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Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based approaches for the study of affinity interactions combined with various sensitive and nontraditional detection techniques. Electrophoresis 2019; 40:625-642. [PMID: 30600537 DOI: 10.1002/elps.201800367] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022]
Abstract
Nearly all processes in living organisms are controlled and regulated by the synergy of many biomolecule interactions involving proteins, peptides, nucleic acids, nucleotides, saccharides, and small molecular weight ligands. There is growing interest in understanding them, not only for the purposes of interactomics as an essential part of system biology, but also in their further elucidation in disease pathology, diagnostics, and treatment. The necessity of detailed investigation of these interactions leads to the requirement of laboratory methods characterized by high efficiency and sensitivity. As a result, many instrumental approaches differing in their fundamental principles have been developed, including those based on capillary electrophoresis. Although capillary electrophoresis offers numerous advantages for such studies, it still has one serious limitation, its poor concentration sensitivity with the most commonly used detection method-ultraviolet-visible spectrometry. However, coupling capillary electrophoresis with a more sensitive detector fulfils the above-mentioned requirement. In this review, capillary electrophoresis combined with fluorescence, mass spectrometry, and several nontraditional detection techniques in affinity interaction studies are summarized and discussed, together with the possibility of conducting these measurements in microchip format.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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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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Kiessig S, Stettler A, Fuhrimann S, Schwarz MA. Affinity Capillary Electrophoresis as a Tool to Characterize Intermolecular Interactions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Park SH, Ban E, Song EJ, Lee H, Chung DS, Yoo YS. Capillary electrophoretic mobility shift assay for binding of DNA with NFAT3, a transcription factor from H9c2 cardiac myoblast cells. Electrophoresis 2011; 32:2174-80. [DOI: 10.1002/elps.201100091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 11/05/2022]
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Szökő É, Tábi T. Analysis of biological samples by capillary electrophoresis with laser induced fluorescence detection. J Pharm Biomed Anal 2010; 53:1180-92. [DOI: 10.1016/j.jpba.2010.07.045] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/23/2010] [Accepted: 07/27/2010] [Indexed: 12/26/2022]
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6
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Xia Z, Li L, Yang J, Xiong C. Investigation of interaction between the drug and cell membrane by capillary electrophoresis. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0156-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gaudreault M, Gingras ME, Lessard M, Leclerc S, Guérin SL. Electrophoretic mobility shift assays for the analysis of DNA-protein interactions. Methods Mol Biol 2009; 543:15-35. [PMID: 19378156 DOI: 10.1007/978-1-60327-015-1_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Electromobility shift assay is a simple, efficient, and rapid method for the study of specific DNA-protein interactions. It relies on the reduction in the electrophoretic mobility conferred to a DNA fragment by an interacting protein. The technique is suitable to qualitative, quantitative, and kinetic analyses. It can also be used to analyze conformational changes.
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Affiliation(s)
- Manon Gaudreault
- Oncology and Molecular Endocrinology Research Center, CHUL, Centre Hospitalier Universitaire de Québec and Laval University, 2705 Laurier Blvd, Québec, QC, Canada, G1V 4G2
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Obubuafo A, Balamurugan S, Shadpour H, Spivak D, McCarley RL, Soper SA. Poly(methyl methacrylate) microchip affinity capillary gel electrophoresis of aptamer-protein complexes for the analysis of thrombin in plasma. Electrophoresis 2008; 29:3436-45. [PMID: 18702051 DOI: 10.1002/elps.200700854] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thrombin generation in blood serves as an important marker for various hemostasis-related diseases and conditions. Analytical techniques currently utilized for determining the thrombin potential of patients rely primarily on the enzymatic activity of thrombin. Microfluidic-based ACE using fluorescently labeled aptamers as affinity probes could provide a simple and efficient technique for the real-time analysis of thrombin levels in plasma. In this study, aptamers were used for the analysis of thrombin by affinity microchip CGE. The CGE used a poly(methyl methacrylate) (PMMA) microfluidic device for the sorting of the affinity complexes with a linear polyacrylamide (LPA) serving as the sieving matrix. Due to the fact that the assay was run under nonequilibrium electrophoresis conditions, the presence of the sieving gel was found to stabilize the affinity complex, providing improved electrophoretic performance compared to free-solution electrophoresis. Two fluorescently labeled aptamer affinity probes, HD1 and HD22, which bind to exosites I and II, respectively, of thrombin were investigated. With an electric field strength of 300 V/cm, two well-resolved peaks corresponding to free aptamer and the thrombin-aptamer complex were obtained in less than 1 min of separation time with a run-to-run and chip-to-chip reproducibility (RSD) of migration times <10% using both aptamers. HD22 affinity assays of thrombin produced baseline-resolved peaks with favorable efficiency due to its higher binding affinity, whereas HD1 assays showed poorer resolution of the free aptamer and complex peaks. HD22 was used in determining the level of thrombin in human plasma. Assays were performed directly on plasma that was diluted to 10% v/v. Thrombin was successfully analyzed by microchip CGE at a concentration level of 543.5 nM for the human plasma sample.
