51
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Ferino A, Xodo LE. Effect of DNA Glycosylases OGG1 and Neil1 on Oxidized G-Rich Motif in the KRAS Promoter. Int J Mol Sci 2021; 22:1137. [PMID: 33498912 PMCID: PMC7865940 DOI: 10.3390/ijms22031137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/28/2022] Open
Abstract
The promoter of the Kirsten ras (KRAS) proto-oncogene contains, upstream of the transcription start site, a quadruplex-forming motif called 32R with regulatory functions. As guanine under oxidative stress can be oxidized to 8-oxoguanine (8OG), we investigated the capacity of glycosylases 8-oxoguanine glycosylase (OGG1) and endonuclease VIII-like 1 (Neil1) to excise 8OG from 32R, either in duplex or G-quadruplex (G4) conformation. We found that OGG1 efficiently excised 8OG from oxidized 32R in duplex but not in G4 conformation. By contrast, glycosylase Neil1 showed more activity on the G4 than the duplex conformation. We also found that the excising activity of Neil1 on folded 32R depended on G4 topology. Our data suggest that Neil1, besides being involved in base excision repair pathway (BER), could play a role on KRAS transcription.
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Affiliation(s)
| | - Luigi E. Xodo
- Laboratory of Biochemistry, Department of Medicine, P.le Kolbe 4, 33100 Udine, Italy;
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52
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Zhao L, Zhou P, Liu X, Zheng H, Zhan K, Luo J, Liu B. Theoretical studies of the ultrafast deactivation mechanism of 8-oxo-guanine on the S 1 and S 2 electronic states in gas phase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118884. [PMID: 32898726 DOI: 10.1016/j.saa.2020.118884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The 8-oxo-deoxyguanosine is the most abundant specie of the DNA oxidative damage. Despite the deleterious effects such as gene mutation it may cause, the 8-oxodG was also reported to have beneficial effect such as repairing the nearby cyclobutane pyrimidine dimer (CPD) after photoexcitation. Due to its strong biological relevance, the photoinduced excited state dynamics behavior of 8-oxo-deoxyguanosine is of particular interest. In this work, a theoretical investigation by combination of complete active space self-consistent field (CASSCF) ab initio calculations and on-the-fly nonadiabatic dynamics simulations are implemented to provide intrinsic deactivation mechanism of its free base 8-oxoguanine after being excited to the S1 and S2 states. Two minimum energy conical intersections (MECIs) characterized by the C3-puckered motion with attractive chiral character are located, which contribute appreciably to the S1 state deactivation process. When the system is being excited to the S2 state directly, a S2 → S1 → S0 two-step decay pattern is proposed. A nearly planar S2/S1 intersection plays a significant role in the S2 → S1 decay process. The subsequent S1 state relaxation process is also dominated by the C3-puckered deformation motion. One decay time is estimated to be 704 fs, which compares well with the experimental observation of 0.9 ± 0.1 ps in solvents. Particular illustration is the fact that the MECIs configurations we located bear an exceptional resemblance with previous reported thymine, cytosine and guanine, suggesting that the current work could lend support for better understanding of the non-natural nucleobases and derivatives.
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Affiliation(s)
- Li Zhao
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China.
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China
| | - Xiaoxu Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China
| | - Haixia Zheng
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China
| | - Kaiyun Zhan
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China
| | - Jianhui Luo
- Research Institute of Petroleum Exploration & Development (RIPED), PetroChina, Beijing 100083, PR China
| | - Bing Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, PR China.
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53
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Wei S, Zhang Z, Liu S, Wang Y. Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation. NEW J CHEM 2021. [DOI: 10.1039/d1nj01653a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The pKa values of reactive protons in 8-oxoG˙+ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.
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Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Zhenhua Zhang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Shijun Liu
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Yinghui Wang
- College of Science
- Chang’an University
- Xi’an 710064
- China
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54
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Hannachi D, El Houda Amrane N, Merzoud L, Chermette H. Exploring the antioxidant activity of thiaflavan compounds: a quantum chemical study. NEW J CHEM 2021. [DOI: 10.1039/d1nj01996a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Conceptual DFT tools (HAT, SPLET, SET-PT, aromaticity index,…) have been used to explore the antioxidant activity of thiaflavan compounds, and predict which derivate should be the best one.
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Affiliation(s)
- Douniazed Hannachi
- Département de Chimie
- Faculté des Sciences
- Université de Setif-1, El Bez
- Setif
- Algeria
| | - Nour El Houda Amrane
- Laboratoire d’Electrochimie
- d’Ingénierie Moléculaire et de Catalyse Redox (LEIMCR), Faculté de Technologie, Université Sétif-1
- Sétif
- Algeria
| | - Lynda Merzoud
- Université de Lyon, Université Claude Bernard Lyon 1
- CNRS UMR 5280, Institut des Sciences Analytiques
- 69622 Villeurbanne Cedex
- France
| | - Henry Chermette
- Université de Lyon, Université Claude Bernard Lyon 1
- CNRS UMR 5280, Institut des Sciences Analytiques
- 69622 Villeurbanne Cedex
- France
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55
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Avagliano D, Tkaczyk S, Sánchez-Murcia PA, González L. Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics. J Phys Chem Lett 2020; 11:10212-10218. [PMID: 33206544 PMCID: PMC7735745 DOI: 10.1021/acs.jpclett.0c03070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/11/2020] [Indexed: 05/10/2023]
Abstract
The urge to discover selective fluorescent binders to G-quadruplexes (G4s) for rapid diagnosis must be linked to understand the effect that those have on the DNA photophysics. Herein, we report on the electronic excited states of a bound merocyanine dye to c-Myc G4 using extensive multiscale quantum mechanics/molecular mechanics calculations. We find that the absorption spectra of c-Myc G4, both without and with the intercalated dye, are mainly composed of exciton states and mixed local/charge-transfer states. The presence of merocyanine hardly affects the energy range of the guanine absorption or the number of guanines excited. However, it triggers a substantial amount (16%) of detrimental pure charge-transfer states involving oxidized guanines. We identify the rigidity introduced by the probe in G4, reducing the overlap among guanines, as the one responsible for the changes in the exciton and charge-transfer states, ultimately leading to a redshift of the absorption maximum.
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Affiliation(s)
- Davide Avagliano
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Sara Tkaczyk
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Pedro A. Sánchez-Murcia
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
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56
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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57
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Diamantis P, Tavernelli I, Rothlisberger U. Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6690-6701. [PMID: 32926773 DOI: 10.1021/acs.jctc.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 ± 0.28 eV and 5.62 ± 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 ± 0.18 eV and 1.00 ± 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
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58
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Landi A, Capobianco A, Peluso A. Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA. J Phys Chem Lett 2020; 11:7769-7775. [PMID: 32830977 PMCID: PMC8154848 DOI: 10.1021/acs.jpclett.0c01996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the framework of a multistep mechanism in which environmental motion triggers comparatively faster elementary electron-transfer steps and stabilizes hole-transfer products, microscopic coherence is crucial for rationalizing the observed yield ratios of oxidative damage to DNA. Interference among probability amplitudes of indistinguishable electron-transfer paths is able to drastically change the final outcome of charge transport, even in DNA oligomers constituted by similar building blocks, and allows for reconciling apparently discordant experimental observations. Properly tailored DNA oligomers appear to be a promising workbench for studying tunneling in the presence of dissipation at the macroscopic level.
