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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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Agafonova L, Zhdanov D, Gladilina Y, Kanashenko S, Shumyantseva V. A pilot study on an electrochemical approach for assessing transient DNA transfection in eukaryotic cells. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Shumyantseva VV, Agafonova LE, Bulko TV, Kuzikov AV, Masamrekh RA, Yuan J, Pergushov DV, Sigolaeva LV. Electroanalysis of Biomolecules: Rational Selection of Sensor Construction. BIOCHEMISTRY (MOSCOW) 2021; 86:S140-S151. [PMID: 33827405 DOI: 10.1134/s0006297921140108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.
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Affiliation(s)
- Victoria V Shumyantseva
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia. .,Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Lubov E Agafonova
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia
| | - Tatiana V Bulko
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia
| | - Alexey V Kuzikov
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Rami A Masamrekh
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Jiayin Yuan
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden
| | - Dmitry V Pergushov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 117991, Russia
| | - Larisa V Sigolaeva
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 117991, Russia
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Sigolaeva LV, Bulko TV, Konyakhina AY, Kuzikov AV, Masamrekh RA, Max JB, Köhler M, Schacher FH, Pergushov DV, Shumyantseva VV. Rational Design of Amphiphilic Diblock Copolymer/MWCNT Surface Modifiers and Their Application for Direct Electrochemical Sensing of DNA. Polymers (Basel) 2020; 12:polym12071514. [PMID: 32650434 PMCID: PMC7407114 DOI: 10.3390/polym12071514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
We demonstrate the application of amphiphilic ionic poly(n-butylmethacrylate)-block- poly(2-(dimethylamino)ethyl methacrylate) diblock copolymers (PnBMA40-b-PDMAEMA40, PnBMA40-b-PDMAEMA120, PnBMA70-b-PDMAEMA120) for dispersing multiwalled carbon nanotubes (MWCNTs) in aqueous media, a subsequent efficient surface modification of screen-printed electrodes (SPEs), and the application of the modified SPEs for DNA electrochemistry. Stable and fine aqueous dispersions of MWCNTs were obtained with PnBMAx-b-PDMAEMAy diblock copolymers, regardless of the structure of the copolymer and the amount of MWCNTs in the dispersions. The effect of the diblock copolymer structure was important when the dispersions of MWCNTs were deposited as modifying layers on surfaces of SPEs, resulting in considerable increases of the electroactive surface areas and great acceleration of the electron transfer rate. The SPE/(PnBMAx-b-PDMAEMAy + MWCNT) constructs were further exploited for direct electrochemical oxidation of the guanine (G) and adenine (A) residues in a model salmon sperm double-stranded DNA (dsDNA). Two well-defined irreversible oxidation peaks were observed at about +600 and +900 mV, corresponding to the electrochemical oxidation of G and A residues, respectively. A multi-parametric optimization of dsDNA electrochemistry enables one to get the limits of detection (LOD) as low as 5 μg/mL (0.25 μM) and 1 μg/mL (0.05 μM) for G and A residues, respectively. The achieved sensitivity of DNA assay enables quantification of the A and G residues of dsDNA in the presence of human serum and DNA in isolated human leukocytes.
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Affiliation(s)
- Larisa V. Sigolaeva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Correspondence: ; Tel.: +7-495-939-40-42
| | - Tatiana V. Bulko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Apollinariya Yu. Konyakhina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
| | - Alexey V. Kuzikov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Rami A. Masamrekh
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Johannes B. Max
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany; (J.B.M.); (M.K.); (F.H.S.)
| | - Moritz Köhler
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany; (J.B.M.); (M.K.); (F.H.S.)
| | - Felix H. Schacher
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany; (J.B.M.); (M.K.); (F.H.S.)
- Jena Center for Soft Matter (JCSM), Friedrich-Schiller-University Jena, D-07743 Jena, Germany
- Center for Energy and Environmental Chemistry (CEEC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany
| | - Dmitry V. Pergushov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
| | - Victoria V. Shumyantseva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia; (T.V.B.); (A.Y.K.); (A.V.K.); (R.A.M.); (D.V.P.); (V.V.S.)
- V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Sigolaeva LV, Bulko TV, Kozin MS, Zhang W, Köhler M, Romanenko I, Yuan J, Schacher FH, Pergushov DV, Shumyantseva VV. Long-term stable poly(ionic liquid)/MWCNTs inks enable enhanced surface modification for electrooxidative detection and quantification of dsDNA. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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