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Szczepaniak O, Ligaj M. May DNA analyses be biased by hidden oxidative damage? Voltammetric study of temperature and oxidation stress effect. PLoS One 2024; 19:e0305590. [PMID: 38875261 PMCID: PMC11178200 DOI: 10.1371/journal.pone.0305590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/01/2024] [Indexed: 06/16/2024] Open
Abstract
The analysis of nucleic acids is one of the fundamental parts of modern molecular biology and molecular diagnostics. The information collected predominantly depends on the condition of the genetic material. All potential damage induced by oxidative stress may affect the final results of the analysis of genetic material obtained using commonly used techniques such as polymerase chain reaction or sequencing. The aim of this work was to evaluate the effects of high temperature and pH on DNA structure in the context of the occurrence of oxidative damage, using square-wave voltammetry and two independent research protocols. We resulted in visible oxidation damage registered in acidic conditions after the thermal denaturation process (pH 4.7) with changes in the intensity of guanine and adenine signals. However, using phosphate buffer (pH 7.0) for DNA denaturation negatively affected the DNA structure, but without any oxidized derivatives present. This leads to the conclusion that oxidation occurring in the DNA melting process results in the formation of various derivatives of nucleobases, both electrochemically active and inactive. These derivatives may distort the results of molecular tests due to the possibility of forming complementary bonds with various nucleobases. For example, 8-oxoguanine can form pairs with both cytosine and adenine.
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Affiliation(s)
- Oskar Szczepaniak
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
| | - Marta Ligaj
- Department of Industrial Products and Packaging Quality, Poznań University of Economics and Business, Poznań, Poland
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2
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Kecel Gunduz S, Budama Kilinc Y, Bicak B, Gok B, Belmen B, Aydogan F, Yolacan C. New Coumarin Derivative with Potential Antioxidant Activity: Synthesis, DNA Binding and In Silico Studies (Docking, MD, ADMET). ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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3
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Gökoğlu E, Kıpçak F, Taskin-Tok T, Duyar H, Seferoğlu Z. Structural analysis and calf thymus DNA/HSA binding properties of new carbazole derivative containing piperazine. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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4
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Rafique B, Kalsoom S, Sajini AA, Ismail H, Iqbal M. Synthesis, Characterization, Biological Evaluation and DNA Interaction Studies of 4-Aminophenol Derivatives: Theoretical and Experimental Approach. Molecules 2022; 27:molecules27041352. [PMID: 35209141 PMCID: PMC8879259 DOI: 10.3390/molecules27041352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 01/27/2023] Open
Abstract
In the present study, five 4-aminophenol derivatives (4-chloro-2-(((4-hydroxyphenyl)imino)methyl)phenol(S-1), 4-((4-(dimethylamino)benzylidene)amino)phenol(S-2), 4-((3-nitrobenzylidene)amino)phenol(S-3), 4-((thiophen-2-ylmethylene)amino)phenol(S-4) and 4-(((E)-3-phenylallylidene)amino)phenol(S-5)) were synthesized and characterized by FT-IR, 1H-NMR, 13C-NMR and elemental analyses. The synthesized compounds were tested for their antimicrobial (Gram-positive and Gram-negative bacteria and Saccharomyces cervesea fungus) and antidiabetic (α-amylase and α-glucosidase inhibitory) activities. All the compounds showed broad-spectrum activities against the Staphylococcus aureus (ATCC 6538), Micrococcus luteus (ATCC 4698), Staphylococcus epidermidis (ATCC 12228), Bacillus subtilis sub. sp spizizenii (ATCC 6633), Bordetella bronchiseptica (ATCC 4617) and Saccharomyces cerevisiae (ATCC 9763) strains. The newly synthesized compounds showed a significant inhibition of amylase (93.2%) and glucosidase (73.7%) in a concentration-dependent manner. Interaction studies of Human DNA with the synthesized Schiff bases were also performed. The spectral bands of S-1, S-2, S-3 and S-5 all showed hyperchromism, whereas the spectral band of S-4 showed a hypochromic effect. Moreover, the spectral bands of the S-2, S-3 and S-4 compounds were also found to exhibit a bathochromic shift (red shift). The present studies delineate broad-spectrum antimicrobial and antidiabetic activities of the synthesized compounds. Additionally, DNA interaction studies highlight the potential of synthetic compounds as anticancer agents. The DNA interaction studies, as well as the antidiabetic activities articulated by the molecular docking methods, showed the promising aspects of synthetic compounds.
