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Suprun EV, Khmeleva SA, Bibik KV, Ptitsyn KG, Kurbatov LK, Radko SP. Polymerase incorporation of fluorescein or rhodamine modified 2'-deoxyuridine-5'-triphosphates into double-stranded DNA for direct electrochemical detection. J Pharm Biomed Anal 2023; 236:115737. [PMID: 37774487 DOI: 10.1016/j.jpba.2023.115737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The 2'-deoxyuridine-5'-triphosphates modified with fluorescein (dUTP-Fl) or rhodamine (dUTP-Rh) were tested as bearers of electroactive labels and as proper substrates for polymerases used in polymerase chain reaction (PCR) and isothermal recombinase polymerase amplification (RPA) with the aim of electrochemical detection of double-stranded DNA (dsDNA) amplification products. For this purpose, electrochemical behavior of free fluorescein and rhodamine as well as the modified nucleotides, dUTP-Fl and dUTP-Rh, was studied by cyclic (CV) and square wave (SWV) voltammetry on carbon screen printed electrodes. Both free fluorescein and dUTP-Fl underwent a two-step oxidation at the peak potentials (Ep) of 0.6-0.7 V and 0.8-0.9 V (phosphate buffer, pH 7.4). The reduction peaks of fluorescein and dUTP-Fl were registered between -0.9 V and -1 V, but they did not depend on concentration. The free rhodamine and dUTP-Rh have demonstrated the well-defined oxidation peaks at 0.8-0.9 V. In addition, the distinct reduction peaks at Ep between -0.8 V and -0.9 V were registered for both rhodamine and dUTP-Rh. The dUTP-Fl and dUTP-Rh were further tested as substrates to incorporate an electroactive label into 210 or 206 base pair long dsDNA amplicons generated either by PCR or RPA. Among two dUTP derivatives tested, dUTP-Fl revealed significantly better compatibility with PCR and RPA, producing the full-size amplicons at 50-90% substitution of dTTP in the reaction mixture. In the PCR, the best compromise between amplicon output and labeling was achieved at the dUTP-Fl : dTTP and dUTP-Rh : dTTP molar ratios of 70% : 30% and 20% : 80% in the PCR mixture, respectively, allowing the direct electrochemical detection of amplicons at micromolar concentrations. Alongside with fluorescence DNA assays, the fluorescein and rhodamine modified dUTP appear as promising electroactive labels to develop direct electrochemical DNA assays for detecting PCR and RPA products.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Konstantin V Bibik
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Konstantin G Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
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Hasoň S, Ostatná V, Fojt L, Fojta M. Arrangements of DNA purine bases on pyrolytic graphite electrode surface. Electrochemical characterization and atomic force microscopy imaging. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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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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Urzúa SA, Sauceda-Oloño PY, García CD, Cooper CD. Predicting the Orientation of Adsorbed Proteins Steered with Electric Fields Using a Simple Electrostatic Model. J Phys Chem B 2022; 126:5231-5240. [PMID: 35819287 DOI: 10.1021/acs.jpcb.2c03118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is a spontaneous process that leads to a rather compact layer of randomly oriented molecules. However, controlling such orientation is critically important for the development of catalytic surfaces. In this regard, the use of electric fields is one of the most promising alternatives. Our work is motivated by experimental observations that show important differences in catalytic activity of a trypsin-covered surface, which depended on the applied potential during the adsorption. Even though adsorption results from the combination of several processes, we were able to determine that (under the selected conditions) mean-field electrostatics play a dominant role, determining the orientation and yielding a difference in catalytic activity. We simulated the electrostatic potential numerically, using an implicit-solvent model based on the linearized Poisson-Boltzmann equation. This was implemented in an extension of the code PyGBe that included an external electric field, and rendered the electrostatic component of the solvation free energy. Our model (extensions available at the Github repository) allowed estimating the overall affinity of the protein with the surface, and their most likely orientation as a function of the potential applied. Our results show that the active sites of trypsin are, on average, more exposed when the electric field is negative, which agrees with the experimental results of catalytic activity, and confirm the premise that electrostatic interactions can be used to control the orientation of adsorbed proteins.
