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Agafonova LE, Zhdanov DD, Gladilina YA, Shishparenok AN, Shumyantseva VV. Electrochemical approach for the analysis of DNA degradation in native DNA and apoptotic cells. Heliyon 2024; 10:e25602. [PMID: 38371963 PMCID: PMC10873663 DOI: 10.1016/j.heliyon.2024.e25602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
The aim of this work was to develop an electrochemical approach for the analysis of DNA degradation and fragmentation in apoptotic cells. DNA damage is considered one of the major causes of human diseases. We analyzed the cleavage processes of the circular plasmid pTagGFP2-N and calf thymus DNA, which were exposed to restriction endonucleases (the restriction endonucleases BstMC I and AluB I and the nonspecific endonuclease I). Genomic DNA from the leukemia K562 cell line was used as a marker of the early and late (mature) stages of apoptosis. Registration of direct electrochemical oxidation of nucleobases of DNA molecules subjected to restriction endonuclease or apoptosis processes was proposed for the detection of these biochemical events. Label-free differential pulse voltammetry (DPV) has been used to measure endonuclease activities and DNA damage using carbon nanotube-modified electrodes. The present DPV technique provides a promising platform for high-throughput screening of DNA hydrolases and for registering the efficiency of apoptotic processes. DPV comparative analysis of the circular plasmid pTagGFP2-N in its native supercoiled state and plasmids restricted to 4 and 23 parts revealed significant differences in their electrochemical behavior. Electrochemical analysis was fully confirmed by means of traditional methods of DNA analysis and registration of apoptotic process, such as gel electrophoresis and flow cytometry.
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Affiliation(s)
- Lyubov E. Agafonova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121, Moscow, Russia
| | - Dmitry D. Zhdanov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121, Moscow, Russia
- Department of Biochemistry, Рeoples’ Friendship University of Russia Named After Patrice Lumumba (RUDN University), Miklukho-Maklaya St. 6, 117198, Moscow, Russia
| | - Yulia A. Gladilina
- Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121, Moscow, Russia
| | | | - Victoria V. Shumyantseva
- Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121, Moscow, Russia
- Department of Biochemistry, Pirogov Russian National Research Medical University, Ostrovitianova St. 1, 117997, Moscow, Russia
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2
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Plucnara M, Eksin E, Erdem A, Fojta M. Electrochemical Detection of SNP in Human Mitochondrial DNA Using Cyclic Primer Extension with Biotinylated Nucletides and Enzymatic Labeling at Disposable Pencil Graphite Electrodes. ELECTROANAL 2018. [DOI: 10.1002/elan.201800314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Medard Plucnara
- Institute of Biophysics Academy of Sciences of the Czech Republic, v.v.i. Královopolská 135 612 65 Brno Czech Republic
| | - Ece Eksin
- Ege University, Faculty of Pharmacy Analytical Chemistry Department 35100 Bornova, Izmir Turkey
- Ege University, Graduate School of Natural and Applied Science Biotechnology Department 35100 Bornova, Izmir Turkey
| | - Arzum Erdem
- Ege University, Faculty of Pharmacy Analytical Chemistry Department 35100 Bornova, Izmir Turkey
- Ege University, Graduate School of Natural and Applied Science Biotechnology Department 35100 Bornova, Izmir Turkey
| | - Miroslav Fojta
- Institute of Biophysics Academy of Sciences of the Czech Republic, v.v.i. Královopolská 135 612 65 Brno Czech Republic
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3
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Varmira K, Saed-Mocheshi M, Jalalvand AR. Electrochemical sensing and bio-sensing of bisphenol A and detection of its damage to DNA: A comprehensive review. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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4
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Fojta M, Daňhel A, Havran L, Vyskočil V. Recent progress in electrochemical sensors and assays for DNA damage and repair. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.11.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kahanda D, Chakrabarti G, Mcwilliams MA, Boothman DA, Slinker JD. Using DNA devices to track anticancer drug activity. Biosens Bioelectron 2016; 80:647-653. [PMID: 26901461 DOI: 10.1016/j.bios.2016.02.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 01/13/2023]
Abstract
It is beneficial to develop systems that reproduce complex reactions of biological systems while maintaining control over specific factors involved in such processes. We demonstrated a DNA device for following the repair of DNA damage produced by a redox-cycling anticancer drug, beta-lapachone (β-lap). These chips supported ß-lap-induced biological redox cycle and tracked subsequent DNA damage repair activity with redox-modified DNA monolayers on gold. We observed drug-specific changes in square wave voltammetry from these chips at therapeutic ß-lap concentrations of high statistical significance over drug-free control. We also demonstrated a high correlation of this change with the specific ß-lap-induced redox cycle using rational controls. The concentration dependence of ß-lap revealed significant signal changes at levels of high clinical significance as well as sensitivity to sub-lethal levels of ß-lap. Catalase, an enzyme decomposing peroxide, was found to suppress DNA damage at a NQO1/catalase ratio found in healthy cells, but was clearly overcome at a higher NQO1/catalase ratio consistent with cancer cells. We found that it was necessary to reproduce key features of the cellular environment to observe this activity. Thus, this chip-based platform enabled tracking of ß-lap-induced DNA damage repair when biological criteria were met, providing a unique synthetic platform for uncovering activity normally confined to inside cells.