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Affiliation(s)
- Bushra Rafique
- Department of Chemistry, School of Natural Sciences, National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan;
| | - Saima Kalsoom
- Department of Chemistry, Preston University, Islamabad 44000, Pakistan;
| | - Abdulrahim A. Sajini
- Healthcare Engineering Innovation Center (HEIC), Department of Biomedical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Hammad Ismail
- Department of Biochemistry and Biotechnology, Umar Al Khayyam Block, Hafiz Hayat Campus, University of Gujrat, Gujrat 50700, Pakistan;
| | - Mudassir Iqbal
- Department of Chemistry, School of Natural Sciences, National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan;
- Correspondence:
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5
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Arul P, Huang ST, Gowthaman NSK, Shankar S. Simultaneous electrochemical determination of DNA nucleobases using AgNPs embedded covalent organic framework. Mikrochim Acta 2021; 188:358. [PMID: 34596766 DOI: 10.1007/s00604-021-05021-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/07/2021] [Indexed: 02/01/2023]
Abstract
An efficient electrochemical biosensor has been developed for the simultaneous evaluation of DNA bases using AgNPs-embedded covalent organic framework (COF). The COF (p-Phenylenediamine and terephthalaldehyde) was synthesized by reflux (DMF; 150 °C; 12 h) and the nanoparticles were embedded from the aqueous solutions of AgNO3 and NaBH4. The nanocomposite-modified COF was confirmed by spectral, microscopic, and electrochemical techniques. The nanocomposite material was deposited on a glassy carbon electrode (GCE) and the redox behavior of AgNPs was confirmed by cyclic voltammetry. The electrocatalytic activities of DNA bases were analyzed by differential pulse voltammetry (DPV) in a physiological environment (PBS; pH = 7.0) based on simple and easy-to-use electrocatalyst. The AgNPs-COF/GCE showed well-defined anodic peak currents for the bases guanine (+ 0.63 V vs. Ag/AgCl), adenine (+ 0.89 V vs. Ag/AgCl), thymine (+ 1.10 V vs. Ag/AgCl), and cytosine (+ 1.26 V vs. Ag/AgCl) in a mixture as well as individuals with respect to the conventional, COF, and AgNPs/GCEs. The AgNPs-COF/GCE showed linear concentration range of DNA bases from 0.2-1000 µM (guanine; (G)), 0.1-500 µM (adenine (A)), 0.25-250 µM (thymine (T)) and 0.15-500 µM (cytosine (C)) and LOD of 0.043, 0.056, 0.062, and 0.051 µM (S/N = 3), respectively. The developed sensor showed reasonable selectivity, reproducibility (RSD = 1.53 ± 0.04%-2.58 ± 0.02% (n = 3)), and stability (RSD = 1.22 ± 0.06%-2.15 ± 0.04%; n = 3) over 5 days of storage) for DNA bases. Finally, AgNPs-COF/GCE was used for the determination of DNA bases in human blood serum, urine and saliva samples with good recoveries (98.60-99.11%, 97.80-99.21%, and 98.69-99.74%, respectively).
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Affiliation(s)
- P Arul
- Institute of Biochemical and Biomedical Engineering, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan, Republic of China.
| | - Sheng-Tung Huang
- Institute of Biochemical and Biomedical Engineering, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan, Republic of China
| | - N S K Gowthaman
- School of Engineering, Monash University, 47500, Bandar Sunway, Malaysia
| | - Sekar Shankar
- School of Material Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
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6
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Bheemanaboina RRY, Wang J, Hu YY, Meng JP, Guan Z, Zhou CH. A facile reaction to access novel structural sulfonyl-hybridized imidazolyl ethanols as potential DNA-targeting antibacterial agents. Bioorg Med Chem Lett 2021; 47:128198. [PMID: 34119615 DOI: 10.1016/j.bmcl.2021.128198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]
Abstract
A novel type of sulfonyl-hybridized imidazolyl ethanols as potential DNA-targeting antibacterial agents was constructed via the unique ring-opened reaction of oxiranes by imidazoles for the first time. Some developed target hybrids showed potential antimicrobial potency against the tested microbes. Especially, imidazole derivative 5f could strongly suppressed the growth of MRSA (MIC = 4 μg/mL), which was 2-fold and 16-fold more potent than the positive control sulfathiazole and norfloxacin. This compound exhibited quite low propensity to induce bacterial resistance. Antibacterial mechanism exploration indicated that compound 5f could embed in MRSA DNA to form steady 5f-DNA complex, which possibly hinder DNA replication to exert antimicrobial behavior. Molecular docking showed that molecule 5f could bind with dihydrofolate synthetase through hydrogen bonds. These results implied that imidazole derivative 5f could be served as a promising molecule for the exploration of novel antibacterial candidates.
