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Tashiro R, Yum JH, Park S, Sugiyama H. Photo-Cross-Linking between Br U and Pyrene Residues in an RNA/DNA Hybrid. Chembiochem 2022; 23:e202100626. [PMID: 35080796 PMCID: PMC10036131 DOI: 10.1002/cbic.202100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/13/2022] [Indexed: 11/11/2022]
Abstract
In this study, we investigated the photoreaction of Br U in a pyrene-labeled DNA duplex, RNA duplex, and DNA/RNA hybrids. We found that the photoreactivity of Br U changed dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when Br U was incorporated into the RNA strand and the pyrene was conjugated to the 5' end of the DNA. These results indicate that the contact manner of pyrene was different between A- and B-form duplexes. This is a rare example of the use of the reactivity of bromouracil to analyze the contact between a small molecule with a weak binding affinity and a nucleic acid.
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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
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Soyoung Park
- Immunology Research Frontier Center (iFReC), Osaka University, Immunology Frontier Research Center, 3-1 Yamadaoka, Suita, 565-0871, Japan
- Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, 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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Wityk P, Kostrzewa-Nowak D, Krawczyk B, Michalik M, Nowak R. X-ray and UV Radiation Damage of dsDNA/Protein Complexes. Molecules 2021; 26:molecules26113132. [PMID: 34073894 PMCID: PMC8197241 DOI: 10.3390/molecules26113132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 01/15/2023] Open
Abstract
Simple Summary One of the most common diseases in the world is cancer. The development of an appropriate treatment pathway for cancer patients seems to be crucial to fight this disease. Therefore, solving the problem that affects more and more people in an aging society is crucial. The study presents the results of radiation and photochemical damage to DNA interacting with proteins (specifically/non-specifically). The obtained results of the analysis of photoliths and radiolites by means of the LC-MS technique allowed to identify possible mechanisms of degradation of DNA interacting with proteins. Results suggest the protective action of protein against hydroxyl radicals or solvated electrons and increased damaging effect when sensitized DNA is irradiated by UV light (280 or 320 nm) compared to the DNA alone (without protein interaction). Abstract Radiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g., buffered solutions of dsDNA or sensitizers alone. To fully understand the sensitization processes and to be able to develop new efficient sensitizers in the future, well established model systems are necessary. In the cell environment, DNA tightly interacts with proteins and incorporating this interaction is necessary to fully understand the DNA sensitization process. In this work, we used dsDNA/protein complexes labeled with photo- and radiosensitizers and investigated degradation pathways using LC-MS and HPLC after X-ray or UV radiation.
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Affiliation(s)
- Paweł Wityk
- Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Al. Gen. J. Halera 107, 80-416 Gdańsk, Poland
- Correspondence:
| | - Dorota Kostrzewa-Nowak
- Centre for Human Structural and Functional Research, Institute of Physical Culture Sciences, University of Szczecin, 17C Narutowicza St., 70-240 Szczecin, Poland; (D.K.-N.); (R.N.)
| | - Beata Krawczyk
- Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
| | | | - Robert Nowak
- Centre for Human Structural and Functional Research, Institute of Physical Culture Sciences, University of Szczecin, 17C Narutowicza St., 70-240 Szczecin, Poland; (D.K.-N.); (R.N.)
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3
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Zhou S, Cai Y, Liu X, Jin L, Wang X, Ma W, Zhang T. Role of H2B mono-ubiquitination in the initiation and progression of cancer. Bull Cancer 2021; 108:385-398. [PMID: 33685627 DOI: 10.1016/j.bulcan.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023]
Abstract
Numerous epigenetic alterations are observed in cancer cells, and dysregulation of mono-ubiquitination of histone H2B (H2Bub1) has often been linked to tumorigenesis. H2Bub1 is a dynamic post-translational histone modification associated with transcriptional elongation and DNA damage response. Histone H2B monoubiquitination occurs in the site of lysine 120, written predominantly by E3 ubiquitin ligases RNF20/RNF40 and deubiquitinated by ubiquitin specific peptidase 22 (USP22). RNF20/40 is often altered in the primary tumors including colorectal cancer, breast cancer, ovarian cancer, prostate cancer, and lung cancer, and the loss of H2Bub1 is usually associated with poor prognosis in tumor patients. The purpose of this review is to summarize the current knowledge of H2Bub1 in transcription, DNA damage response and primary tumors. This review also provides novel options for exploiting the potential therapeutic target H2Bub1 in personalized cancer therapy.
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Affiliation(s)
- Sa Zhou
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Yuqiao Cai
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Xinyi Liu
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Lijun Jin
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Xiaoqin Wang
- Beijing University of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing 102206, PR China
| | - Wenjian Ma
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China; Qilu Institute of Technology, Shandong 250200, PR China.
| | - Tongcun Zhang
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China; Wuhan University of Science and Technology, Institute of Biology and Medicine, Wuhan 430081, PR China.
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4
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Fujimoto K, Ishida K, Xue L, Nakamura S. Effect of linker length on photo-cross-linking position mediated by click chemistry via [2 + 2] photocycloaddition†. Photochem Photobiol Sci 2020; 19:776-782. [PMID: 33856676 DOI: 10.1039/d0pp00098a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/12/2020] [Indexed: 12/28/2022]
Abstract
Ultrafast reversible DNA/RNA photo-cross-linking is a powerful tool for regulating the target strand in living cells. In particular, 3-cyanovinylcarbazole (CNVK) and 3-cyanovinylcarbazole modified by D-threoninol (CNVD) can photo-cross-link to pyrimidine bases within a few seconds of photoirradiation. However, these photo-cross-linkers can only cross-link to the counter base if it is adjacent to the 5'-side (-1 position). In this study, we synthesized novel photo-cross-linkers with varying linker lengths capable of photo-cross-linking with pyrimidine bases at locations other than the -1 position via click chemistry. The photo-cross-linking site was dependent on linker length.