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Affiliation(s)
- Anne Obubuafo
- Department of Chemistry, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
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Yang Q, Zhao YC, Xiong Q, Cheng J. Rapid chip-based capillary electrophoretic mobility shift assay with negative pressure injection for the binding study of transcription factor Abf1 inSaccharomyces cerevisiae. Electrophoresis 2008; 29:5003-9. [DOI: 10.1002/elps.200800218] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Pedersen JT, Østergaard J, Houen G, Heegaard NHH. Affinity capillary electrophoresis for identification and investigation of human Gc-globulin (vitamin D-binding protein) and its isoforms interacting with G-actin. Electrophoresis 2008; 29:1723-33. [DOI: 10.1002/elps.200700618] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Fundador E, Rusling J. Detection of labeled abasic sites in damaged DNA by capillary electrophoresis with laser-induced fluorescence. Anal Bioanal Chem 2007; 387:1883-90. [PMID: 17206410 DOI: 10.1007/s00216-006-1041-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/19/2006] [Accepted: 11/22/2006] [Indexed: 11/29/2022]
Abstract
Removal of nucleobases from the DNA backbone leads to the formation of abasic sites. The rate of abasic site formation is significantly increased for chemically damaged nucleobases. Thus, abasic sites serve as general biomarkers for the quantification of DNA damage. Herein, we show that capillary electrophoresis with laser-induced fluorescence (CE-LIF) can be used to detect the amount of abasic sites with very high sensitivity. For proof of concept, DNA was incubated with methylmethane sulfonate (MMS) and the damaged bases were removed by incubation at 80 degrees C. The resulting abasic sites were then tagged with a fluorescent aldehyde-reactive probe (FARP). The DNA was precipitated with ethanol, and then analyzed by CE-LIF. CE-LIF and HPLC analysis shows that the fluorescently tagged DNA (DNA-FARP) had a peak area directly proportional to the amount of N-7 methyl guanines. The CE-LIF method had a detection limit of 1.2 abasic sites per 1,000,000 bases or ca. 20 attomoles of abasic sites. This provides a general method for detecting DNA damage that is not only faster but also has comparable or better sensitivity than the alternative ELISA-like method.
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Affiliation(s)
- Erwin Fundador
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA
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Xiao Y, Zhou Y, Wang J, Yu M, Wang G, Jin J, Xiao J. Selection and identification of human Gonadotropin-releasing hormone promoter binding peptides by phage display-CEMSA. J Mol Recognit 2007; 20:51-7. [PMID: 17136792 DOI: 10.1002/jmr.811] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Specific interactions between transcription factors and cis-acting DNA sequences form the molecular basis of gene expression regulation. Here, we applied phage display technology to DNA-protein interaction studies. A phage-displayed peptide library was used to select Gonadotropin-releasing hormone promoter (GP) binding peptides. After four sequential rounds of biopanning on GP-conjugated magnetic beads, phage clones encoding GQPTPRNAGLPL (B6), SRLNVEPLTTYS (B3), and TTLHWASLTTGR (B11) were enriched. Phages bearing these peptides showed specific binding to GP in solution by capillary electrophoresis mobility shift assay (CEMSA). In addition, some human transcription factors were speculated as the potential transcription factors or co-activators of GnRH gene by bioinformatic analysis. These results suggest that phage display-CEMSA methodology should be a powerful tool to screen and identify site-specific DNA-binding peptides.
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Affiliation(s)
- Yichuan Xiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
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Babu SCV, Song EJ, Babar SME, Yoo YS. Capillary electrophoresis of signaling molecules. Biomed Chromatogr 2007; 21:890-7. [PMID: 17583878 DOI: 10.1002/bmc.867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The emerging field of quantitative systems biology uses high-throughput bioanalytical measurements to gain a deeper understanding of biological phenomena. With the advent of instrumentation platforms, capillary electrophoresis spans a very wide range of biological applications. This short article focuses on the exploitation of capillary electrophoresis for the systems-level analysis of cell signaling molecules.
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Affiliation(s)
- Suresh C V Babu
- Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, Korea
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Ostergaard J, Heegaard NHH. Bioanalytical interaction studies executed by preincubation affinity capillary electrophoresis. Electrophoresis 2006; 27:2590-608. [PMID: 16732622 DOI: 10.1002/elps.200600047] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The versatility of CE is beneficial for the study of many types of molecular interactions, because different experimental designs can be made to suit the characteristics of a particular interaction. A very versatile starting point is the preequilibration type of affinity CE that has been used extensively for characterizing biomolecular interactions in the last 15 years. We review this field here and include a comprehensive overview of the existing preincubation ACE modes including their advantages and limitations as well as the methodological developments and applications within the bioanalytical field.