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Affiliation(s)
- Rammohan R Yadav Bheemanaboina
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Juan Wang
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yuan-Yuan Hu
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Jiang-Ping Meng
- National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, College of Pharmacy, Chongqing University of Arts and Sciences, Chongqing 402160, China.
| | - Zhi Guan
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
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7
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Yang Y, Lin M, Feng S, Gu Q, Chen Y, Wang Y, Song D, Gao M. Chemical composition, antibacterial activity, and mechanism of action of essential oil from
Litsea cubeba
against foodborne bacteria. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yu‐Jing Yang
- Key Laboratory for Food Microbial Technology of Zhejiang Province Zhejiang Gongshang University Hangzhou PR China
| | - Meng‐Yi Lin
- Key Laboratory for Food Microbial Technology of Zhejiang Province Zhejiang Gongshang University Hangzhou PR China
| | - Shu‐Yi Feng
- Key Laboratory for Food Microbial Technology of Zhejiang Province Zhejiang Gongshang University Hangzhou PR China
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province Zhejiang Gongshang University Hangzhou PR China
| | - Yi‐Cun Chen
- State Key Laboratory of Tree Genetics and Breeding Chinese Academy of Forestry Beijing PR China
- Institute of Subtropical Forestry Chinese Academy of Forestry Hangzhou PR China
| | - Yang‐Dong Wang
- State Key Laboratory of Tree Genetics and Breeding Chinese Academy of Forestry Beijing PR China
- Institute of Subtropical Forestry Chinese Academy of Forestry Hangzhou PR China
| | - Da‐feng Song
- Key Laboratory for Food Microbial Technology of Zhejiang Province Zhejiang Gongshang University Hangzhou PR China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding Chinese Academy of Forestry Beijing PR China
- Institute of Subtropical Forestry Chinese Academy of Forestry Hangzhou PR China
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8
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Phadte AA, Banerjee S, Mate NA, Banerjee A. Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines. Biochem Biophys Rep 2019; 18:100629. [PMID: 30993216 PMCID: PMC6449707 DOI: 10.1016/j.bbrep.2019.100629] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022] Open
Abstract
Push-pull dibenzodioxins and phenazines having ‘anthracene-like’ planar structures and good charge transfer character had been previously synthesised in our laboratory. The dibenzodioxins had earlier proven their anti-proliferative nature against HeLa tumor cell lines. Since phenazines are structural analogues of the former, these molecules were evaluated in course of the current study for their cytotoxic action against HeLa cell lines and they exhibited strong anti-tumor activity. This behavior could be related to their good DNA binding property. The DNA binding modes of molecules 1–4 (Fig. 1) were evaluated using various experimental techniques and they interacted with DNA in a non-covalently by both intercalative as well as groove binding mechanisms. Molecule 1 follows predominantly intercalative binding mode whereas molecules 2 and 3 have nearly equal and opposite preferences for both groove binding and intercalative modes. For molecule 4, groove binding is preferred mode of binding to DNA. A rationale for such differential binding behaviour is provided based on the subtle structural differences in our synthesised dibenzodioxins and phenazines. Elucidation of the mode of a molecule-DNA-binding event is relevant for understanding the mechanism of action of these molecules and will help promote further research into designing better DNA targeting small molecules. DNA binding modes of push-pull planar dibenzodioxins and phenazines were elucidated. DNA binding mechanistic details were obtained by spectroscopic and viscometric techniques. The molecular shape and geometry has a bearing on its choice of binding mode.