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Affiliation(s)
- Kenzo Fujimoto
- School of advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan.
| | - Kenta Ishida
- School of advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Li Xue
- School of advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- School of advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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5
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Wang S, Ding J, Liu P, Xie S, Xie D, Zhang M, Cheng F. Theoretical studies on the purine radical induced purine-purine type intrastrand cross-links. Org Biomol Chem 2019; 17:892-897. [PMID: 30629064 DOI: 10.1039/c8ob02882f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
At the density functional theory (DFT) level, addition reactions between the guanine-8-yl radical and its 3'/5' neighboring purine deoxynucleosides forming the purine-purine type intrastrand cross-links were studied. It is found that addition of the guanine-8-yl radical to the C8 site of its 5' neighboring deoxyguanosine or deoxyadenosine is a two-step reaction consisting of a structurally relatively unfavourable conformational transformation step, while the corresponding 3' C8 addition is straightforward and kinetically more efficient. The 3' C8 preference of the guanine-8-yl radical additions indicates the existence of an obvious sequence effect, which is completely opposite to that observed in the formation of pyrimidine radicals induced DNA intrastrand cross-links. The detrimental effects from steric hindrance and stabilizing weak interactions make these addition reactions markedly suppressed in double stranded DNA. This work broadens our knowledge about the possible types of DNA intrastrand cross-links.
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Affiliation(s)
- Shoushan Wang
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials, School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan 523808, People's Republic of China.
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6
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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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7
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Saha A, Bombard S, Granzhan A, Teulade-Fichou MP. Probing of G-Quadruplex Structures via Ligand-Sensitized Photochemical Reactions in BrU-Substituted DNA. Sci Rep 2018; 8:15814. [PMID: 30361545 PMCID: PMC6202380 DOI: 10.1038/s41598-018-34141-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/12/2018] [Indexed: 01/18/2023] Open
Abstract
We studied photochemical reactions of BrU-substituted G-quadruplex (G4) DNA substrates with two pyrene-substituted polyazamacrocyclic ligands, M-1PY and M-2PY. Both ligands bind to and stabilize G4-DNA structures without altering their folding topology, as demonstrated by FRET-melting experiments, fluorimetric titrations and CD spectroscopy. Notably, the bis-pyrene derivative (M-2PY) behaves as a significantly more affine and selective G4 ligand, compared with its mono-pyrene counterpart (M-1PY) and control compounds. Upon short UVA irradiation (365 nm) both ligands, in particular M-2PY, efficiently sensitize photoreactions at BrU residues incorporated in G4 structures and give rise to two kinds of photoproducts, namely DNA strand cleavage and covalent ligand-DNA photoadducts. Remarkably, the photoinduced strand cleavage is observed exclusively with G4 structures presenting BrU residues in lateral or diagonal loops, but not with parallel G4-DNA structures presenting only propeller loops. In contrast, the formation of fluorescent photoadducts is observed with all BrU-substituted G4-DNA substrates, with M-2PY giving significantly higher yields (up to 27%) than M-1PY. Both ligand-sensitized photoreactions are specific to BrU-modified G4-DNA structures with respect to double-stranded or stem-loop substrates. Thus, ligand-sensitized photoreactions with BrU-substituted G4-DNA may be exploited (i) as a photochemical probe, allowing "photofootprinting" of G4 folding topologies in vitro and (ii) for covalent trapping of G4 structures as photoadducts with pyrene-substituted ligands.
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Affiliation(s)
- Abhijit Saha
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France. .,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France. .,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France.
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8
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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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9
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Wang S, Zhang M, Liu P, Xie S, Cheng F, Wang L. DNA intrastrand cross-links induced by the purine-type deoxyguanosine-8-yl radical: a DFT study. Phys Chem Chem Phys 2018; 19:16621-16628. [PMID: 28617503 DOI: 10.1039/c7cp02725g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Currently, all known DNA intrastrand cross-links are found to be induced by pyrimidine-type radicals; however, whether or not purine-type radicals are able to cause DNA intrastrand cross-links remains unclear. In the present study, probable additions of the highly reactive deoxyguanosine-8-yl radical to its 3'/5' neighboring pyrimidine nucleotides in four model compounds, 5'-G˙T-3', 5'-TG˙-3', 5'-G˙C-3', and 5'-CG˙-3', were studied using density functional theory (DFT) methods. In single-stranded DNA, the deoxyguanosine-8-yl radical is preferred to efficiently attack the C5 site of its 3' neighboring deoxythymidine or deoxycytidine, forming the G[8-5]T or G[8-5]C intrastrand cross-link rather than the C6 site forming the G[8-6]T or G[8-6]C intrastrand cross-link. The four corresponding sequence isomers, namely T[5-8]G, T[6-8]G, C[5-8]G, and C[6-8]G, formed by additions of deoxyguanosine-8-yl radical to its 5' neighboring pyrimidine nucleotides are predicted to be formed inefficiently. In double-stranded DNA, considering the detrimental effects of stabilizing weak interactions on related structural adjustments required in each addition reaction path, relatively lower reaction yields are suggested for the G[8-5]T and G[8-5]C intrastrand cross-links, while the formation of the other six intrastrand cross-links becomes quite difficult. All calculations definitely demonstrate that, in addition to pyrimidine-type radicals, the purine-type deoxyguanosine-8-yl radical is able to attack its 3'/5' neighboring pyrimidine nucleotides forming several DNA intrastrand cross-links.