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Affiliation(s)
- Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, United States
| | - Gaurab Chakrabarti
- Departments of Pharmacology, Oncology and Radiation Oncology, Laboratory of Molecular Stress Responses and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, ND2.210K 601 Forest Park Drive, Dallas, TX 75390-8807, United States
| | - Marc A Mcwilliams
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, United States
| | - David A Boothman
- Departments of Pharmacology, Oncology and Radiation Oncology, Laboratory of Molecular Stress Responses and the Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, ND2.210K 601 Forest Park Drive, Dallas, TX 75390-8807, United States
| | - Jason D Slinker
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Rd., PHY 36, Richardson, TX 75080, United States.
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Electrochemical behavior of 7-deazaguanine- and 7-deazaadenine-modified DNA at the hanging mercury drop electrode. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-015-1584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Wu Y, Yang X, Zhang B, Guo LH. An electrochemiluminescence biosensor for 8-oxo-7,8-dihydro-2′-deoxyguanosine quantification and DNA repair enzyme activity analysis using a novel bifunctional probe. Biosens Bioelectron 2015; 69:235-40. [DOI: 10.1016/j.bios.2015.02.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/13/2015] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
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8
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Němcová K, Sebest P, Havran L, Orság P, Fojta M, Pivoňková H. Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode. Anal Bioanal Chem 2014; 406:5843-52. [PMID: 25056872 DOI: 10.1007/s00216-014-7996-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 06/22/2014] [Accepted: 06/24/2014] [Indexed: 11/28/2022]
Abstract
In this paper, we present an electrochemical DNA-protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT20 tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed.
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Affiliation(s)
- Kateřina Němcová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
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Sensitive and selective real-time electrochemical monitoring of DNA repair. Biosens Bioelectron 2014; 54:541-6. [DOI: 10.1016/j.bios.2013.11.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/24/2013] [Accepted: 11/10/2013] [Indexed: 11/23/2022]
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10
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Hvastkovs EG, Schenkman JB, Rusling JF. Metabolic toxicity screening using electrochemiluminescence arrays coupled with enzyme-DNA biocolloid reactors and liquid chromatography-mass spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:79-105. [PMID: 22482786 PMCID: PMC3399491 DOI: 10.1146/annurev.anchem.111808.073659] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
New chemicals or drugs must be guaranteed safe before they can be marketed. Despite widespread use of bioassay panels for toxicity prediction, products that are toxic to a subset of the population often are not identified until clinical trials. This article reviews new array methodologies based on enzyme/DNA films that form and identify DNA-reactive metabolites that are indicators of potentially genotoxic species. This molecularly based methodology is designed in a rapid screening array that utilizes electrochemiluminescence (ECL) to detect metabolite-DNA reactions, as well as biocolloid reactors that provide the DNA adducts and metabolites for liquid chromatography-mass spectrometry (LC-MS) analysis. ECL arrays provide rapid toxicity screening, and the biocolloid reactor LC-MS approach provides a valuable follow-up on structure, identification, and formation rates of DNA adducts for toxicity hits from the ECL array screening. Specific examples using this strategy are discussed. Integration of high-throughput versions of these toxicity-screening methods with existing drug toxicity bioassays should allow for better human toxicity prediction as well as more informed decision making regarding new chemical and drug candidates.
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Affiliation(s)
- Eli G. Hvastkovs
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858;
| | - John B. Schenkman
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06269;
| | - James F. Rusling
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06269;
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269;
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11
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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12
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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13
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Kostečka P, Havran L, Bittová M, Pivoňková H, Fojta M. Sensing mispaired thymines in DNA heteroduplexes using an electroactive osmium marker: towards electrochemical SNP probing. Anal Bioanal Chem 2011; 400:197-204. [DOI: 10.1007/s00216-011-4794-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/08/2011] [Accepted: 02/08/2011] [Indexed: 11/28/2022]
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14
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Zhang W, Yang T, Li W, Li G, Jiao K. Rapid and sensitive electrochemical sensing of DNA damage induced by V2O5 nanobelts/HCl/H2O2 system in natural dsDNA layer-by-layer films. Biosens Bioelectron 2010; 25:2370-4. [DOI: 10.1016/j.bios.2010.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 02/27/2010] [Accepted: 03/01/2010] [Indexed: 11/28/2022]
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15
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Horáková P, Těsnohlídková L, Havran L, Vidláková P, Pivoňková H, Fojta M. Determination of the Level of DNA Modification with Cisplatin by Catalytic Hydrogen Evolution at Mercury-Based Electrodes. Anal Chem 2010; 82:2969-76. [DOI: 10.1021/ac902987x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Petra Horáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic, and Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Lucie Těsnohlídková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic, and Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Luděk Havran
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic, and Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Pavlína Vidláková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic, and Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Hana Pivoňková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic, and Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic, and Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
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Voltammetric detection of damage to DNA caused by nitro derivatives of fluorene using an electrochemical DNA biosensor. Anal Bioanal Chem 2010; 397:233-241. [DOI: 10.1007/s00216-010-3517-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/04/2010] [Accepted: 01/27/2010] [Indexed: 10/19/2022]
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17
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Wachholz F, Duwensee H, Schmidt R, Zwanzig M, Gimsa J, Fiedler S, Flechsig GU. Template-Free Galvanic Nanostructuring of Gold Electrodes for Sensitive Electrochemical Biosensors. ELECTROANAL 2009. [DOI: 10.1002/elan.200904665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Hasoň S, Fojt L, Šebest P, Fojta M. Improved Electrochemical Detection of Purine Nucleobases at Mechanically Roughened Edge-Plane Pyrolytic Graphite Electrode. ELECTROANAL 2009. [DOI: 10.1002/elan.200804437] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Paleček E, Trefulka M, Fojta M. End-labeling of peptide nucleic acid with osmium complex. Voltammetry at carbon and mercury electrodes. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2008.11.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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