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59
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Ijsselsteijn R, Jansen JG, de Wind N. DNA mismatch repair-dependent DNA damage responses and cancer. DNA Repair (Amst) 2020; 93:102923. [DOI: 10.1016/j.dnarep.2020.102923] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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60
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Role of Poly [ADP-ribose] Polymerase 1 in Activating the Kirsten ras ( KRAS) Gene in Response to Oxidative Stress. Int J Mol Sci 2020; 21:ijms21176237. [PMID: 32872305 PMCID: PMC7504130 DOI: 10.3390/ijms21176237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
In pancreatic Panc-1 cancer cells, an increase of oxidative stress enhances the level of 7,8-dihydro-8-oxoguanine (8OG) more in the KRAS promoter region containing G4 motifs than in non-G4 motif G-rich genomic regions. We found that H2O2 stimulates the recruitment to the KRAS promoter of poly [ADP-ribose] polymerase 1 (PARP-1), which efficiently binds to local G4 structures. Upon binding to G4 DNA, PARP-1 undergoes auto PARylation and thus becomes negatively charged. In our view this should favor the recruitment to the KRAS promoter of MAZ and hnRNP A1, as these two nuclear factors, because of their isoelectric points >7, are cationic in nature under physiological conditions. This is indeed supported by pulldown assays which showed that PARP-1, MAZ, and hnRNP A1 form a multiprotein complex with an oligonucleotide mimicking the KRAS G4 structure. Our data suggest that an increase of oxidative stress in Panc-1 cells activates a ROS-G4-PARP-1 axis that stimulates the transcription of KRAS. This mechanism is confirmed by the finding that when PARP-1 is silenced by siRNA or auto PARylation is inhibited by Veliparib, the expression of KRAS is downregulated. When Panc-1 cells are treated with H2O2 instead, a strong up-regulation of KRAS transcription is observed.
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61
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Zhu H, Tamura T, Fujisawa A, Nishikawa Y, Cheng R, Takato M, Hamachi I. Imaging and Profiling of Proteins under Oxidative Conditions in Cells and Tissues by Hydrogen-Peroxide-Responsive Labeling. J Am Chem Soc 2020; 142:15711-15721. [DOI: 10.1021/jacs.0c02547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hao Zhu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Alma Fujisawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuki Nishikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Rong Cheng
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mikiko Takato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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62
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Balanikas E, Banyasz A, Douki T, Baldacchino G, Markovitsi D. Guanine Radicals Induced in DNA by Low-Energy Photoionization. Acc Chem Res 2020; 53:1511-1519. [PMID: 32786340 DOI: 10.1021/acs.accounts.0c00245] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Guanine (G) radicals are precursors to DNA oxidative damage, correlated with carcinogenesis and aging. During the past few years, we demonstrated clearly an intriguing effect: G radicals can be generated upon direct absorption of UV radiation with energy significantly lower than the G ionization potential. Using nanosecond transient absorption spectroscopy, we studied the primary species, ejected electrons and guanine radicals, which result from photoionization of various DNA systems in aqueous solution.The DNA propensity to undergo electron detachment at low photon energies greatly depends on its secondary structure. Undetected for monomers or unstacked oligomers, this propensity may be 1 order of magnitude higher for G-quadruplexes than for duplexes. The experimental results suggest nonvertical processes, associated with the relaxation of electronic excited states. Theoretical studies are required to validate the mechanism and determine the factors that come into play. Such a mechanism, which may be operative over a broad excitation wavelength range, explains the occurrence of oxidative damage observed upon UVB and UVA irradiation.Quantification of G radical populations and their time evolution questions some widespread views. It appears that G radicals may be generated with the same probability as pyrimidine dimers, which are considered to be the major lesions induced upon absorption of low-energy UV radiation by DNA. As most radical cations undergo deprotonation, the vast majority of the final reaction products is expected to stem from long-lived deprotonated radicals. Consequently, when G radical cations are involved, the widely used oxidation marker 8-oxodG is not representative of the oxidative damage.Beyond the biological consequences, photogeneration of electron holes in G-quadruplexes may inspire applications in nanoelectronics; although four-stranded structures are currently studied as molecular wires, their behavior as photoconductors has not been explored so far.In the present Account, after highlighting some key experimental issues, we first describe the photoionization process, and then, we focus on radicals. We use as show-cases new results obtained for genomic DNA and Oxytricha G-quadruplexes. Generation and reaction dynamics of G radicals in these systems provide a representative picture of the phenomena reported previously for duplexes and G-quadruplexes, respectively.
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Affiliation(s)
| | - Akos Banyasz
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble France
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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63
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Huang SR, Tureček F. Cation Radicals of Hachimoji Nucleobases. Canonical Purine and Noncanonical Pyrimidine Forms Generated in the Gas Phase and Characterized by UV–Vis Photodissociation Action Spectroscopy. J Phys Chem A 2020; 124:7101-7112. [DOI: 10.1021/acs.jpca.0c06227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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64
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Kaczmarek R, Ward S, Debnath D, Jacobs T, Stark AD, Korczyński D, Kumar A, Sevilla MD, Denisov SA, Shcherbakov V, Pernot P, Mostafavi M, Dembinski R, Adhikary A. One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate. Chemistry 2020; 26:9495-9505. [PMID: 32059063 PMCID: PMC7416487 DOI: 10.1002/chem.202000247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/09/2020] [Indexed: 12/26/2022]
Abstract
The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S- )=S was calculated to be slightly lower than that of guanine in 5'-dGMP. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S- . 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S- . 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S- . 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.
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Affiliation(s)
- Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Alexander D Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Sergey A Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Roman Dembinski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
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65
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Liu X, Hu JY. Effect of DNA sizes and reactive oxygen species on degradation of sulphonamide resistance sul1 genes by combined UV/free chlorine processes. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122283. [PMID: 32086093 DOI: 10.1016/j.jhazmat.2020.122283] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Nowadays, antibiotic resistance genes (ARGs) have been characterized as an emerging environmental contaminant, as the spread of ARGs may increase the difficulty of bacterial infection treatments. This study evaluates the combination of ultraviolet (UV) irradiation and chlorination, the two most commonly applied disinfection methods, on the degradation of sulphonamide resistance sul1 genes. The results revealed that although both of individual UV and chlorination processes were relatively less effective, two of the four combined processes, namely UV followed by chlorination (UV-Cl2) and simultaneous combination of UV and chlorination (UV/Cl2), delivered a better removal rate (up to 1.5 logs) with an observation of synergetic effects up to 0.609 log. The mechanisms analysis found that the difference of DNA size affected sul1 genes degradation by UV and chlorination; targeted genes on larger DNA fragments could be more effectively degraded by UV (1.09 logs for large fragments and 0.12 log for small fragments when UV dose reached 432 mJ/cm2), while to degrade ARGs on smaller DNA fragments required less free chlorine dosage (10 mg/L for small fragments and 40 mg/L for large fragments). The sequential combination of UV and chlorination (UV-Cl2) used the corresponding reactivity of both processes, which could be the reason for the synergetic effect. For UV/Cl2 process, the formation of reactive oxygen species (ROS) contributed to the synergetic effect. Scavenger analysis showed that the contribution of ROS to the sul1 gene reduction was 0.004 to 0.273 log (up to 45.5 % of the total synergy values), and among the two major reactive species in UV/Cl2 system, HO was the more important radical, while the contribution of Cl was negligible. Besides, UV/Cl2 process also used the corresponding reactivity of both processes to generate the remaining synergy values when excluding the contribution by reactive radicals. These findings provide a thorough understanding of the effects of UV and free chlorine on the degradation of ARGs and indicate the potential to utilize the combined processes of UV and free chlorine in water or wastewater treatment practice to control the dissemination of antibiotic resistance.