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Affiliation(s)
- Shoushan Wang
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials, School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan 523808, People's Republic of China.
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10
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Wang S, Zhang M, Liu P, Xie S, Cheng F, Wang L. Formation of pyrimidine-pyrimidine type DNA intrastrand cross-links: a theoretical verification. Phys Chem Chem Phys 2018; 19:28907-28916. [PMID: 29057416 DOI: 10.1039/c7cp06452g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyrimidine-type radicals have been demonstrated to be able to attack their 3' or 5' neighboring purine nucleotides forming diverse DNA intrastrand cross-links, but whether or not these radicals can attack their surrounding pyrimidine nucleotides forming pyrimidine-pyrimidine type DNA intrastrand cross-links remains unclear. To resolve this question, probable additions of the uracil-5-methyl (˙UCH2) radical to the C5[double bond, length as m-dash]C6 double bond of its 3'/5' neighboring pyrimidine nucleotides in the four models, 5'-T(˙UCH2)-3', 5'-C(˙UCH2)-3', 5'-(˙UCH2)T-3', and 5'-(˙UCH2)C-3', are explored in the present work employing density functional theory (DFT) methods. The C6 site of its 5' neighboring thymidine is the preferred target for ˙UCH2 radical addition, while additions of the ˙UCH2 radical to the C6 and C5 sites of its 5' neighboring deoxycytidine are found to be competitive reactions. The ˙UCH2 radical can react with both the C6 and C5 sites of its 3' neighboring pyrimidine nucleotides, but the efficiencies of these reactions are predicted to be much lower than those of the corresponding addition reactions to its 5' neighboring pyrimidine nucleotides, indicating the existence of an obvious sequence effect. All the addition products could be finally transformed into closed-shell intrastrand cross-links, the molecular masses of which are found to be exactly the same as certain MS values determined in a recent study of an X-irradiated deoxygenated aqueous solution of calf thymus DNA. The present study thus not only definitely corroborates the fact that the reactive ˙UCH2 radical can attack its 3'/5' neighboring pyrimidine nucleotides forming several pyrimidine-pyrimidine type DNA intrastrand cross-links, but also provides a plausible explanation for the identities of these structurally unknown intrastrand cross-links.
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Affiliation(s)
- Shoushan Wang
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials, School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan 523808, People's Republic of China.
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11
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Wang S, Zhang M, Liu P, Xie S, Cheng F, Wang L. Mechanism studies of addition reactions between the pyrimidine type radicals and their 3′/5′ neighboring deoxyguanosines. RSC Adv 2018; 8:2777-2785. [PMID: 35541474 PMCID: PMC9077473 DOI: 10.1039/c7ra12713h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/06/2018] [Indexed: 11/21/2022] Open
Abstract
To clarify the biologically significant sequence effect existing in the formation of the pyrimidine-type radicals induced DNA intrastrand cross-links, addition mechanisms between the uridine-5-methyl (˙UCH2), 6-hydroxy-5,6-dihydrothymidine-5-yl (˙T6OH), and 6-hydroxy-5,6-dihydrocytidine-5-yl (˙C6OH) radicals and their 3′/5′ neighboring deoxyguanosines (dG) are explored in the present study employing the model 5′-G(˙UCH2)-3′, 5′-(˙UCH2)G-3′, 5′-G(˙T6OH)-3′, 5′-(˙T6OH)G-3′, 5′-G(˙C6OH)-3′, and 5′-(˙C6OH)G-3′ sequences. It is found that the 5′ G/C8 additions of the three radicals are all simple direct one-step reactions inducing only relatively small structural changes, while a conformational adjustment involving orientation transitions of both nucleobase moieties and twisting of the DNA backbone is indispensable for each 3′ G/C8 addition. Furthermore, markedly positive reaction free energy requirements are estimated for these conformational transformations making the 3′ G/C8 additions of the three radicals thermodynamically much more unfavorable than the corresponding 5′ G/C8 additions. Such essential conformational adjustments along the 3′ G/C8 addition paths that structurally greatly influence the local DNA structures and thermodynamically substantially reduce the addition efficiencies may be the reasons responsible for the differences in the formation yields and biological consequences of the pyrimidine-type radicals induced DNA intrastrand cross-link lesions. For each radical, the 5′ G/C8 addition is a simple direct one-step reaction, while a structurally significant and thermodynamically markedly unfavorable conformational adjustment is indispensable for the 3′ G/C8 addition.![]()
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Affiliation(s)
- Shoushan Wang
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- People's Republic of China
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials
| | - Min Zhang
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials
- School of Environment and Civil Engineering
- Dongguan University of Technology
- Dongguan 523808
- People's Republic of China
| | - Peng Liu
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials
- School of Environment and Civil Engineering
- Dongguan University of Technology
- Dongguan 523808
- People's Republic of China
| | - Shilei Xie
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials
- School of Environment and Civil Engineering
- Dongguan University of Technology
- Dongguan 523808
- People's Republic of China
| | - Faliang Cheng
- Guangdong Engineering and Technology Research Center for Advanced Nanomaterials
- School of Environment and Civil Engineering
- Dongguan University of Technology
- Dongguan 523808
- People's Republic of China
| | - Lishi Wang
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- People's Republic of China
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12
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Wang S, Zhang M, Liu P, Xie S, Cheng F, Wang L. 5-(Halomethyl)uridine derivatives as potential antitumor radiosensitizers: A DFT study. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.12.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Wityk P, Wieczór M, Makurat S, Chomicz-Mańka L, Czub J, Rak J. Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics. J Chem Theory Comput 2017; 13:6415-6423. [PMID: 29117674 DOI: 10.1021/acs.jctc.7b00978] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Brominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide leads to a reactive C8 adenosyl radical known to generate a range of DNA lesions. In the current work, we propose a multiscale computational approach to elucidate the mechanism by which this unstable radical causes further damage in genomic DNA. We employed a combination of classical molecular dynamics conformational sampling and QM/MM metadynamics to study the thermodynamics and kinetics of plausible reaction pathways in a realistic model, bridging between different time scales of the key processes and accounting for the spatial constraints in DNA. The obtained data allowed us to build a kinetic model that correctly predicts the products predominantly observed in experimental settings-cyclopurine and β-elimination (single strand break) lesions-with their ratio and yield dependent on the effective lifetime of the radical species. To date, our study provides the most complete description of purine radical reactivity in double stranded DNA, explaining the radiosensitizing action of electrophilic purines in molecular detail as well as providing a conceptual framework for the computational modeling of competing reaction pathways in biomolecules.