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Affiliation(s)
- Jesper Ostergaard
- Department of Pharmaceutics and Analytical Chemistry, The Danish University of Pharmaceutical Sciences, Copenhagen, Denmark.
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Abstract
This review article with 304 references describes recent developments in CE of proteins, and covers the two years since the previous review (Hutterer, K., Dolník, V., Electrophoresis 2003, 24, 3998-4012) through Spring 2005. It covers topics related to CE of proteins, including modeling of the electrophoretic migration of proteins, sample pretreatment, wall coatings, improving separation, various forms of detection, special electrophoretic techniques such as affinity CE, CIEF, and applications of CE to the analysis of proteins in real-world samples including human body fluids, food and agricultural samples, protein pharmaceuticals, and recombinant protein preparations.
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Tran NT, Taverna M, Miccoli L, Angulo JF. Poly(ethylene oxide) facilitates the characterization of an affinity between strongly basic proteins with DNA by affinity capillary electrophoresis. Electrophoresis 2005; 26:3105-12. [PMID: 16047314 DOI: 10.1002/elps.200400091] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In order to study kin17 protein-DNA affinity, we have developed a fast and reproducible capillary electrophoresis (CE) analysis of a strongly basic protein: kin17 protein, using a nonpermanent coating based on poly(ethylene oxide) (PEO) to avoid adsorption of kin17. The coating procedure was optimized to provide a residual and stable electroosmotic flow (EOF = 5 x 10(-5) cm(2)/V x s), exhibiting RSD of 0.3% and excellent long-term stability. Good intraday and interday reproducibility of kin17 migration times (0.8 and 0.3% relative standard deviation (RSD), respectively) enabled us to consider that the recovery percentage obtained for kin17 protein was satisfactory (79%). The potential of this PEO-based coating procedure was evaluated for affinity CE method in order to study the affinity of kin17 protein for two single-stranded DNA (ssDNA) models: polydeoxyadenylic acid and polydeoxycytidilic acid (pdA and pdC). Binding constants (1.5 x 10(7) +/- 17% and 1.7 x 10(7) + 25%M(-1)) were evaluated assuming a 1:1 affinity between kin17 and pdA or pdC, respectively.
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Affiliation(s)
- Nguyet Thuy Tran
- Groupe de Chimie Analytique Paris-Sud, EA 3343, Faculté de Pharmacie, Université Paris XI, F-92290 Châtenay-Malabry, France.
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Liu S, Liu Y, Li J, Guo M, Nie L, Yao S. Study on the interaction between DNA and protein induced by anticancer drug carboplatin. ACTA ACUST UNITED AC 2005; 63:125-36. [PMID: 15896850 DOI: 10.1016/j.jbbm.2005.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Accepted: 04/04/2005] [Indexed: 11/25/2022]
Abstract
The interaction of DNA and human serum albumin (HSA) in the presence of anticancer drug carboplatin was studied with piezoelectric quartz crystal impedance (PQCI) and electrochemistry techniques. In the PQCI analysis, the correlative parameters including the frequency (f0), the motional resistance (R(m)), and the static capacitance (C0) in the experiment were obtained and discussed in detail. Additionally, the kinetics parameters of the cross-linking process were investigated and a response kinetics model was deduced. The values of association rate constant k1, dissociation rate constant k(-1) and the reaction equilibrium constant K were estimated to be 1.895 mg/ml(-1) s(-1), 4.7 x 10(-5) s(-1) and 4.03 x 10(4) (mg/ml)-1, respectively. Furthermore, cyclic voltammetry (CV) and electrochemical AC impedance techniques were employed to testify the cross-linking process.
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Affiliation(s)
- Shanchao Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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Gayton-Ely M, Pappas TJ, Holland LA. Probing affinity via capillary electrophoresis: advances in 2003–2004. Anal Bioanal Chem 2005; 382:570-80. [PMID: 15703915 DOI: 10.1007/s00216-004-3033-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 12/09/2004] [Indexed: 10/25/2022]
Abstract
This review addresses recent advances in capillary electrophoresis of biological-based molecular interaction from a broader perspective, based on applications reported during the period 2003-2004. These capillary electrophoresis-based studies of molecular interactions include affinity capillary electrophoresis, electrokinetic chromatography, and free zone electrophoresis. The review is written as a general synopsis of applications and does not cover the theory or protocol involved in the implementation of the analyses.
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Affiliation(s)
- Melissa Gayton-Ely
- Department of Chemistry, West Virginia University, 217 Clark Hall, P.O.Box 6045, Morgantown, WV 26506, USA
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Laser literature watch. Photomed Laser Surg 2004; 22:261-76. [PMID: 15315736 DOI: 10.1089/1549541041438588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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