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Affiliation(s)
- Sergio A Urzúa
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, Valparaíso, 2390123, Chile
| | - Perla Y Sauceda-Oloño
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Carlos D García
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Christopher D Cooper
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, Valparaíso, 2390123, Chile.,Centro Científico Tecnológico de Valparaíso, Valparaíso, 2390123, Chile
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Agafonova LE, Bulko TV, Kuzikov AV, Masamrekh RA, Shumyantseva VV. Sensors for analysis of drugs, drug-drug interactions, and catalytic activity of enzymes. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Development of highly sensitive methods for drug analysis is an ongoing challenge posed by modern bioanalytical and pharmaceutical chemistry. Drug analysis is essential to monitor the quality and purity of pharmaceuticals, study the delivery vehicles for therapeutic agents, to assess the effectiveness of the substance incorporation into the drug delivery system, to estimate the kinetic parameters of reactions, catalyzed by enzymes involved in xenobiotic metabolism, and to study the mechanisms of the drug-DNA interactions from the perspective of pharmacogenomics. The study was aimed to develop an electrochemical technique for detection of a number of drugs. The method is based on electrochemical oxidation of organic molecules at positive potentials between +(0÷1.6) V. The commercially available three-contact electrodes obtained by screen printing with unmodified graphite working electrode were used for analysis. It is shown that electrochemical technique allows for simultaneous detection of several compounds at various working electrode potentials, and for detection of drugs over a wide range of the clinically meaningful drug concentrations (50 µM – 10 mМ), which could be used when working with biological fluids (blood plasma, blood serum, blood, urine), as well as when performing drug monitoring and drug–drug interaction analysis.
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Affiliation(s)
- LE Agafonova
- Institute of Biomedical Chemistry (IBMC), Moscow, Russia
| | - TV Bulko
- Institute of Biomedical Chemistry (IBMC), Moscow, Russia
| | - AV Kuzikov
- Institute of Biomedical Chemistry (IBMC), Moscow, Russia
| | - RA Masamrekh
- Institute of Biomedical Chemistry (IBMC), Moscow, Russia
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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: 0.7] [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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Suprun EV. Direct electrochemistry of proteins and nucleic acids: The focus on 3D structure. Electrochem commun 2021. [DOI: 10.1016/j.elecom.2021.106983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Suprun EV, Kutdusova GR, Khmeleva SA, Radko SP. Towards deeper understanding of DNA electrochemical oxidation on carbon electrodes. Electrochem commun 2021. [DOI: 10.1016/j.elecom.2021.106947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Shumyantseva VV, Bulko TV, Tikhonova EG, Sanzhakov MA, Kuzikov AV, Masamrekh RA, Pergushov DV, Schacher FH, Sigolaeva LV. Electrochemical studies of the interaction of rifampicin and nanosome/rifampicin with dsDNA. Bioelectrochemistry 2020; 140:107736. [PMID: 33494014 DOI: 10.1016/j.bioelechem.2020.107736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/31/2022]
Abstract
The interactions of dsDNA with rifampicin (RF) or with rifampicin after encapsulation in phospholipid micelles (nanosome/rifampicin) (NRF) were studied electrochemically. Screen-printed electrodes (SPEs) modified by stable dispersions of multi-wolled carbon nanotubes (MWCNTs) in aqueous solution of poly(1,2-butadiene)-block-poly(2-(dimethylamino)ethyl methacrylate) (PB290-b-PDMAEMA240) diblock copolymer were used for quantitative electrochemical investigation of direct electrochemical oxidation of guanine at E = 0.591 V (vs. Ag/AgCl) and adenine at E = 0.874 V (vs. Ag/AgCl) of dsDNA and its change in the presence of RF or NRF. Due to RF or NRF interaction with dsDNA, the differential pulse voltammetry (DPV) peak currents of guanine and adenine decreased and the peak potentials shifted to more positive values with increasing drug concentration (RF or NRF). Binding constants (Kb) of complexes RF-dsDNA and NRF-dsDNA were calculated based on adenine and guanine oxidation signals. The Kb values for RF-dsDNA were 1.48 × 104 M-1/8.56 × 104 M-1, while for NRF-dsDNA were 2.51 × 104 M-1/1.78 × 103 M-1 (based on adenine or guanine oxidation signals, respectively). The values of Kb revealed intercalation mode of interaction with dsDNA for RF and mixed type of interaction (intercalation and electrostatic mode) for NRF. The estimated values of ΔG (Gibbs free energy) of the complex formation confirmed that drug-dsDNA interactions are spontaneous and favourable reactions.
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Affiliation(s)
- Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street 1, 117997 Moscow, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia.
| | - Tatiana V Bulko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Elena G Tikhonova
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
| | - Maxim A Sanzhakov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia
| | - Alexey V Kuzikov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street 1, 117997 Moscow, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street 1, 117997 Moscow, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Dmitry V Pergushov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Felix H Schacher
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany; 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
| | - Larisa V Sigolaeva
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
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Suprun EV, Khmeleva SA, Kutdusova GR, Duskaev IF, Kuznetsova VE, Lapa SA, Chudinov AV, Radko SP. Deoxyuridine triphosphates modified with tyrosine or tryptophan aromatic groups for direct electrochemical detection of double-stranded DNA. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.137105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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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: 7] [Impact Index Per Article: 1.8] [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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