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Shumyantseva VV, Pronina VV, Bulko TV, Agafonova LE. Electroanalysis in Pharmacogenomic Studies: Mechanisms of Drug Interaction with DNA. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S224-S233. [PMID: 38621752 DOI: 10.1134/s0006297924140128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 04/17/2024]
Abstract
The review discusses electrochemical methods for analysis of drug interactions with DNA. The electroanalysis method is based on the registration of interaction-induced changes in the electrochemical oxidation potential of heterocyclic nitrogenous bases in the DNA molecule and in the maximum oxidation current amplitude. The mechanisms of DNA-drug interactions can be identified based on the shift in the electrooxidation potential of heterocyclic nitrogenous bases toward more negative (cathodic) or positive (anodic) values. Drug intercalation into DNA shifts the electrochemical oxidation potential to positive values, indicating thermodynamically unfavorable process that hinders oxidation of nitrogenous bases in DNA. The potential shift toward the negative values indicates electrostatic interactions, e.g., drug binding in the DNA minor groove, since this process does not interfere with the electrochemical oxidation of bases. The concentration-dependent decrease in the intensity of electrochemical oxidation of DNA bases allows to quantify the type of interaction and calculate the binding constants.
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Affiliation(s)
- Victoria V Shumyantseva
- Orekhovich Research Institute of Biomedical Chemistry, Laboratory of Bioelectrochemistry, Moscow, 119121, Russia.
- Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Veronica V Pronina
- Orekhovich Research Institute of Biomedical Chemistry, Laboratory of Bioelectrochemistry, Moscow, 119121, Russia
| | - Tatiana V Bulko
- Orekhovich Research Institute of Biomedical Chemistry, Laboratory of Bioelectrochemistry, Moscow, 119121, Russia
| | - Lyubov E Agafonova
- Orekhovich Research Institute of Biomedical Chemistry, Laboratory of Bioelectrochemistry, Moscow, 119121, Russia
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2
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A decoloration/recoloration cycling-associated photo-stimulated fuel cell to assess potential health risks caused by TiO2 nanoparticles and tris(hydroxymethyl)aminomethane. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Lima D, Hacke ACM, Inaba J, Pessôa CA, Kerman K. Electrochemical detection of specific interactions between apolipoprotein E isoforms and DNA sequences related to Alzheimer's disease. Bioelectrochemistry 2019; 133:107447. [PMID: 32006858 DOI: 10.1016/j.bioelechem.2019.107447] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/14/2019] [Accepted: 12/15/2019] [Indexed: 12/26/2022]
Abstract
Apolipoprotein E4 (ApoE4) has a key role on the onset and progression of Alzheimer's disease (AD), since it favours the deposition of toxic amyloid-beta (Aβ) aggregates in the brain. These effects might result from the interaction between ApoE4 and specific DNA promoters related to cellular autophagy pathways and to the expression of neuroprotective proteins, like sirtuin-1. Herein, we modified gold electrodes with mixed self-assembled monolayers of 6-mercapto-1-hexanol and thiolated DNA oligonucleotides related to CLEAR (associated with autophagic processes that enable the clearance of toxic species, such as Aβ) and SirT1 (related to the expression of sirtuin-1) promoter sequences. The interactions of the immobilized DNA sequences with isoforms of ApoE (ApoE4/ApoE3/ApoE2) were investigated by differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) measurements. By monitoring current and charge transfer resistance (Rct) variations, CLEAR showed to interact specifically with ApoE4, whereas SirT1 showed a higher affinity to ApoE4 compared to ApoE3 and ApoE2. To the best of our knowledge, this is the first report about the application of electrochemical techniques to investigate the sequence-specific interaction between ApoE isoforms and CLEAR and SirT1 oligonucleotides.
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Affiliation(s)
- Dhésmon Lima
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Ana Carolina M Hacke
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Juliana Inaba
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Christiana A Pessôa
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Kagan Kerman
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, M1C 1A4 Toronto, ON, Canada.