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Affiliation(s)
- Xiaochen Liu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Jiang Yong Hu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore.
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66
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Zheng L, Greenberg MM. Independent Generation and Reactivity of 2'-Deoxyguanosin- N1-yl Radical. J Org Chem 2020; 85:8665-8672. [PMID: 32525316 DOI: 10.1021/acs.joc.0c01095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
2'-Deoxyguanosin-N1-yl radical (dG(N1-H)•) is the thermodynamically favored one-electron oxidation product of 2'-deoxyguanosine (dG), the most readily oxidized native nucleoside. dG(N1-H)• is produced by the formal dehydration of a hydroxyl radical adduct of dG as well as by deprotonation of the corresponding radical cation. dG(N1-H)• were formed as a result of the indirect and direct effects of ionizing radiation, among other DNA damaging agents. dG(N1-H)• was generated photochemically (λmax = 350 nm) from an N-aryloxy-naphthalimide precursor (3). The quantum yield for photochemical conversion of 3 is ∼0.03 and decreases significantly in the presence O2, suggesting that bond scission occurs from a triplet excited state. dG is formed quantitatively in the presence of excess β-mercaptoethanol. In the absence of a reducing agent, dG(N1-H)• oxidizes 3, decreasing the dG yield to ∼50%. Addition of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) as a sacrificial reductant results in a quantitative yield of dG and two-electron oxidation products of 8-oxodGuo. N-Aryloxy-naphthalimide 3 is an efficient and high-yielding photochemical precursor of dG(N1-H)• that will facilitate mechanistic studies on the reactivity of this important reactive intermediate involved in DNA damage.
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Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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67
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Stratigopoulou M, van Dam TP, Guikema JEJ. Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences. Front Immunol 2020; 11:1084. [PMID: 32547565 PMCID: PMC7272602 DOI: 10.3389/fimmu.2020.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.
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Affiliation(s)
- Maria Stratigopoulou
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tijmen P van Dam
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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68
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Tungmunnithum D, Abid M, Elamrani A, Drouet S, Addi M, Hano C. Almond Skin Extracts and Chlorogenic Acid Delay Chronological Aging and Enhanced Oxidative Stress Response in Yeast. Life (Basel) 2020; 10:E80. [PMID: 32481725 PMCID: PMC7345664 DOI: 10.3390/life10060080] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Almond (Prunus dulcis (Mill.) D.A.Webb) is one of the largest nut crops in the world. Recently, phenolic compounds, mostly stored in almond skin, have been associated with much of the health-promoting behavior associated with their intake. The almond skin enriched fraction obtained from cold-pressed oil residues of the endemic Moroccan Beldi ecotypes is particularly rich in chlorogenic acid. In this study, both almond skin extract (AE) and chlorogenic acid (CHL) supplements, similar to traditional positive control resveratrol, significantly increased the chronological life-span of yeast compared to the untreated group. Our results showed that AE and CHL significantly reduced the production of reactive oxygen and nitrogen species (ROS/RNS), most likely due to their ability to maintain mitochondrial function during aging, as indicated by the maintenance of normal mitochondrial membrane potential in treated groups. This may be associated with the observed activation of the anti-oxidative stress response in treated yeast, which results in activation at both gene expression and enzymatic activity levels for SOD2 and SIR2, the latter being an upstream inducer of SOD2 expression. Interestingly, the differential gene expression induction of mitochondrial SOD2 gene at the expense of the cytosolic SOD1 gene confirms the key role of mitochondrial function in this regulation. Furthermore, AE and CHL have contributed to the survival of yeast under UV-C-induced oxidative stress, by reducing the development of ROS/RNS, resulting in a significant reduction in cellular oxidative damage, as evidenced by decreased membrane lipid peroxidation, protein carbonyl content and 8-oxo-guanine formation in DNA. Together, these results demonstrate the interest of AE and CHL as new regulators in the chronological life-span and control of the oxidative stress response of yeast.
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Affiliation(s)
- Duangjai Tungmunnithum
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, 45067 Orléans CEDEX 2, France;
- Bioactifs et Cosmetiques, CNRS GDR 3711, 45067 Orléans CEDEX 2, France
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand;
| | - Malika Abid
- Laboratoire de Biologie des plantes et des micro-organismes, Faculté des Sciences, Université Mohamed Ier, Oujda 60000, Morocco; (M.A.); (A.E.)
| | - Ahmed Elamrani
- Laboratoire de Biologie des plantes et des micro-organismes, Faculté des Sciences, Université Mohamed Ier, Oujda 60000, Morocco; (M.A.); (A.E.)
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, 45067 Orléans CEDEX 2, France;
- Bioactifs et Cosmetiques, CNRS GDR 3711, 45067 Orléans CEDEX 2, France
| | - Mohamed Addi
- Laboratoire de Biologie des plantes et des micro-organismes, Faculté des Sciences, Université Mohamed Ier, Oujda 60000, Morocco; (M.A.); (A.E.)
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, 45067 Orléans CEDEX 2, France;
- Bioactifs et Cosmetiques, CNRS GDR 3711, 45067 Orléans CEDEX 2, France
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69
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Zhang J, Zeng W, Wu K, Ye J, Cheng Y, Cheng Y, Zou T, Peng N, Wu X, Zhao Y, Wang F. Unexpected Thymine Oxidation and Collision-Induced Thymine-Pt-guanine Cross-Linking on 5'-TpG and 5'-GpT by a Photoactivatable Diazido Pt(IV) Anticancer Complex. Inorg Chem 2020; 59:8468-8480. [PMID: 32450042 DOI: 10.1021/acs.inorgchem.0c00894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photochemical products of dinucleotides 5'-TpG/5'-GpT with a photoactivatable anticancer Pt(IV) complex (trans,trans,trans-[Pt(N3)2(OH)2(py)2], py = pyridine; 1) were characterized by electrospray ionization mass spectrometry. The primary MS showed the main products were monoplatinated and diplatinated adducts for both the dinucleotides accompanied by the formation of minor triplatinated dinucleotides, indicating that T-N3 and G-N1 may be platination sites additional to the well-known G-N7 site. Surprisingly, a series of minor platinated adducts with oxidation of guanine and/or thymine were observed. Although guanine is more sensitive to oxidation than thymine, thymine can compete with guanine for complex 1-induced oxidation, of which the oxidation adducts were identified as cis- and trans-diastereomers of 5,6-dihydroxy-5,6-dihydrothymidine (cis,trans-ThdGly), 5-formyl-2'-deoxyuridine (5-FormdUrd), and 5-(hydroxymethyl)-2'-deoxyuridine (5-HMdUrd), respectively. While for guanine, apart from 8-hydroxyguanine (8-OH-G) and N-formylamidoiminohydantoin (RedSp), other guanine oxidized adducts such as spiroiminodihydantoin (Sp), dehydroguanidinohydantoin (DGh), and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) were also identified. MS/MS analysis showed that unique fragments with a Pt moiety [Pt(N3)(py)] cross-linking the G and T bases were formed during the fragmentation of monoplatinated dinucleotides. Such binding mode to and oxidative damages on DNA bases imposed by the diazido Pt(IV) complex are apparently distinct from those of cisplatin, perhaps accounting for its unique mechanism of action.