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Affiliation(s)
- Paweł Wityk
- Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - Miłosz Wieczór
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology , Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Samanta Makurat
- Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - Lidia Chomicz-Mańka
- Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology , Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-952 Gdańsk, Poland
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14
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Jian Y, Maximowitsch E, Liu D, Adhikari S, Li L, Domratcheva T. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. Chemistry 2017; 23:7526-7537. [PMID: 28370554 DOI: 10.1002/chem.201700045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,School of Chemistry & Chemical Engineering, Shaanxi Normal University (SNNU), No. 620, West Chang'an Avenue, Xi'an, Shaanxi, 710119, P. R. China
| | - Egle Maximowitsch
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
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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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16
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Yu Y, Cui Y, Niedernhofer LJ, Wang Y. Occurrence, Biological Consequences, and Human Health Relevance of Oxidative Stress-Induced DNA Damage. Chem Res Toxicol 2016; 29:2008-2039. [PMID: 27989142 DOI: 10.1021/acs.chemrestox.6b00265] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A variety of endogenous and exogenous agents can induce DNA damage and lead to genomic instability. Reactive oxygen species (ROS), an important class of DNA damaging agents, are constantly generated in cells as a consequence of endogenous metabolism, infection/inflammation, and/or exposure to environmental toxicants. A wide array of DNA lesions can be induced by ROS directly, including single-nucleobase lesions, tandem lesions, and hypochlorous acid (HOCl)/hypobromous acid (HOBr)-derived DNA adducts. ROS can also lead to lipid peroxidation, whose byproducts can also react with DNA to produce exocyclic DNA lesions. A combination of bioanalytical chemistry, synthetic organic chemistry, and molecular biology approaches have provided significant insights into the occurrence, repair, and biological consequences of oxidatively induced DNA lesions. The involvement of these lesions in the etiology of human diseases and aging was also investigated in the past several decades, suggesting that the oxidatively induced DNA adducts, especially bulky DNA lesions, may serve as biomarkers for exploring the role of oxidative stress in human diseases. The continuing development and improvement of LC-MS/MS coupled with the stable isotope-dilution method for DNA adduct quantification will further promote research about the clinical implications and diagnostic applications of oxidatively induced DNA adducts.
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Affiliation(s)
| | | | - Laura J Niedernhofer
- Department of Metabolism and Aging, The Scripps Research Institute Florida , Jupiter, Florida 33458, United States
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17
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Wang Y, Lin Z, Fan H, Peng X. Photoinduced DNA Interstrand Cross-Link Formation by Naphthalene Boronates via a Carbocation. Chemistry 2016; 22:10382-6. [DOI: 10.1002/chem.201601504] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yibin Wang
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Zechao Lin
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Heli Fan
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
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18
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Wang Y, Liu S, Lin Z, Fan Y, Wang Y, Peng X. Photochemical Generation of Benzyl Cations That Selectively Cross-Link Guanine and Cytosine in DNA. Org Lett 2016; 18:2544-7. [PMID: 27191599 PMCID: PMC5609456 DOI: 10.1021/acs.orglett.6b00755] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UV irradiation of several aryl boronates efficiently produced bifunctional benzyl cations that selectively form guanine-cytosine cross-links in DNA. Photoinduced homolysis of the C-Br bond took place with the aryl boronate bromides 3a and 4a, generating free radicals that were oxidized to benzyl cations via electron transfer. However, photoirradiation of the quaternary ammonium salts 3b and 4b led to heterolysis of C-N bond, directly producing benzyl cations. The electron-donating group in the aromatic ring greatly enhanced cross-linking efficiency.
