Study of molecular interactions by nonequilibrium capillary electrophoresis of equilibrium mixtures: Originations, developments, and applications.

Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 8204476 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1522-2683 (Electronic) Linking ISSN: 01730835 NLM ISO Abbreviation: Electrophoresis Subsets: MEDLINE

Publication: : Weinheim : Wiley-VCH
Original Publication: [Weinheim, Germany] : Verlag Chemie, [1980-

Proteins* ; Aptamers, Nucleotide*/chemistry; Oligonucleotides/chemistry ; Thermodynamics ; Electrophoresis, Capillary/methods

Molecular interactions play a vital role in regulating various physiological and biochemical processes in vivo. Kinetic capillary electrophoresis (KCE) is an analytical platform that offers significant advantages in studying the thermodynamic and kinetic parameters of molecular interactions. It enables the simultaneous analysis of these parameters within an interaction pattern and facilitates the screening of binding ligands with predetermined kinetic parameters. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was the first proposed KCE method, and it has found widespread use in studying molecular interactions involving proteins/aptamers, proteins/small molecules, and peptides/small molecules. The successful applications of NECEEM have demonstrated its promising potential for further development and broader application. However, there has been a dearth of recent reviews on NECEEM. To address this gap, our study provides a comprehensive description of NECEEM, encompassing its origins, development, and applications from 2015 to 2022. The primary focus of the applications section is on aptamer selection and screening of small-molecule ligands. Furthermore, we discuss important considerations in NECEEM experimental design, such as buffer suitability, detector selection, and protein adsorption. By offering this thorough review, we aim to contribute to the understanding, advancement, and wider utilization of NECEEM as a valuable tool for studying molecular interactions and facilitating the identification of potential ligands and targets.
(© 2023 Wiley-VCH GmbH.)