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Dual redox labeling of DNA as a tool for electrochemical detection of p53 protein-DNA interactions. Anal Chim Acta 2019; 1050:123-131. [DOI: 10.1016/j.aca.2018.10.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/04/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
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5
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Zhong S, Zou D, Zhao B, Zhang D, Li X, Wang H. Electrophoretic behavior of DNA-methyl-CpG-binding domain protein complexes revealed by capillary electrophoreses laser-induced fluorescence. Electrophoresis 2015; 36:3088-93. [DOI: 10.1002/elps.201500336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Shangwei Zhong
- College of Chemistry and Chemical Engineering; University of Chinese Academy of Sciences; Beijing P. R. China
| | - Dandan Zou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
| | - Bailin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
| | - Xiangjun Li
- College of Chemistry and Chemical Engineering; University of Chinese Academy of Sciences; Beijing P. R. China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing P. R. China
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Macazo F, Karpel RL, White RJ. Monitoring cooperative binding using electrochemical DNA-based sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:868-75. [PMID: 25517392 PMCID: PMC4303326 DOI: 10.1021/la504083c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/15/2014] [Indexed: 05/20/2023]
Abstract
Electrochemical DNA-based (E-DNA) sensors are utilized to detect a variety of targets including complementary DNA, small molecules, and proteins. These sensors typically employ surface-bound single-stranded oligonucleotides that are modified with a redox-active molecule on the distal 3' terminus. Target-induced flexibility changes of the DNA probe alter the efficiency of electron transfer between the redox active methylene blue and the electrode surface, allowing for quantitative detection of target concentration. While numerous studies have utilized the specific and sensitive abilities of E-DNA sensors to quantify target concentration, no studies to date have demonstrated the ability of this class of collision-based sensors to elucidate biochemical-binding mechanisms such as cooperativity. In this study, we demonstrate that E-DNA sensors fabricated with various lengths of surface-bound oligodeoxythymidylate [(dT)n] sensing probes are able to quantitatively distinguish between cooperative and noncooperative binding of a single-stranded DNA-binding protein. Specifically, we demonstrate that oligo(dT) E-DNA sensors are able to quantitatively detect nM levels (50 nM-4 μM) of gene 32 protein (g32p). Furthermore, the sensors exhibit signal that is able to distinguish between the cooperative binding of the full-length g32p and the noncooperative binding of the core domain (*III) fragment to single-stranded DNA. Finally, we demonstrate that this binding is both probe-length- and ionic-strength-dependent. This study illustrates a new quantitative property of this powerful class of biosensor and represents a rapid and simple methodology for understanding protein-DNA binding mechanisms.
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Affiliation(s)
- Florika
C. Macazo
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Richard L. Karpel
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Ryan J. White
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
- E-mail:
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Zhuang J, He Y, Chen G, Tang D. Binding-induced internal-displacement of inverted aptamer beacon: Toward a novel electrochemical detection platform. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Gholivand MB, Jalalvand AR, Goicoechea HC. Multivariate analysis for resolving interactions of carbidopa with dsDNA at a fullerene-C60/GCE. Int J Biol Macromol 2014; 69:369-81. [DOI: 10.1016/j.ijbiomac.2014.05.074] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 11/25/2022]
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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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Taleat Z, Cristea C, Marrazza G, Mazloum-Ardakani M, Săndulescu R. Electrochemical immunoassay based on aptamer–protein interaction and functionalized polymer for cancer biomarker detection. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2014.01.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Fotouhi L, Hashkavayi AB, Heravi MM. Interaction of sulfadiazine with DNA on a MWCNT modified glassy carbon electrode: Determination of DNA. Int J Biol Macromol 2013. [DOI: 10.1016/j.ijbiomac.2012.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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12
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Syntheses and in vitro antitumor activities of ferrocene-conjugated Arg-Gly-Asp peptides. J Inorg Biochem 2012; 116:19-25. [DOI: 10.1016/j.jinorgbio.2012.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/11/2012] [Accepted: 06/25/2012] [Indexed: 11/24/2022]
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13
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Barou E, Bouvet M, Heintz O, Meunier-Prest R. Electrochemistry of methylene blue at an alkanethiol modified electrode. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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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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Label-free detection of protein–DNA interactions using electrochemical impedance spectroscopy. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.06.063] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Mandler D, Kraus-Ophir S. Self-assembled monolayers (SAMs) for electrochemical sensing. J Solid State Electrochem 2011. [DOI: 10.1007/s10008-011-1493-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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A protein-based electrochemical method for label-free characterization of sequence-specific protein–DNA interactions. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.04.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Alessio P, Aoki PHB, De Saja Saez JA, Rodríguez-Méndez ML, Constantino CJL. Combining SERRS and electrochemistry to characterize sensors based on biomembrane mimetic models formed by phospholipids. RSC Adv 2011. [DOI: 10.1039/c1ra00141h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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He X, Xu J, Liu Y, Peng R, Lee ST, Kang Z. Carbon nanospheres for highly sensitive electrochemical detection of sequence-specific protein–DNA interactions. Chem Commun (Camb) 2011; 47:8316-8. [DOI: 10.1039/c1cc12375k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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