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Affiliation(s)
- Yibin Wang
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Shuo Liu
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Zechao Lin
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Yukai Fan
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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Churchill CDM, Eriksson LA, Wetmore SD. DNA Distortion Caused by Uracil-Containing Intrastrand Cross-Links. J Phys Chem B 2016; 120:1195-204. [PMID: 26830475 DOI: 10.1021/acs.jpcb.5b10381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Four uracil-containing intrastrand cross-links have been detected in human cells upon UV irradiation of 5-bromouracil-containing DNA, namely 5'-G[8-5]U-3', 5'-U[5-8]G-3', 5'-A[8-5]U-3', and 5'-A[2-5]U-3'. These lesions feature unique composition and connectivity compared with other intrastrand cross-links reported in the literature. For the first time, structural information obtained using molecular dynamics (MD) simulations reveal that all four lesions distort the DNA helix, which can involve an extrahelical location of the cross-link, changes in the helical interactions of the complementary nucleotides, or disruption of hydrogen bonding in the flanking base pairs up to two positions from the cross-linked site; however, the degree of distortion varies between the cross-links, being affected by the sequence, nucleobase-nucleobase connectivity, and the purine involved. Most importantly, the relative distortion of the damaged DNA provides the first structural explanation for the observed abundances of the four uracil-containing cross-links. Furthermore, the highly distorted conformations suggest that these lesions will likely have severe implications for DNA replication and repair processes in cells.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg , Box 462, Göteborg 405 30, Sweden
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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20
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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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21
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Price NE, Catalano MJ, Liu S, Wang Y, Gates KS. Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA. Nucleic Acids Res 2015; 43:3434-41. [PMID: 25779045 PMCID: PMC4402519 DOI: 10.1093/nar/gkv174] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/20/2015] [Indexed: 01/11/2023] Open
Abstract
A new type of interstrand DNA–DNA cross-link between abasic (Ap) sites and 2′-deoxyadenosine (dA) residues was recently reported, but the chemical structure and properties of this lesion were not rigorously established. Here we characterized the nucleoside cross-link remnant released by enzymatic digestion of duplex DNA containing the dA-Ap cross-link. A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N6-amino group of dA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that the synthetic material 6 matched the authentic cross-link remnant released by enzymatic digestion of cross-linked DNA. These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA. Both the nucleoside cross-link remnant 6 and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes.
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Affiliation(s)
- Nathan E Price
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Michael J Catalano
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
| | - Shuo Liu
- Environmental Toxicology Graduate Program, University of California-Riverside, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California-Riverside, Riverside, CA 92521-0403, USA Department of Chemistry, University of California-Riverside, Riverside, CA 92521-0403, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
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22
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Brem R, Zhang X, Xu YZ, Karran P. UVA photoactivation of DNA containing halogenated thiopyrimidines induces cytotoxic DNA lesions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 145:1-10. [PMID: 25747491 PMCID: PMC4376468 DOI: 10.1016/j.jphotobiol.2015.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 11/20/2022]
Abstract
Growing cells incorporate thio-iodo-deoxyuridine and thio-bromo-deoxyuridine into DNA. They are non-toxic but act as powerful UVA photosensitisers. UVA lesions include DNA-protein and DNA–DNA crosslinks. Singlet oxygen is involved in the formation of this potentially lethal damage. Thio-halo-deoxynucleosides offer a potential selective therapeutic option.
Photochemotherapy, the combination of a photosensitiser and ultraviolet (UV) or visible light, is an effective treatment for skin conditions including cancer. The high mutagenicity and non-selectivity of photochemotherapy regimes warrants the development of alternative approaches. We demonstrate that the thiopyrimidine nucleosides 5-bromo-4-thiodeoxyuridine (SBrdU) and 5-iodo-4-thiodeoxyuridine (SIdU) are incorporated into the DNA of cultured human and mouse cells where they synergistically sensitise killing by low doses of UVA radiation. The DNA halothiopyrimidine/UVA combinations induce DNA interstrand crosslinks, DNA-protein crosslinks, DNA strand breaks, nucleobase damage and lesions that resemble UV-induced pyrimidine(6-4)pyrimidone photoproducts. These are potentially lethal DNA lesions and cells defective in their repair are hypersensitive to killing by SBrdU/UVA and SIdU/UVA. DNA SIdU and SBrdU generate lethal DNA photodamage by partially distinct mechanisms that reflect the different photolabilities of their C–I and C–Br bonds. Although singlet oxygen is involved in photolesion formation, DNA SBrdU and SIdU photoactivation does not detectably increase DNA 8-oxoguanine levels. The absence of significant collateral damage to normal guanine suggests that UVA activation of DNA SIdU or SBrdU might offer a strategy to target hyperproliferative skin conditions that avoids the extensive formation of a known mutagenic DNA lesion.
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Affiliation(s)
- Reto Brem
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts. EN6 3LD, UK.
| | - Xiaohui Zhang
- College of Environment and Chemical Engineering, Dalian University, Dalian 116622, China
| | - Yao-Zhong Xu
- Department of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK
| | - Peter Karran
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts. EN6 3LD, UK
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23
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Garrec J, Dumont E. Are dinucleoside monophosphates relevant models for the study of DNA intrastrand cross-link lesions? The example of g[8-5m]T. Chem Res Toxicol 2014; 27:1133-41. [PMID: 24911289 DOI: 10.1021/tx4004616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxidatively generated tandem lesions such as G[8-5m]T pose a potent threat to genome integrity. Direct experimental studies of the kinetics and thermodynamics of a specific lesion within DNA are very challenging, mostly due to the variety of products that can be formed in oxidative conditions. Dinucleoside monophosphates (DM) involving only the reactive nucleobases in water represent appealing alternative models on which most physical chemistry and structural techniques can be applied. However, it is not yet clear how relevant these models are. Here, we present QM/MM MD simulations of the cyclization step involved in the formation of G[8-5m]T from the guanine-thymine (GpT) DM in water, with the aim of comparing our results to our previous investigation of the same reaction in DNA ( Garrec , J. , Patel , C. , Rothlisberger , U. , and Dumont , E. ( 2012 ) J. Am. Chem. Soc. 134 , 2111 - 2119 ). We show that, despite the different levels of preorganization of the two systems, the corresponding reactions share many energetic and structural characteristics. The main difference lies in the angle between the G and T bases, which is slightly higher in the transition state (TS) and product of the reaction in water than in the reaction in DNA. This effect is due to the Watson-Crick H-bonds, which are absent in the {GpT+water} system and restrain the relative positioning of the reactive nucleobases in DNA. However, since the lesion is accommodated easily in the DNA macromolecule, the induced energetic penalty is relatively small. The high similarity between the two reactions strongly supports the use of GpT in water as a model of the corresponding reaction in DNA.