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Affiliation(s)
- Jishuai Zhang
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Kui Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Juan Ye
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yiyu Cheng
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Yang Cheng
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Tao Zou
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Na Peng
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Xiaoqin Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials; School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences; National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,Basic Medical College, Shandong University of Chinese Traditional Medicine, Jinan 250355, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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70
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Ye L, Qiu L, Feng B, Jiang C, Huang Y, Zhang H, Zhang H, Hong H, Liu J. Role of Blood Oxygen Saturation During Post-Natal Human Cardiomyocyte Cell Cycle Activities. JACC Basic Transl Sci 2020; 5:447-460. [PMID: 32478207 PMCID: PMC7251192 DOI: 10.1016/j.jacbts.2020.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/28/2022]
Abstract
Blood oxygen saturation (SaO2) is one of the most important environmental factors in clinical heart protection. This study used human heart samples and human induced pluripotent stem cell-cardiomyocytes (iPSC-CMs) to assess how SaO2 affects human CM cell cycle activities. The results showed that there were significantly more cell cycle markers in the moderate hypoxia group (SaO2: 75% to 85%) than in the other 2 groups (SaO2 <75% or >85%). In iPSC-CMs 15% and 10% oxygen (O2) treatment increased cell cycle markers, whereas 5% and rapid change of O2 decreased the markers. Moderate hypoxia is beneficial to the cell cycle activities of post-natal human CMs.
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Key Words
- CHD, congenital heart disease
- CM, cardiomyocytes
- IF, immunofluorescence
- LV, lentivirus
- O2, oxygen
- SaO2, blood oxygen saturation
- TOF, tetralogy of Fallot
- YAP1, yes-associated protein 1
- blood oxygen saturation
- cardiomyocyte
- congenital heart disease
- iPSC, induced pluripotent stem cell
- pATM, phosphorylated ataxia telangiectasia mutated
- pHH3, phospho-histone H3
- pediatric patients
- proliferation
- qPCR, quantitative polymerase chain reaction
- sh, short hairpin
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Affiliation(s)
- Lincai Ye
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lisheng Qiu
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bei Feng
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chuan Jiang
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanhui Huang
- Department of Anesthesiology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haibo Zhang
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hao Zhang
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haifa Hong
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jinfen Liu
- Shanghai Institute for Pediatric Congenital Heart Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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71
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Huang SR, Liu Y, Tureček F. UV–vis Photodissociation Action Spectroscopy Reveals Cytosine–Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Reduction. J Phys Chem B 2020; 124:3505-3517. [DOI: 10.1021/acs.jpcb.0c01693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Yue Liu
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
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72
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Repolês BM, Machado CR, Florentino PTV. DNA lesions and repair in trypanosomatids infection. Genet Mol Biol 2020; 43:e20190163. [PMID: 32236391 PMCID: PMC7197992 DOI: 10.1590/1678-4685-gmb-2019-0163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/21/2019] [Indexed: 12/22/2022] Open
Abstract
Pathological processes such as bacterial, viral and parasitic infections can generate a plethora of responses such as, but not restricted to, oxidative stress that can be harmful to the host and the pathogen. This stress occurs when there is an imbalance between reactive oxygen species produced and antioxidant factors produced in response to the infection. This imbalance can lead to DNA lesions in both infected cells as well as in the pathogen. The effects of the host response on the parasite lead to several kinds of DNA damage, causing alterations in the parasite's metabolism; the reaction and sensitivity of the parasite to these responses are related to the DNA metabolism and life cycle of each parasite. The present review will discuss the survival strategies developed by host cells and Trypanosoma cruzi, focusing on the DNA repair mechanisms of these organisms throughout infection including the relationship between DNA damage, stress response features, and the unique characteristics of these diseases.
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Affiliation(s)
- Bruno M Repolês
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e Imunologia, Belo Horizonte MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e Imunologia, Belo Horizonte MG, Brazil
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73
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Hu L, Liu J, Zhang J, Zhang H, Xu P, Chen Z, Xiao E. A novel ratiometric fluorescent probe for rapid detection of hydrogen peroxide in living cells. RSC Adv 2019; 9:39532-39535. [PMID: 35540638 PMCID: PMC9076112 DOI: 10.1039/c9ra07517h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/24/2019] [Indexed: 12/17/2022] Open
Abstract
In this work, we present a new ratiometric fluorescent probe JNY-1 for rapid and convenient detection of H2O2. The probe could selectively and sensitively respond to H2O2 within 10 min. In addition, this probe was successfully applied for monitoring and imaging of H2O2 in liver cancer HepG2 cells under physiological conditions. A new ratiometric fluorescent probe JNY-1 for sensitive detection of H2O2 is presented with selectivity over other reactive oxygen species, reactive nitrogen species, and biologically relevant species. Imaging of H2O2 in liver cancer HepG2 cells was achieved.![]()
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Affiliation(s)
- Linan Hu
- Departments of Radiology, The Second Xiangya Hospital, Central South University Changsha Hunan 410011 P. R. China.,Departments of Radiology, Zhuzhou Central Hospital Zhuzhou Hunan 412000 P. R. China
| | - Jiayi Liu
- Departments of Radiology, The Second Xiangya Hospital, Central South University Changsha Hunan 410011 P. R. China
| | - Jie Zhang
- Departments of Radiology, The Second Xiangya Hospital, Central South University Changsha Hunan 410011 P. R. China
| | - Hailiang Zhang
- Institute of Clinical Pharmacy & Pharmacology, Jining First People's Hospital, Jining Medical University Jining 272000 P. R. China
| | - Pengfei Xu
- Institute of Clinical Pharmacy & Pharmacology, Jining First People's Hospital, Jining Medical University Jining 272000 P. R. China
| | - Zhu Chen
- Departments of Radiology, The Second Xiangya Hospital, Central South University Changsha Hunan 410011 P. R. China
| | - Enhua Xiao
- Departments of Radiology, The Second Xiangya Hospital, Central South University Changsha Hunan 410011 P. R. China
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74
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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75
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Abe YS, Sasaki S. The adduct formation between the thioguanine-polyamine ligands and DNA with the AP site under UVA irradiated and non-irradiated conditions. Bioorg Med Chem 2019; 27:115160. [PMID: 31706680 DOI: 10.1016/j.bmc.2019.115160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022]
Abstract
The AP sites are representative of DNA damage and known as an intermediate in the base excision repair (BER) pathway which is involved in the repair of damaged nucleobases by reactive oxygen species, UVA irradiation, and DNA alkylating agents. Therefore, it is expected that the inhibition or modulation of the AP site repair pathway may be a new type of anticancer drug. In this study, we investigated the effects of the thioguanine-polyamine ligands (SG-ligands) on the affinity and the reactivity for the AP site under UVA irradiated and non-irradiated conditions. The SG-ligands have a photo-reactivity with the A-F-C sequence where F represents a tetrahydrofuran AP site analogue. Interestingly, the SG-ligands promoted the β-elimination of the AP site followed by the formation of a covalent bond with the β-eliminated fragment without UVA irradiation.
