of the hydroxyl ion from the radical anion of thymine glycol in DNA.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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Koch TH, Smith D, Tabacman E, Zichi DA. Kinetic analysis of site-specific photoaptamer-protein cross-linking. J Mol Biol 2004; 336:1159-73. [PMID: 15037076 DOI: 10.1016/j.jmb.2004.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 12/29/2003] [Accepted: 01/05/2004] [Indexed: 10/26/2022]
Abstract
ssDNA oligonucleotides containing bromodeoxyuridine, BrdU-photoaptamers, are rapidly emerging as specific protein capture reagents in protein microarray technologies. A mathematical model for the kinetic analysis of photoaptamer-protein photocross-linking reactions is presented. The model is based on specific aptamer/protein binding followed by laser excitation that can lead to either covalent cross-linking of the photoaptamer and protein in the complex or irreversible photodamage to the aptamer. Two distinct kinetic regimes, (1) frozen and (2) rapid equilibrium, are developed analytically to model binding kinetics between laser pulses. The models are used to characterize the photocross-linking between three photoaptamers and their cognate protein targets; photoaptamers 0650 and 0615 cross-link human basic fibroblast growth factor and 0518 cross-links HIV MN envelope glycoprotein. Data for cross-linking reaction yields as a function of both laser energy dose and target protein concentration are analyzed for affinity constants and cross-link reaction rates. The binding dissociation constants derived from the cross-linking data are in good accord with independent measurements; the rapid equilibrium model appears to produce results more consistent with the experimental observations, although there is significant overlap between the two models for most conditions explored here. The rate of photodamage for 0615 and 0518 is 3.5 and 2.5 times that of the specific cross-link, giving low maximum reaction yields of approximately 20% and approximately 30%, whereas 0650 cross-links with a rate over five times higher than its photodamage rate and has a maximum reaction yield exceeding 80%. Quantum yields for the three systems are estimated from the data; photoaptamer 0650 has a reasonably high quantum yield of approximately 0.2 for protein cross-linking, while 0518 and 0615 have quantum yields of 0.07 and 0.02. The work presented here provides a useful set of metrics that allow for refinement of photoaptamer properties.
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Affiliation(s)
- Tad H Koch
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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