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Affiliation(s)
- Julian Garrec
- CNRS, Théorie-Modélisation-Simulation, SRSMC, Vandoeuvre-lès-Nancy F-54506, France
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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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25
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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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Fujii Y, Genet MD, Roybal EJ, Kubota N, Okayasu R, Miyagawa K, Fujimori A, Kato TA. Comparison of the bromodeoxyuridine-mediated sensitization effects between low-LET and high-LET ionizing radiation on DNA double-strand breaks. Oncol Rep 2013; 29:2133-9. [PMID: 23525528 DOI: 10.3892/or.2013.2354] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/17/2012] [Indexed: 11/06/2022] Open
Abstract
The incorporation of halogenated pyrmidines such as bromo- and iodo-deoxyuridines (BrdU, IdU) into DNA as thymidine analogs enhances cellular radiosensitivity when high-linear energy transfer (LET) radiation is not used. Although it is known that high-LET ionizing radiation confers fewer biological effects resulting from halogenated pyrimidine incorporation, the exact mechanisms of reduced radiosensitivity with high-LET radiation are not clear. We investigated the radiosensitization effects of halogenated pyrimidines with high-LET radiation using accelerated carbon and iron ions. Cells synchronized into the G1 phase after unifilar (1 cell cycle) and bifilar (2 cell cycles) substitution with 10 µM BrdU were exposed to various degrees of LET with heavy ions and X-rays. We then carried out a colony formation assay to measure cell survival. The γ-H2AX focus formation assay provided a measure of DNA double-strand break (DSB) formation and repair kinetics. Chromosomal aberration formations for the first post-irradiation metaphase were also scored. For both low-LET X-rays and carbon ions (13 keV/µm), BrdU incorporation led to impaired DNA repair kinetics, a larger initial number of DNA DSBs more frequent chromosomal aberrations at the first post-irradiated metaphase, and increased radiosensitivity for cell lethality. The enhancement ratio was higher after bifilar substitution. In contrast, no such synergistic enhancements were observed after high-LET irradiation with carbon and iron ions (70 and 200 keV/µm, respectively), even after bifilar substitution. Our results suggest that BrdU substitution did not modify the number and quality of DNA DSBs produced by high-LET radiation. The incorporation of halogenated pyrimidines may produce more complex/clustered DNA damage along with radicals formed by low-LET ionizing radiation. In contrast, the severity of damage produced by high-LET radiation may undermine the effects of BrdU and account for the observed minimal radiosensitization effects.
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Affiliation(s)
- Yoshihiro Fujii
- Department of Radiological Sciences, Ibaraki Prefectural University of Health Sciences, Inashiki, Ibaraki 300-0394, Japan
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Patel C, Garrec J, Dupont C, Dumont E. What Singles Out the G[8–5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations. Biochemistry 2013; 52:425-31. [DOI: 10.1021/bi301198h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Chandan Patel
- Université de Lyon, Institut
de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon,
46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Julian Garrec
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Céline Dupont
- Université de Lyon, Institut
de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon,
46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Elise Dumont
- Université de Lyon, Institut
de Chimie de Lyon, CNRS, Ecole normale supérieure de Lyon,
46 allée d’Italie, 69364 Lyon Cedex 07, France
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Nuclease digestion and mass spectrometric characterization of oligodeoxyribonucleotides containing 1,2-GpG, 1,2-ApG, and 1,3-GpXpG cisplatin intrastrand cross-links. Clin Chim Acta 2012; 420:160-70. [PMID: 23266768 DOI: 10.1016/j.cca.2012.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 12/05/2012] [Indexed: 12/22/2022]
Abstract
BACKGROUND The primary mode of action for cis-diamminedichloroplatinum (II), referred to as cisplatin, toward the treatment of solid malignancies is through formation of cross-links with DNA at purine sites, especially guanines. METHODS We prepared oligodeoxyribonucleotides (ODNs) containing a 1,2-GpG, 1,2-ApG, or 1,3-GpXpG cisplatin intrastrand cross-link and the corresponding ODNs modified with (15)N2-labeled cisplatin, and characterized these ODNs with electrospray ionization mass spectrometry (ESI-MS) and tandem MS (MS/MS). We also employed LC-MS/MS to characterize the digestion products of these ODNs after treatment with a cocktail of 4 enzymes (nuclease P1, phosphodiesterases I and II, and alkaline phosphatase). RESULTS 1,2-GpG was released from the ODNs as a dinucleoside monophosphate or a dinucleotide. Analyses of the digestion products of ODNs containing a 1,2-GpG cross-link on the 5' or 3' terminus revealed that the dinucleotide carries a terminal 5' phosphate. On the other hand, digestion of the 1,3-GpXpG intrastrand cross-link yielded 3 dinucleoside products with 0, 1, or 2 phosphate groups. CONCLUSION The availability of the ODNs carrying the stable isotope-labeled lesions, MS/MS analyses of the cisplatin-modified ODNs, and the characterization of the enzymatic digestion products of these ODNs set the stage for the future LC-MS/MS quantification of the 1,2-GpG, 1,2-ApG, and 1,3-GpXpG lesions in cellular DNA.