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Affiliation(s)
- Yukiko S Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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76
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Cercola R, Uleanya KO, Dessent CEH. Electron detachment dynamics of the iodide-guanine cluster: does ionization occur from the iodide or from guanine? Mol Phys 2019. [DOI: 10.1080/00268976.2019.1679402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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77
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78
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Martínez Fernández L, Cerezo J, Asha H, Santoro F, Coriani S, Improta R. The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lara Martínez Fernández
- Departamento de Química, Facultad de Ciencias, Mòdulo13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco 28049 Madrid Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Mòdulo13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco 28049 Madrid Spain
| | - Haritha Asha
- Istituto di Biostrutture e Bioimmagini-CNR Via Mezzocannone 6 I-80134 Napoli
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)Area della Ricerca del CNR Via Moruzzi 1 I-56124 Pisa
| | - Sonia Coriani
- DTU ChemistryTechnical University of Denmark, Kemitorvet Building 207 DK-2800 Kongens Lyngby Denmark
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR Via Mezzocannone 6 I-80134 Napoli
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79
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Cogoi S, Ferino A, Miglietta G, Pedersen EB, Xodo LE. The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription. Nucleic Acids Res 2019; 46:661-676. [PMID: 29165690 PMCID: PMC5778462 DOI: 10.1093/nar/gkx1142] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleotides mimicking the KRAS G4-motif and found that 8-oxoG impacts folding and stability of the G-quadruplex. Dimethylsulphate-footprinting showed that the G-run carrying 8-oxoG is excluded from the G-tetrads and replaced by a redundant G-run in the KRAS G4-motif. Chromatin immunoprecipitation revealed that the base-excision repair protein OGG1 is recruited to the KRAS promoter when the level of 8-oxoG in the G4 region is raised by H2O2. Polyacrylamide gel electrophoresis evidenced that OGG1 removes 8-oxoG from the G4-motif in duplex, but when folded it binds to the G-quadruplex in a non-productive way. We also found that 8-oxoG enhances the recruitment to the KRAS promoter of MAZ and hnRNP A1, two nuclear factors essential for transcription. All this suggests that 8-oxoG in the promoter G4 region could have an epigenetic potential for the control of gene expression.
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Affiliation(s)
- Susanna Cogoi
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Annalisa Ferino
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | | | - Erik B Pedersen
- Nucleic Acid Center, Institute of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Luigi E Xodo
- Department of Medicine, University of Udine, 33100 Udine, Italy
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80
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Nagarajan K, Soundarapandian K, Thorne RF, Li D, Li D. Activation of Pyroptotic Cell Death Pathways in Cancer: An Alternative Therapeutic Approach. Transl Oncol 2019; 12:925-931. [PMID: 31085408 PMCID: PMC6518321 DOI: 10.1016/j.tranon.2019.04.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
Cancer can be considered the result of a series of genetic variations that lead to a normal cell being transformed into a malignant one while avoiding cell death-atypical characteristics of tumor development. Although a large number of genomics and epigenetic alterations have been identified in cells undergoing apoptotic, autophagic or necrotic cell death, the treatment of cancer remains thought-provoking. Pyroptosis is differentiated from other types of programmed cell death and is mainly activated by Caspase-1. To initiate pyroptosis, cells receive specific "death" messages, produce cytokines, swell, burst, and ultimately die. The deficiency of Caspase-1 expression may lead to inflammation-mediated tumor progression. Hence, the molecular mechanisms for the Caspase-1 activation in tumor tissues are yet to be exploited extensively. This review aims to summarise the latest discoveries about pyroptosis and its new exciting role in inducing cancer cell death.
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Affiliation(s)
- Kanipandian Nagarajan
- Department of Hepato-Biliary Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan Province, People's Republic of China
| | - Kannan Soundarapandian
- Proteomics and Molecular Cell Physiology Laboratory, Department of Zoology, Periyar University, Salem - 636 011, Tamil Nadu, India
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan Province, People's Republic of China
| | - Dongxiao Li
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, People's Republic of China.
| | - Deyu Li
- Department of Hepato-Biliary Pancreatic Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan Province, People's Republic of China.
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81
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Populations and Dynamics of Guanine Radicals in DNA strands-Direct versus Indirect Generation. Molecules 2019; 24:molecules24132347. [PMID: 31247883 PMCID: PMC6651618 DOI: 10.3390/molecules24132347] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 01/17/2023] Open
Abstract
Guanine radicals, known to be involved in the damage of the genetic code and aging, are studied by nanosecond transient absorption spectroscopy. They are generated in single, double and four-stranded structures (G-quadruplexes) by one and two-photon ionization at 266 nm, corresponding to a photon energy lower than the ionization potential of nucleobases. The quantum yield of the one-photon process determined for telomeric G-quadruplexes (TEL25/Na+) is (5.2 ± 0.3) × 10−3, significantly higher than that found for duplexes containing in their structure GGG and GG sequences, (2.1 ± 0.4) × 10−3. The radical population is quantified in respect of the ejected electrons. Deprotonation of radical cations gives rise to (G-H1)• and (G-H2)• radicals for duplexes and G-quadruplexes, respectively. The lifetimes of deprotonated radicals determined for a given secondary structure strongly depend on the base sequence. The multiscale non-exponential dynamics of these radicals are discussed in terms of inhomogeneity of the reaction space and continuous conformational motions. The deviation from classical kinetic models developed for homogeneous reaction conditions could also be one reason for discrepancies between the results obtained by photoionization and indirect oxidation, involving a bi-molecular reaction between an oxidant and the nucleic acid.
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Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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82
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Flood DT, Asai S, Zhang X, Wang J, Yoon L, Adams ZC, Dillingham BC, Sanchez BB, Vantourout JC, Flanagan ME, Piotrowski DW, Richardson P, Green SA, Shenvi RA, Chen JS, Baran PS, Dawson PE. Expanding Reactivity in DNA-Encoded Library Synthesis via Reversible Binding of DNA to an Inert Quaternary Ammonium Support. J Am Chem Soc 2019; 141:9998-10006. [PMID: 31136164 PMCID: PMC7033622 DOI: 10.1021/jacs.9b03774] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA Encoded Libraries have proven immensely powerful tools for lead identification. The ability to screen billions of compounds at once has spurred increasing interest in DEL development and utilization. Although DEL provides access to libraries of unprecedented size and diversity, the idiosyncratic and hydrophilic nature of the DNA tag severely limits the scope of applicable chemistries. It is known that biomacromolecules can be reversibly, noncovalently adsorbed and eluted from solid supports, and this phenomenon has been utilized to perform synthetic modification of biomolecules in a strategy we have described as reversible adsorption to solid support (RASS). Herein, we present the adaptation of RASS for a DEL setting, which allows reactions to be performed in organic solvents at near anhydrous conditions opening previously inaccessible chemical reactivities to DEL. The RASS approach enabled the rapid development of C(sp2)-C(sp3) decarboxylative cross-couplings with broad substrate scope, an electrochemical amination (the first electrochemical synthetic transformation performed in a DEL context), and improved reductive amination conditions. The utility of these reactions was demonstrated through a DEL-rehearsal in which all newly developed chemistries were orchestrated to afford a compound rich in diverse skeletal linkages. We believe that RASS will offer expedient access to new DEL reactivities, expanded chemical space, and ultimately more drug-like libraries.
