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Wityk P, Zdrowowicz M, Wiczk J, Rak J. UV-induced electron transfer between triethylamine and 5-bromo-2'-deoxyuridine. A puzzle concerning the photochemical debromination of labeled DNA. J Pharm Biomed Anal 2017; 142:262-269. [PMID: 28528145 DOI: 10.1016/j.jpba.2017.04.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/14/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
Abstract
5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding in the labeled DNA is dramatically changed due to the photoinduced electron transfer (PET) between the photoexcited BrdU and the ground state TEA. For the first time, we demonstrated that the latter process produces 2'-deoxyuridne2'-deoxyuridine (debromination) in the labeled DNA instead of the expected strand break. PET between TEA and BrdU was additionally confirmed by the UV irradiations of aqueous solutions containing both species. Indeed, the efficient formation of 2'-deoxyuridine was observed in the studied photolytes. Moreover, we showed the formation of an additional product in these binary mixtures, i.e. imidazole derivative, that is not formed in DNA and was reported in the literature in the context of dark rather than photochemical processes. Using mass spectrometry we demonstrated that the amount of TEA impurity in the commercial samples of oligos exceeds up to 3 orders of magnitude that of the purchased DNA.
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Affiliation(s)
- Paweł Wityk
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Magdalena Zdrowowicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Justyna Wiczk
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.
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Dai X, Song D, Liu K, Su H. Photoinduced C—I bond homolysis of 5-iodouracil: A singlet predissociation pathway. J Chem Phys 2017; 146:025103. [DOI: 10.1063/1.4973650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Xiaojuan Dai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kunhui Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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3
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Zdrowowicz M, Chomicz L, Miloch J, Wiczk J, Rak J, Kciuk G, Bobrowski K. Reactivity pattern of bromonucleosides induced by 2-hydroxypropyl radicals: photochemical, radiation chemical, and computational studies. J Phys Chem B 2015; 119:6545-54. [PMID: 25971814 DOI: 10.1021/acs.jpcb.5b01904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bromonucleosides (BrdX's) 5-bromo-2'-deoxyuridine (BrdU), 5-bromo-2'-deoxycytidine (BrdC), 8-bromo-2'-deoxyadenosine (BrdA), and 5-bromo-2'-deoxyguanosine (BrdG) may substitute for ordinary nucleosides in DNA. As indicated by electron-stimulated desorption experiments, such a modified biopolymer is greater than 2-3-fold more sensitive to damage induced by excess electrons. The other major product of water radiolysis, the (•)OH radical, may form a number of other radicals in chemical reactions with the complex content of the cell. Thus, the well-proved BrdU-labeled DNA radiosensitivity may be, at least in part, related to secondary organic radicals. Therefore, in the current study, the propensity of BrdX's to damage induced by 2-hydroxypropyl radical (OHisop(•))-a prototype radical species-was investigated. The HPLC and LC-MS analyses revealed the formation of two major products from the brominated pyrimidine nucleosides, a native nucleoside and an adduct of BrdX and OHisop(•) , and only an adduct of BrdX from the bromopurine nucleosides. Quantum chemical calculations ascribed this evident difference between purines and pyrimidines to the electron transfer from OHisop(•) to BrdX that is especially favorable in pyrimidines.
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Affiliation(s)
- Magdalena Zdrowowicz
- †Faculty of Chemistry, University of Gdañsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Lidia Chomicz
- †Faculty of Chemistry, University of Gdañsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Justyna Miloch
- †Faculty of Chemistry, University of Gdañsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Justyna Wiczk
- †Faculty of Chemistry, University of Gdañsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Janusz Rak
- †Faculty of Chemistry, University of Gdañsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Gabriel Kciuk
- ‡Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Krzysztof Bobrowski
- ‡Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, 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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Reductive dehalogenation of 5-bromouracil by aliphatic organic radicals in aqueous solutions; electron transfer and proton-coupled electron transfer mechanisms. Radiat Phys Chem Oxf Engl 1993 2011. [DOI: 10.1016/j.radphyschem.2011.02.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Polska K, Zielonka J, Chomicz L, Czerwicka M, Stepnowski P, Guzow K, Wiczk W, Smużyńska M, Kasprzykowski F, Żylicz-Stachula A, Skowron P, Rak J. Unexpected photoproduct generated via the acetone-sensitized photolysis of 5-bromo-2'-deoxyuridine in a water/isopropanol solution: experimental and computational studies. J Phys Chem B 2010; 114:16902-7. [PMID: 21117683 DOI: 10.1021/jp1071499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The acetone-sensitized photolysis of 5-bromo-2'-deoxyuridine (5-BrdU) in a water/isopropanol solution with 300 nm photons leads to the formation of 2'-deoxyuridine (dU) and a comparable amount of another photoproduct that has not been reported in the literature so far. The negative and positive mass spectra recorded for this species indicate that they originate from the molecular mass of 286 Da, which corresponds to an adduct of 2'-deoxyuridine and 2-propanol. Quantum chemical calculations carried out at the DFT and TDDFT levels reveal both the structure and the UV spectrum of that adduct. The latter computational characteristic matches well the experimental UV spectrum of the new photoproduct. Our findings indicate that the acetone-sensitized photolysis of 5-BrdU is more complicated than has hitherto been assumed. Nevertheless, since electron transfer is one of the pathways responsible for 5-BrdU decay, acetone-sensitized photolysis of the halogen derivatives of nucleobases could be a convenient tool for studying their radiosensitivity in aqueous solutions.
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Affiliation(s)
- Katarzyna Polska
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Gruen H, Görner H. Reduction of the polynuclear quinonoid dyes 16,17-dihydroxy- and dimethoxyviolanthrone with photogenerated radicals. Photochem Photobiol Sci 2009; 8:1164-71. [DOI: 10.1039/b907913k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bose A, Basu S. Laser Flash Photolysis and Magnetic Field Effect Studies on the Interaction of Uracil and Its Derivatives with Menadione and 9,10-Anthraquinone. J Phys Chem A 2008; 112:12045-53. [DOI: 10.1021/jp805632j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adity Bose
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata−700 064, India
| | - Samita Basu
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata−700 064, India
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Norris CL, Meisenheimer KM, Koch TH. Mechanistic Studies Relevant to Bromouridine-Enhanced Nucleoprotein Photocrosslinking: Possible Involvement of an Excited Tyrosine Residue of the Protein. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1997.tb08546.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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