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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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Garrec J, Patel C, Rothlisberger U, Dumont E. Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations. J Am Chem Soc 2012; 134:2111-9. [DOI: 10.1021/ja2084042] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julian Garrec
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Chandan Patel
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
| | - Ursula Rothlisberger
- Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Elise Dumont
- Université de Lyon, Institut de Chimie de Lyon, CNRS, Ecole normale
supérieure de Lyon, 46 allée d’Italie, 69364
Lyon Cedex 07, France
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31
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Churchill CDM, Eriksson LA, Wetmore SD. Formation mechanism and structure of a guanine-uracil DNA intrastrand cross-link. Chem Res Toxicol 2011; 24:2189-99. [PMID: 22060045 DOI: 10.1021/tx2003239] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The formation and structure of the 5'-G[8-5]U-3' intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine-pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5'-G[8-5]U-3' within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5'-G[8-5]U-3', may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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32
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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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Rakhmetova SI, Rad'ko SP, Gnedenko OV, Bodoev NV, Ivanov AS, Archakov AI. [Photoaptamer heterodimeric constructs as a new approach to enhance the efficiency of formation of photocrosslinking with a target protein]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2011; 56:72-81. [PMID: 21328912 DOI: 10.18097/pbmc20105601072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Using two DNA aptamers selectively recognizing anion-binding exosites 1 and 2 of thrombin as a model, it has been demonstrated that their conjugation by a poly-(dT)-linker (ranging from 5 to 65 nt in length) to produce aptamer heterodimeric constructs results into affinity enhancement. The apparent dissociation constant (Kd(app)) measured at the optical biosensor Biacore-3000 for complexes of thrombin with the heterodimeric constructs reached minimum values (Kd(app) = 0.2-0.4 nM) which were approximately 30-fold less than for the complexes with the primary aptamers. A photoaptamer heterodimeric construct was designed connecting photoaptamer and aptamer sequences with the poly-(dT)-linker of 35 nt long. The photoaptamer used could form photo-induced cross-links with the exosite 2 of thrombin and the aptamer used could bind to the exosite 1. The measured value of Kd(app) for the photoaptamer construct was approximately 40-fold less than that for the primary photoaptamer (5.3 and 190 nM, respectively). Upon exposure to the UV radiation at 308 nm of the equimolar mixtures of thrombin with the photoaptamer construct, the equal yield of the crosslinked complexes was observed at concentrations which were lower by two orders of magnitude than in the case of the primary photoaptamer. It was found that concurrently with crosslinking to thrombin a photo-induced inactivation of the photoaptamer occurs presumably due to formation of the intermolecular crosslinking.
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Lin G, Zhang J, Zeng Y, Luo H, Wang Y. Conformation-dependent formation of the G[8-5]U intrastrand cross-link in 5-bromouracil-containing G-quadruplex DNA induced by UVA irradiation. Biochemistry 2010; 49:2346-50. [PMID: 20166754 DOI: 10.1021/bi901861w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-quadruplex motifs are known to be present in telomeres of human and other organisms. Recent bioinformatic studies also revealed the widespread existence of these motifs in promoter regions of human genes. Treatment of cultured cells with 5-bromo-2'-deoxyuridine ((Br)dU) is known to result in the substitution of DNA thymidine with (Br)dU; such replacement has been shown to sensitize cells to killing induced by UV light. Our previous studies revealed that the exposure of (Br)dU-carrying duplex DNA or (Br)dU-treated MCF-7 cells to UVB light could lead to the facile formation of intrastrand cross-link products initiated from (Br)dU. Here we found that the exposure of (Br)dU-bearing G-quadruplex DNA to UVA light could also give rise to the efficient formation of the G[8-5]U intrastrand cross-link, where the C8 of guanine in the external G-tetrad is covalently linked with the C5 of its adjacent 3' uracil in the loop region. In addition, the yield for the cross-link product is dependent on the conformation of the G-quadruplex. Together, the formation of intrastrand cross-link in G-quadruplex motifs may account for the photocytotoxic effect induced by (Br)dU incorporation, and the (Br)dU-mediated photo-cross-linking may constitute a useful method for monitoring the different conformations of G-quadruplex folding.
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Affiliation(s)
- Guangxin Lin
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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Dextraze ME, Cecchini S, Bergeron F, Girouard S, Turcotte K, Wagner JR, Hunting DJ. Reaching for the other side: generating sequence-dependent interstrand cross-links with 5-bromodeoxyuridine and gamma-rays. Biochemistry 2009; 48:2005-11. [PMID: 19216505 DOI: 10.1021/bi801684t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interstrand cross-links impede critical cellular processes such as transcription and replication and are thus considered to be one of the most toxic types of DNA damage. Although several studies now point to the existence of gamma-radiation-induced cross-links in cellular DNA, little is known about the characteristics required for their creation. Recently, we reported the formation of interstrand cross-links that were specific for mismatched nucleotides within 5-bromo-2'-deoxyuridine-substituted DNA. Given the structural specificity for interstrand cross-link formation, it is likely that open or mismatched regions of DNA in cells may be particularly favorable for cross-link production. Herein, we investigated the effect of the local DNA sequence on the formation of interstrand cross-links, using 5-bromo-2'-deoxyuridine to generate radicals in a mismatched region of DNA. We investigated a total of 12 variations of bases in the mismatched region. The oligonucleotides were irradiated with gamma-rays, and interstrand cross-link formation was analyzed by denaturing gel electrophoresis. We found that the efficiency of cross-link formation was highly dependent on the nature of mismatched bases and, on the basis of electrophoretic mobility, observed several distinctive cross-link structures with specific DNA sequences. This study provides new insights into the reactivity of mismatched DNA and the mechanisms leading to interstrand cross-link formation. The potential application of 5-bromo-2'-deoxyuridine-induced interstrand cross-links to the field of DNA repair is discussed.