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Affiliation(s)
- Dillon T. Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shota Asai
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Xuejing Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jie Wang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Leonard Yoon
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Zoë C. Adams
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Blythe C. Dillingham
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brittany B. Sanchez
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mark E. Flanagan
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - David W. Piotrowski
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive, San Diego, CA 92121, United States
| | - Samantha A. Green
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason S. Chen
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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83
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Miro P, Gomez-Mendoza M, Sastre G, Cuquerella MC, Miranda MA, Marin ML. Generation of the Thymine Triplet State by Through-Bond Energy Transfer. Chemistry 2019; 25:7004-7011. [PMID: 30920069 DOI: 10.1002/chem.201900830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Indexed: 01/12/2023]
Abstract
Benzophenone (BP) and drugs containing the BP chromophore, such as the non-steroidal anti-inflammatory drug ketoprofen, have been widely reported as DNA photosensitizers through triplet-triplet energy transfer (TTET). In the present work, a direct spectroscopic fingerprint for the formation of the thymine triplet (3 Thy*) by through-bond (TB) TTET from 3 BP* has been uncovered. This has been achieved in two new systems that have been designed and synthesized with one BP and one thymine (Thy) covalently linked to the two ends of the rigid skeleton of the natural bile acids cholic and lithocholic acid. The results shown here prove that it is possible to achieve triplet energy transfer to a Thy unit even when the photosensitizer is at a long (nonbonding) distance.
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Affiliation(s)
- Paula Miro
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior, de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Miguel Gomez-Mendoza
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior, de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
- Present address: Photoactivated Processes Unit, IMDEA Energy Institute, Avda Ramon de la Sagra 3, 28935 Mostoles, Madrid, Spain
| | - Germán Sastre
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior, de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - M Consuelo Cuquerella
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior, de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Miguel A Miranda
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior, de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - M Luisa Marin
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior, de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
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84
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Landi A, Borrelli R, Capobianco A, Peluso A. Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires. J Phys Chem Lett 2019; 10:1845-1851. [PMID: 30939015 DOI: 10.1021/acs.jpclett.9b00650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.
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Affiliation(s)
- Alessandro Landi
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science , University of Torino , Via Leonardo da Vinci 44 , I-10095 Grugliasco , Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
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85
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Dai L, Xia J, Sahin O, Zhang Q. Identification of a nth-Like Gene Encoding an Endonuclease III in Campylobacter jejuni. Front Microbiol 2019; 10:698. [PMID: 31024487 PMCID: PMC6467930 DOI: 10.3389/fmicb.2019.00698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/20/2019] [Indexed: 01/31/2023] Open
Abstract
Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. As a microaerobic pathogen, C. jejuni is subjected to DNA damages caused by various stresses such as reactive oxygen species (ROS) and UV radiations. The base excision repair (BER) system plays an important role in preventing mutations associated with oxidative DNA damage, but the system remains poorly characterized in Campylobacter. In this study, a BER homolog encoded by cj0595c (named nth) in C. jejuni was analyzed for endonuclease III activity and for its role in maintaining genomic stability. It was found that inactivation of nth resulted in elevated frequencies of spontaneous fluoroquinolone-resistant (FQR) and oxidative stress resistant (OXR) mutants, compared with the wild-type strain in C. jejuni. Sequencing analysis of the FQR and OXR mutants revealed that the elevated mutation rates were associated with C → T or G → A transition in gyrA (FQR mutants) or perR (for OXR mutants). In an in vitro assay, a purified recombinant C. jejuni Nth protein demonstrated endonuclease III activity that recognized and excised the thymine glycol (Tg) base from a double stranded DNA. These findings indicate that Nth functions as a BER repair enzyme in C. jejuni and is important for the repair of DNA damage, protecting the bacteria from stresses encountered within a host and in the environment.
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Affiliation(s)
- Lei Dai
- Departments of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jing Xia
- Departments of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Orhan Sahin
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Qijing Zhang
- Departments of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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86
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Liu ZQ. Enhancing Antioxidant Effect against Peroxyl Radical-Induced Oxidation of DNA: Linking with Ferrocene Moiety! CHEM REC 2019; 19:2385-2397. [PMID: 30946536 DOI: 10.1002/tcr.201800201] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023]
Abstract
As a major member in the family of reactive oxygen species, peroxyl radical is able to abstract hydrogen atom from 4-position of ribose, leading to the collapse of DNA strand. Thus, inhibiting oxidative stress with exogenous antioxidants acts as a promising strategy to protect the integrity of DNA structure and is thereby suggested to be a pathway against developments of related diseases. Ferrocene as an organometallic scaffold is widely applied in the design of organometallic drugs, and redox of Fe(II)/Fe(III) in ferrocene offers advantage for providing electron to radicals. Presented herein are our ongoing studies on ferrocene-appended antioxidants, including McMurry reaction applied to construct ferrocifen; Aldol condensation used to prepare ferrocenyl curcumin; Povarov reaction employed to prepare ferrocenyl quinoline; Biginelli reaction used to construct ferrocenyl dihydropyrimidine; Groebke reaction used to synthesize ferrocenyl imidazo[1,2-a]pyridine; and Passerini three-component reaction as well as Ugi four-component reaction applied to synthesize α-acyloxycarboxamide and bisamide, respectively. It is found that ferrocene moiety is able to enhance antioxidative effect of the aforementioned scaffolds even without the aid of phenolic hydroxyl group. The role of ferrocene in enhancing antioxidative effect can be attributable to trapping radicals, decreasing oxidative potential, and increasing the affinity toward DNA strand. Therefore, ferrocene is worthy to be taken into consideration in the design of drugs in relation to DNA oxidation.
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Affiliation(s)
- Zai-Qun Liu
- Department of Organic Chemistry, College of Chemistry, Jilin University, No.2519 Jiefang Road, Changchun, 130021, China
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87
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Okumura K, Nishihara S, Inoue YH. Genetic identification and characterization of three genes that prevent accumulation of oxidative DNA damage in Drosophila adult tissues. DNA Repair (Amst) 2019; 78:7-19. [PMID: 30947023 DOI: 10.1016/j.dnarep.2019.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 01/29/2023]
Abstract
Reactive oxygen species generated in the process of energy production represent a major cause of oxidative DNA damage. Production of the oxidized guanine base, 8-oxo-guanine (8-oxoG), results in mismatched pairing with adenine and subsequently leads to G:C to T:A transversions after DNA replication. Our previous study demonstrated that Drosophila CG1795 encodes an ortholog of Ogg1, which is essential for the elimination of 8-oxoG. Moreover, the Drosophila ribosomal protein S3 (RpS3) possesses N-glycosylase activity that eliminates 8-oxoG in vitro. In this study, we show that RpS3 heterozygotes hyper-accumulate 8-oxoG in midgut cell nuclei after oxidant feeding, suggesting thatRpS3 is required for the elimination of 8-oxoG in Drosophila adults. We further showed that several muscle-aging phenotypes were significantly accelerated in RpS3 heterozygotes. Ogg1 is localized in the nucleus, while RpS3 is in the cytoplasm, closely associated with endoplasmic reticulum networks. Results of genetic analyses also suggest that these two proteins operate similarly but independently in the elimination of oxidized guanine bases from genomic DNA. Next, we obtained genetic evidence suggesting that CG42813 functions as the Drosophila ortholog of mammalian Mth1 in the elimination of oxidized dGTP (8-oxo-dGTP) from the nucleotide pool. Depletion of this gene significantly increased the number of DNA damage foci in the nuclei of Drosophila midgut cells. Furthermore, several aging-related phenotypes such as age-dependent loss of adult locomotor activities and accumulation of polyubiquitylated proteins in adult muscles were also significantly accelerated in CG42813-depleted flies. Lastly, we investigated the phenotype of adults depleted of CG9272, which encodes a protein with homology to mammalian Nth1 that is essential for the elimination of oxidized thymine. Excessive accumulation of oxidized bases was observed in the epithelial cell nuclei after oxidant feeding. In conclusion, three genes that prevent accumulation of oxidative DNA damage were identified in Drosophila.