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Affiliation(s)
- Apeksha Ashok Phadte
- Department of Chemistry, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
| | - Subhadeep Banerjee
- Department of Chemistry, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
| | - Nayan Anand Mate
- Department of Biological Sciences, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
| | - Arnab Banerjee
- Department of Biological Sciences, BITS Pilani KK Birla Goa Campus, Zuarinagar, Goa, 403726, India
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9
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Jing R, Wang H, Ju S, Cui M. Reference materials for molecular diagnostics: Current achievements and future strategies. Clin Biochem 2018; 56:11-17. [DOI: 10.1016/j.clinbiochem.2018.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 04/08/2018] [Accepted: 04/17/2018] [Indexed: 02/06/2023]
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10
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Terent'yeva YG, Yashchuk VM, Zaika LA, Snitserova OM, Losytsky MY. The manifestation of optical centers in UV-Vis absorption and luminescence spectra of white blood human cells. Methods Appl Fluoresc 2016; 4:044010. [PMID: 28192303 DOI: 10.1088/2050-6120/4/4/044010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A white blood human cells spectral investigation is presented. The aim of this series of experiments was to obtain and analyze the absorption and luminescence (fluorescence and phosphorescence) spectra at room temperature and at 78 K of newly isolated white blood human cells and their organelles. As a result the optical centers and possible biochemical components that form the studied spectra where identified. Also the differences between the spectra of abnormal cells (B-cell chronic lymphocytic leukemia BCLL) and normal ones were studied for the whole cells and individual organelles.
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11
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Barchanski A, Hashimoto N, Petersen S, Sajti CL, Barcikowski S. Impact of spacer and strand length on oligonucleotide conjugation to the surface of ligand-free laser-generated gold nanoparticles. Bioconjug Chem 2012; 23:908-15. [PMID: 22475043 DOI: 10.1021/bc200462b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Gold nanoparticles conjugated to nucleic acids are widely used for biomedical targeting and sensing applications; however, little is known about the conjugation chemistry covering the impact of steric dimension and strand orientation of single-stranded oligonucleotides (ssO) on the conjugation process and binding efficiencies. In this context, we present an extensive investigation concerning the attachment of thiolated ssO to the surface of laser-generated gold nanoparticles, altering both strand length and binding orientation by the insertion of different spacer types at either the 3' or 5' ssO terminus. A significant reduction of conjugation efficiency of about 30-50% is determined for spacer-prolonged bionanoconjugates due to coiling effects of the flexible ssO strand on the particle surface which increases deflection angle of oligonucleotides and limits the number of biomolecules attached to the nanoparticles.
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Affiliation(s)
- A Barchanski
- Laser Zentrum Hannover e.V., Hollerithallee 8, 30419 Hannover, Germany
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Jury F, Morris J, Davis E, Ollier W, Yuille M. Sources of variability between biobanks in the estimation of DNA concentration. Biopreserv Biobank 2012; 10:55-61. [PMID: 24849754 DOI: 10.1089/bio.2011.0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
In biobank networks, accrual, aggregation, and retrieval of samples and data are impeded if minimal standards are not agreed in advance by the network members. The critical requirement is that outputs be standardized between biobanks. To start to address this problem of minimal standards, we undertook a pilot study and now report a follow-up study with 79 centers to identify sources of variability in a common measurement-the estimation of DNA concentration. Our main findings include confirmation of the results of the pilot study on overall variability between centers; fluorescence spectroscopy yields lower estimates of concentration and has less accuracy than absorption spectroscopy; and the 2 technologies differ in their sensitivity to mixing of the samples before measurement. We found that more recent servicing of liquid handling devices contributes to accuracy (at least when deploying absorption spectroscopy). We conclude that, while further study is required, there is a need to promote the development of complete Standard Operating Procedures in academic and commercial laboratories with the implementation of management systems that ensure full adherence to those procedures. There also needs to be a consensus on how much variability in measurements is acceptable for each downstream platform for technologies, including genotyping, sequencing, and epigenetics.
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Affiliation(s)
- Francine Jury
- 1 Centre for Integrated Genomic Medical Research, The University of Manchester/Manchester Academic Health Science Centre , Manchester, United Kingdom
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