Chu Y, Cheng C. Affinity capillary electrophoresis in biomolecular recognition. Cell Mol Life Sci. 1998;54:663-83.
Nguyen HH, Park J, Kang S, Kim M. Surface plasmon resonance: a versatile technique for biosensor applications. Sensors. 2015;15:10481-510.
Pattnaik P. Surface plasmon resonance: applications in understanding receptor-ligand interaction. Appl Biochem Biotechnol. 2005;126:79-92.
Concepcion J, Witte K, Wartchow C, Choo S, Yao D, Persson H, et al. Label-free detection of biomolecular interactions using BioLayer interferometry for kinetic characterization. Comb Chem High Throughput Screen. 2009;12:791-800.
Desai M, Di R, Fan H. Application of biolayer interferometry (BLI) for studying protein-protein interactions in transcription. JoVE. 2019;149, e59687.
Dam TK, Brewer CF. Thermodynamic studies of lectin-carbohydrate interactions by isothermal titration calorimetry. Chem Rev. 2002;102:387-429.
Doyle ML. Characterization of binding interactions by isothermal titration calorimetry. Curr Opin Biotechnol. 1997;8:31-5.
Grolier J, del Rio J. Isothermal titration calorimetry: a thermodynamic interpretation of measurements. J Chem Thermodyn. 2012;55:193-202.
Cala O, Guilliere F, Krimm I. NMR-based analysis of protein-ligand interactions. Anal Bioanal Chem. 2014;406:943-56.
Sirajuddin M, Ali S, Badshah A. Drug-DNA interactions and their study by UV-visible, fluorescence spectroscopies and cyclic voltametry. J Photochem Photobiol B: Biol. 2013;124:1-19.
Muhammad S, Han S, Xie X, Wang S, Aziz M. Overview of online two-dimensional liquid chromatography based on cell membrane chromatography for screening target components from traditional Chinese medicines. J Sep Sci. 2018;40:299-313.
Hage DS. Affinity chromatography: a review of clinical applications. Clin Chem. 1999;45:593-615.
Iftekhar S, Ovbude ST, Hage DS. Kinetic analysis by affinity chromatography. Front Chem. 2019;7:673.
Shimura K, Kasai K. Affinity capillary electrophoresis: a sensitive tool for the study of molecular interactions and its use in microscale analyses. Anal Biochem. 1997;251:1-16.
Yan Y, Marriott G. Analysis of protein interactions using fluorescence technologies. Curr Opin Chem Biol. 2003;7:635-40.
Dodero V, Quirolo Z, Sequeira M. Biomolecular studies by circular dichroism. Front Biosci Landmark. 2011;16:61-73.
Ostergaard J, Heegaard NHH. Bioanalytical interaction studies executed by preincubation affinity capillary electrophoresis. Electrophoresis. 2006;27:2590-608.
Krylov SN. Kinetic CE: foundation for homogeneous kinetic affinity methods. Electrophoresis. 2007;28:69-88.
Le ATH, Krylova SM, Krylov SN. Kinetic capillary electrophoresis in screening oligonucleotide libraries for protein binders. TrAC Trends Anal Chem. 2023;162:117061.
Siroka J, Jac P, Polasek M. Use of inorganic, complex-forming ions for selectivity enhancement in capillary electrophoretic separation of organic compounds. TrAC Trends Anal Chem. 2011;30:142-52.
Pobozy E, Trojanowicz M. Application of capillary electrophoresis for determination of inorganic analytes in waters. Molecules. 2022;26:6972.
Roesch T, Troffer J, Huhn C. Indirect CE-UV detection for the characterization of organic and inorganic ions of a broad mobility and pK(a) range in engine coolants. Electrophoresis. 2019;40:2806-9.
Kaur H, Beckman J, Zhang Y, Li ZJ, Szigeti M, Guttman A. Capillary electrophoresis and the biopharmaceutical industry: therapeutic protein analysis and characterization. TrAC Trends Anal Chem. 2021;144:116407.
Wu Y, Wang W, Fang Y, Chen M, Feng R. Capillary electrophoresis becoming an effective tool for explaining inconsistent results of interactions between nonionic polymers and phosphate surfactants. J ElectroAnal Chem. 2019;832:105-11.
Zhou W, Zhang B, Liu Y, Wang C, Sun W, Li W, et al. Advances in capillary electrophoresis-mass spectrometry for cell analysis. TrAC Trends Anal Chem. 2019;117:316-30.
Chu YH, Avila LZ, Biebuyck HA, Whitesides GM. Use of affinity capillary electrophoresis to measure binding constants of ligands to proteins. J Med Chem. 1992;35:2915-7.
Albishri HM, Deeb SE, AlGarabli N, AlAstal R, Alhazmi HA, Nachbar M, et al. Recent advances in affinity capillary electrophoresis for binding studies. Bioanalysis. 2015;6:3369-92.
Schou C, Heegaard NHH. Recent applications of affinity interactions in capillary electrophoresis. Electrophoresis. 2006;27:44-59.
Dubsky P, Dvorak M, Ansorge M. Affinity capillary electrophoresis: the theory of electromigration. Anal Bioanal Chem. 2017;408:8623-41.
Heegaard NH, Guzman NA. Affinity capillary electrophoresis: important application areas and some recent developments. J Chromatogr B: Biomed Sci Appl. 1998;715:29-54.
Ansorge M, Dubsky P, Uselova K. Into the theory of the partial-filling affinity capillary electrophoresis and the determination of apparent stability constants of analyte-ligand complexes. Electrophoresis. 2018;39:742-51.
Mlcochova H, Ratih R, Michalcova L, Watzig H, Glatz Z, Stein M. Comparison of mobility shift affinity capillary electrophoresis and capillary electrophoresis frontal analysis for binding constant determination between human serum albumin and small drugs. Electrophoresis. 2022;43:1724-34.