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Affiliation(s)
- Kazuko Okumura
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan
| | - Shunta Nishihara
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan
| | - Yoshihiro H Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan.
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88
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Abstract
The chemistry of DNA and its repair selectivity control the influence of genomic oxidative stress on the development of serious disorders such as cancer and heart diseases. DNA is oxidized by endogenous reactive oxygen species (ROS) in vivo or in vitro as a result of high energy radiation, non-radiative metabolic processes, and other consequences of oxidative stress. Some oxidations of DNA and tumor suppressor gene p53 are thought to be mutagenic when not repaired. For example, site-specific oxidations of p53 tumor suppressor gene may lead to cancer-related mutations at the oxidation site codon. This review summarizes the research on the primary products of the most easily oxidized nucleobase guanine (G) when different oxidation methods are used. Guanine is by far the most oxidized DNA base. The primary initial oxidation product of guanine for most, but not all, pathways is 8-oxoguanine (8-oxoG). With an oxidation potential much lower than G, 8-oxoG is readily susceptible to further oxidation, and the products often depend on the oxidants. Specific products may control the types of subsequent mutations, but mediated by gene repair success. Site-specific oxidations of p53 tumor suppressor gene have been reported at known mutation hot spots, and the codon sites also depend on the type of oxidants. Modern methodologies using LC-MS/MS for codon specific detection and identification of oxidation sites are summarized. Future work aimed at understanding DNA oxidation in nucleosomes and interactions between DNA damage and repair is needed to provide a better picture of how cancer-related mutations arise.
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Affiliation(s)
- Di Jiang
- Department of ChemistryUniversity of ConnecticutStorrsCT 06269United States
| | - James F. Rusling
- Department of ChemistryUniversity of ConnecticutStorrsCT 06269United States
- Department of SurgeryNeag Cancer Center, UConn HealthFarmingtonCT 06032United States
- Institute of Material ScienceUniversity of ConnecticutStorrsCT 06269United States
- School of ChemistryNational University of Ireland at GalwayIreland
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89
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Aslam S, Lan XR, Zhang BW, Chen ZL, Wang L, Niu DK. Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have. BMC Evol Biol 2019; 19:35. [PMID: 30691392 PMCID: PMC6350292 DOI: 10.1186/s12862-019-1365-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/17/2019] [Indexed: 12/17/2022] Open
Abstract
Background Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results. Results When aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes. Conclusions The positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1365-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sidra Aslam
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xin-Ran Lan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zheng-Lin Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Li Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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90
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Cadet J, Wagner JR, Angelov D. Biphotonic Ionization of DNA: From Model Studies to Cell. Photochem Photobiol 2018; 95:59-72. [PMID: 30380156 DOI: 10.1111/php.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule LBMC, CNRS-UMR 5239, Université de Lyon, École Normale Supérieure de Lyon, Lyon, France
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91
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Karwowski BT. The AT Interstrand Cross-Link: Structure, Electronic Properties, and Influence on Charge Transfer in dsDNA. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:665-685. [PMID: 30500729 PMCID: PMC6258832 DOI: 10.1016/j.omtn.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 12/01/2022]
Abstract
The interaction of chemical and physical agents with genetic material can lead to almost 80 different DNA damage formations. The targeted intentional DNA damage by radiotherapy or chemotherapy is a front-line anticancer therapy. An interstrand cross-link can result from ionization radiation or specific chemical agents, such as trans-/cisplatin activity. Here, the influence of the adenine and thymidine (AT) interstrand linkage, the covalent bond between the adenine N6 and thymidine C5 methylene group, on the isolated base pair as well as double-stranded DNA (dsDNA) was taken into quantum mechanical/molecular mechanical (QM/MM) consideration at the m062x/6-31+G*:UFF level of theory in the aqueous phase. All the results presented in this article, for the first time, show that an AT-interstrand cross-link (ICL) changes the positive and negative charge migration process due to a higher activation energy forced by the cross-link’s presence. However, the final radical cation destination in cross-linked DNA is left in the same place as in a native double-stranded-deoxyoligonucleotide. Additionally, the direction of the radical anion transfer was found to be opposite to that of native dsDNA. Therefore, it can be postulated that the appearance of the AT-ICL does not disturb the hole migration in the double helix, with subsequent effective changes in the electron migration process.
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Affiliation(s)
- Boleslaw T Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland.