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Affiliation(s)
- Marie-Eve Dextraze
- Center for Research in Radiotherapy (CR2), Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
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Cao H, Wang Y. Fragmentation of isomeric intrastrand crosslink lesions of DNA in an ion-trap mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:611-617. [PMID: 19103496 PMCID: PMC2691995 DOI: 10.1016/j.jasms.2008.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 11/24/2008] [Accepted: 11/25/2008] [Indexed: 05/27/2023]
Abstract
The collision-induced dissociation pathways of isomeric cytosine-guanine and cytosine-adenine intrastrand crosslink-containing dinucleoside monophosphates were investigated with the stable isotope-labeled compounds to gain insights into the effects of chemical structure on the fragmentation pathways of these DNA modifications. A Dimroth-like rearrangement, which was reported for protonated 2'-deoxycytidine and involved the switching of the exocyclic N4 with the ring N3 nitrogen atom, was also observed for the cytosine component in the protonated ions of C[5-8]G, C[5-2]A, and C[5-8]A, but not C[5-N(2)]G or C[5-N(6)]A. In these two sets of crosslinks, the C5 of cytosine is covalently bonded with its neighboring purine base via a carbon atom on the aromatic ring and an exocyclic nitrogen atom, respectively. On the contrary, the rearrangement could occur for the deprotonated ions of C[5-N(2)]G, C[5-N(6)]A, and unmodified cytosine, but not C[5-8]G, C[5-2]A, or C[5-8]A. In addition, ammonia could be lost more readily from C[5-N(2)]G and C[5-N(6)]A than from C[5-8]G, C[5-2]A, and C[5-8]A. The results from the present study afforded important guidance for the application of mass spectrometry for the structure elucidation of other intrastrand/interstrand crosslink lesions.
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Affiliation(s)
| | - Yinsheng Wang
- To whom correspondence should be addressed: Telephone: (951) 827-2700. Fax: (951) 827-4713. E-mail:
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Liu Y, Sen D. A contact photo-cross-linking investigation of the active site of the 8-17 deoxyribozyme. J Mol Biol 2008; 381:845-59. [PMID: 18586041 DOI: 10.1016/j.jmb.2008.06.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/30/2008] [Accepted: 06/08/2008] [Indexed: 11/19/2022]
Abstract
The small RNA-cleaving 8-17 deoxyribozyme (DNAzyme) has been the subject of extensive mechanistic and structural investigation, including a number of recent single-molecule studies of its global folding. Little detailed insight exists, however, into this DNAzyme's active site; for instance, the identity of specific nucleotides that are proximal to or in contact with the scissile site in the substrate. Here, we report a systematic replacement of a number of bases within the magnesium-folded DNAzyme-substrate complex with thio- and halogen-substituted base analogues, which were then photochemically activated to generate contact cross-links within the complex. Mapping of the cross-links revealed a striking pattern of DNAzyme-substrate cross-links but an absence of significant intra-DNAzyme cross-links. Notably, the two nucleotides directly flanking the scissile phosphodiester cross-linked strongly with functionally important elements within the DNAzyme, the thymine of a G.T wobble base pair, a WCGR bulge loop, and a terminal AGC loop. Mutation of the wobble base pair to a G-C pair led to a significant folding instability of the DNAzyme-substrate complex. The cross-linking patterns obtained were used to generate a model for the DNAzyme's active site that had the substrate's scissile phosphodiester sandwiched between the DNAzyme's wobble thymine and its AGC and WCGR loops.
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Affiliation(s)
- Yong Liu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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Cao H, Wang Y. Quantification of oxidative single-base and intrastrand cross-link lesions in unmethylated and CpG-methylated DNA induced by Fenton-type reagents. Nucleic Acids Res 2007; 35:4833-44. [PMID: 17626047 PMCID: PMC1976268 DOI: 10.1093/nar/gkm497] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methylation of cytosine at CpG sites in mammalian cells plays an important role in the epigenetic regulation of gene expression. Here, we assessed the formation of single-nucleobase lesions and intrastrand cross-link lesions (i.e. G[8-5]C, C[5-8]G, mC[5m-8]G, and G[8-5m]mC, where ‘mC’ represents 5-methylcytosine) in unmethylated and the corresponding CpG-methylated synthetic double-stranded DNA upon treatment with Fenton-type reagents [i.e. H2O2, ascorbate together with Cu(II) or Fe(II)]. Our results showed that the yields of oxidative single-nucleobase lesions were considerably higher than those of the intrastrand cross-link lesions. Although no significant differences were found for the yields of single-base lesions induced from cytosine and mC, the G[8-5m]mC cross-link was induced ∼10 times more efficiently than the G[8-5]C cross-link. In addition, the mC[5m-8]G was induced at a level that was ∼15 times less than G[8-5m]mC, whereas the corresponding C[5-8]G intrastrand cross-link lesion was not detectable. Moreover, Cu(II) is ∼10-fold as effective as Fe(II) in inducing oxidative DNA lesions. These results suggest that oxidative intrastrand cross-link lesions formed at methylated-CpG sites may account for the previously reported mCG→TT tandem double mutations induced by Fenton-type reagents.
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Affiliation(s)
| | - Yinsheng Wang
- *To whom correspondence should be addressed.+1 951 827 2700+1 951 827 4713
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