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92
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Liu Y, Korn JA, Dang A, Tureček F. Hydrogen-Rich Cation Radicals of DNA Dinucleotides: Generation and Structure Elucidation by UV-Vis Action Spectroscopy. J Phys Chem B 2018; 122:9665-9680. [PMID: 30269486 DOI: 10.1021/acs.jpcb.8b07925] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hydrogen-rich DNA dinucleotide cation radicals (dGG + 2H)+•, (dCG + 2H)+•, and (dGC + 2H)+• represent transient species comprising protonated and hydrogen atom adducted nucleobase rings that serve as models for proton and radical migrations in ionized DNA. These DNA cation radicals were generated in the gas phase by electron-transfer dissociation of dinucleotide dication-crown-ether complexes and characterized by UV-vis photodissociation action spectra, ab initio calculations of structures and relative energies, and time-dependent density functional theory calculations of UV-vis absorption spectra. Theoretical calculations indicate that (dGG + 2H)+• cation radicals formed by electron transfer underwent an exothermic conformational collapse that was accompanied by guanine ring stacking and facile internucleobase hydrogen atom transfer, forming 3'-guanine C-8-H radicals. In contrast, exothermic hydrogen transfer from the 5'-cytosine radical onto the guanine ring in (dCG + 2H)+• was kinetically hampered, resulting in the formation of a mixture of 5'-cytosine and 3'-guanine radicals. Conformational folding and nucleobase stacking were energetically unfavorable in (dGC + 2H)+• that retained its structure of a 3'-cytosine radical, as formed by one-electron reduction of the dication. Hydrogen-rich guanine (G + H)• and cytosine (C + H)• radicals were calculated to have vastly different basicities in water, as illustrated by the respective p Ka values of 20.0 and 4.6, which is pertinent to their different abilities to undergo proton-transfer reactions in solution.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
| | - Joseph A Korn
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
| | - Andy Dang
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
| | - František Tureček
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
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93
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Banyasz A, Martínez-Fernández L, Improta R, Ketola TM, Balty C, Markovitsi D. Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation. Phys Chem Chem Phys 2018; 20:21381-21389. [PMID: 30101268 DOI: 10.1039/c8cp02588f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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94
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Martínez‐Fernández L, Banyasz A, Markovitsi D, Improta R. Topology Controls the Electronic Absorption and Delocalization of Electron Holes in Guanine Quadruplexes. Chemistry 2018; 24:15185-15189. [DOI: 10.1002/chem.201803222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | | | - Roberto Improta
- LIDYL, CEA, CNRSUniversité Paris-Saclay 91191 Gif-sur-Yvette France
- Istituto di Biostrutture e BioimmaginiCNR Via Mezzocannone 16 80134 Napoli Italy
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95
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Sun H, Zheng L, Greenberg MM. Independent Generation of Reactive Intermediates Leads to an Alternative Mechanism for Strand Damage Induced by Hole Transfer in Poly(dA-T) Sequences. J Am Chem Soc 2018; 140:11308-11316. [PMID: 30169029 DOI: 10.1021/jacs.8b05484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Purine radical cations (dA•+ and dG•+) are the primary hole carriers of DNA hole migration due to their favorable oxidation potential. Much less is known about the reactivity of higher energy pyrimidine radical cations. The thymidine radical cation (T•+) was produced at a defined position in DNA from a photochemical precursor for the first time. T•+ initiates hole transfer to dGGG triplets in DNA. Hole localization in a dGGG sequence accounts for ∼26% of T•+ formed under aerobic conditions in 9. Reduction to yield thymidine is also quantified. 5-Formyl-2'-deoxyuridine is formed in low yield in DNA when T•+ is independently generated. This is inconsistent with mechanistic proposals concerning product formation from electron transfer in poly(dA-T) sequences, following hole injection by a photoexcited anthraquinone. Additional evidence that is inconsistent with the original mechanism was obtained using hole injection by a photoexcited anthraquinone in DNA. Instead of requiring the intermediacy of T•+, the strand damage patterns observed in those studies, in which thymidine is oxidized, are reproduced by independent generation of 2'-deoxyadenosin- N6-yl radical (dA•). Tandem lesion formation by dA• provides the basis for an alternative mechanism for thymidine oxidation ascribed to hole migration in poly(dA-T) sequences. Overall, these experiments indicate that the final products formed following DNA hole transfer in poly(dA-T) sequences do not result from deprotonation or hydration of T•+, but rather from deprotonation of the more stable dA•+, to form dA•, which produces tandem lesions in which 5'-flanking thymidines are oxidized.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Liwei Zheng
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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96
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Capobianco A, Landi A, Peluso A. Modeling DNA oxidation in water. Phys Chem Chem Phys 2018; 19:13571-13578. [PMID: 28513687 DOI: 10.1039/c7cp02029e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, I-84084 Fisciano (SA), Italy.
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97
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Sowlati-Hashjin S, Wetmore SD. Structural Insight into the Discrimination between 8-Oxoguanine Glycosidic Conformers by DNA Repair Enzymes: A Molecular Dynamics Study of Human Oxoguanine Glycosylase 1 and Formamidopyrimidine-DNA Glycosylase. Biochemistry 2018; 57:1144-1154. [PMID: 29320630 DOI: 10.1021/acs.biochem.7b01292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
hOgg1 and FPG are the primary DNA repair enzymes responsible for removing the major guanine (G) oxidative product, namely, 7,8-dihydro-8-oxoguanine (OG), in humans and bacteria, respectively. While natural G adopts the anti conformation and forms a Watson-Crick pair with cytosine (C), OG can also adopt the syn conformation and form a Hoogsteen pair with adenine (A). hOgg1 removes OG paired with C but is inactive toward the OG:A pair. In contrast, FPG removes OG from OG:C pairs and also exhibits appreciable (although diminished) activity toward OG:A pairs. As a first step toward understanding this difference in activity, we have employed molecular dynamics simulations to examine how the anti and syn conformers of OG are accommodated in the hOgg1 and FPG active sites. When anti-OG is bound, hOgg1 active site residues are properly aligned to initiate catalytic base departure, while geometrical parameters required for the catalytic reaction are not conserved for syn-OG. On the other hand, the FPG catalytic residues are suitably aligned for both OG conformers, with anti-OG being more favorably bound. Thus, our data suggests that the differential ability of hOgg1 and FPG to accommodate the anti- and syn-OG glycosidic conformations is an important factor that contributes to the relative experimental excision rates. Nevertheless, the positions of the nucleophiles with respect to the lesion in the active sites suggest that the reactant complex is poised to initiate catalysis through a similar mechanism for both repair enzymes and supports a recently proposed mechanism in which sugar-ring opening precedes nucleoside deglycosylation.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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98
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Dang A, Nguyen HTH, Ruiz H, Piacentino E, Ryzhov V, Tureček F. Experimental Evidence for Noncanonical Thymine Cation Radicals in the Gas Phase. J Phys Chem B 2017; 122:86-97. [DOI: 10.1021/acs.jpcb.7b09872] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andy Dang
- Department
of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Huong T. H. Nguyen
- Department
of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Heather Ruiz
- Department
of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Elettra Piacentino
- Department
of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Victor Ryzhov
- Department
of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - František Tureček
- Department
of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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99
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Lenz SAP, Wetmore SD. QM/MM Study of the Reaction Catalyzed by Alkyladenine DNA Glycosylase: Examination of the Substrate Specificity of a DNA Repair Enzyme. J Phys Chem B 2017; 121:11096-11108. [PMID: 29148771 DOI: 10.1021/acs.jpcb.7b09646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair pathway to excise structurally diverse oxidized and alkylated DNA purines. Specifically, AAG uses a water molecule activated by a general base and a nonspecific active site lined with aromatic residues to cleave the N-glycosidic bond. Despite broad substrate specificity, AAG does not target the natural purines (adenine (A) and guanine (G)). Using the ONIOM(QM:MM) methodology, we provide fundamental atomic level details of AAG bound to DNA-containing a neutral substrate (hypoxanthine (Hx)), a nonsubstrate (G), or a cationic substrate (7-methylguanine (7MeG)) and probe changes in the reaction pathway that occur when AAG targets different nucleotides. We reveal that subtle differences in protein-DNA contacts upon binding different substrates within the flexible AAG active site can significantly affect the deglycosylation reaction. Notably, we predict that AAG excises Hx in a concerted mechanism that is facilitated through correct alignment of the (E125) general base due to hydrogen bonding with a neighboring aromatic amino acid (Y127). Hx departure is further stabilized by π-π interactions with aromatic amino acids and hydrogen bonds with active site water. Despite possessing a similar structure to Hx, G is not excised since the additional exocyclic amino group leads to misalignment of the general base due to disruption of the key E125-Y127 hydrogen bond, the catalytically unfavorable placement of water within the active site, and weakened π-contacts between aromatic amino acids and the nucleobase. In contrast, cationic 7MeG does not occupy the same position within the AAG active site as G due to steric clashes with the additional N7 methyl group, which results in the correct alignment of the general base and permits nucleobase excision as observed for neutral Hx. Overall, our structural data rationalizes the observed substrate specificity of AAG and contributes to our fundamental understanding of enzymes with flexible active sites and broad substrate specificities.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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100
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Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
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Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
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