Rudnev AV, Aleksenko SS, Semenova O, Hartinger CG, Timerbaev AR, Keppler BK. Determination of binding constants and stoichiometries for platinum anticancer drugs and serum transport proteins by capillary electrophoresis using the Hummel-Dreyer method. J Sep Sci. 2005;28:121-7.
Busch MHA, Carels LB, Boelens HFM, Kraak JC, Poppe H. Comparison of five methods for the study of drug-protein binding in affinity capillary electrophoresis. J Chromatogr A. 1997;777:311-28.
Dvorak M, Svobodova J, Benes M, Gas B. Applicability and limitations of affinity capillary electrophoresis and vacancy affinity capillary electrophoresis methods for determination of complexation constants. Electrophoresis. 2013;34:761-7.
Fermas S, Gonnet F, Varenne A, Gareil P, Daniel R. Frontal analysis capillary electrophoresis hyphenated to electrospray ionization mass spectrometry for the characterization of the antithrombin/heparin pentasaccharide complex. Anal Chem. 2007;79:4987-93.
Petrov A, Okhonin V, Berezovski M, Krylov SN. Kinetic capillary electrophoresis (KCE): a conceptual platform for kinetic homogeneous affinity methods. J Am Chem Soc. 2005;127:17104-10.
Berezovski M, Krylov SN. Nonequilibrium capillary electrophoresis of equilibrium mixtures-a single experiment reveals equilibrium and kinetic parameters of protein-DNA interactions. J Am Chem Soc. 2002;124:13674-5.
Berezovski M, Krylov SN. Using nonequilibrium capillary electrophoresis of equilibrium mixtures for the determination of temperature in capillary electrophoresis. Anal Chem. 2004;76:7114-7.
Berezovski M, Krylov SN. Thermochemistry of protein-DNA interaction studied with temperature-controlled nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem. 2005;77:1526-9.
Okhonin V, Berezovski M, Krylov SN. Sweeping capillary electrophoresis: a non-stopped-flow method for measuring bimolecular rate constant of complex formation between protein and DNA. J Am Chem Soc. 2004;126:7166-7.
Kanoatov M, Mehrabanfar S, Krylov SN. Systematic approach to optimization of experimental conditions in nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem. 2016;88:9300-8.
Krylov SN. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM): a novel method for biomolecular screening. J Biomol Screen. 2006;11:115-22.
Cherney LT, Kanoatov M, Krylov SN. Method for determination of peak areas in nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem. 2011;83:8617-22.
Yan J, Xiong H, Cai S, Wen N, He Q, Liu Y, et al. Advances in aptamer screening technologies. Talanta. 2019;200:124-44.
Dausse E, Taouji S, Evade L, Di Primo C, Chevet E, Toulme J-J. HAPIscreen, a method for high-throughput aptamer identification. J Nanobiotechnol. 2011;9:25.
Berezovski M, Musheev M, Drabovich A, Krylov SN. Non-SELEX selection of aptamers. J Am Chem Soc. 2006;128:1410-1.
Kudłak B, Wieczerzak M. Aptamer based tools for environmental and therapeutic monitoring: a review of developments, applications, future perspectives. Crit Rev Environ Sci Technol. 2019;50:816-67.
Tok J, Lai J, Leung T, Li S. Selection of aptamers for signal transduction proteins by capillary electrophoresis. Electrophoresis. 2010;31:2055-62.
Hagiwara K, Kasahara Y, Fujita H, Kuwahara M. Non-equilibrium capillary electrophoresis of equilibrium mixtures-based affinity separation and selective enrichment of a long-length DNA aptamer. Aust J Chem. 2016;69:1102-7.
Kanoatov M, Galievsky VA, Krylova SM, Cherney LT, Krylov SN, Jankowski HK. Using non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) for simultaneous determination of concentration and equilibrium constant. Anal Chem. 2015;87:3099-106.
Riley KR, Gagliano J, Xiao J, Libby K, Saito S, Yu G, et al. Combining capillary electrophoresis and next-generation sequencing for aptamer selection. Anal Biochem Chem. 2015;407:1527-32.
Behjati S, Tarpey P. What is next generation sequencing? Arch Dis Child: Educ Pract Ed. 2013;98:236-8.
Ric A, Ecochard V, Iacovoni JS, Boutonnet A, Ginot F, Ong-Mean V, et al. G-quadruplex aptamer selection using capillary electrophoresis-LED-induced fluorescence and Illumina sequencing. Anal Bioanal Chem. 2018;410:1991-2000.
Le ATH, Krylova SM, Kanoatov M, Desai S, Krylov SN. Ideal-filter capillary electrophoresis (IFCE) facilitates the one-step selection of aptamers. Angew Chem Int Ed. 2019;58:2739-43.
Le ATH, Wang TY, Krylova SM, Beloborodov SS, Krylov SN. Quantitative characterization of partitioning in selection of DNA aptamers for protein targets by capillary electrophoresis. Anal Chem. 2022;94:2578-88.
Drabovich AP, Berezovski MV, Musheev MU, Krylov SN. Selection of smart small-molecule ligands: the proof of principle. Anal Chem. 2009;81:490-4.
Bao J, Krylova SM, Cherney LT, Hale RL, Belyanskaya SL, Chiu CH, et al. Predicting electrophoretic mobility of protein-ligand complexes for ligands from DNA-encoded libraries of small molecules. Anal Chem. 2016;88:5498-506.
Beloborodov SS, Krylova SM, Krylov SN. Spherical-shape assumption for protein-aptamer complexes facilitates prediction of their electrophoretic mobility. Anal Chem. 2019;91:12680-7.
Guo X, Chen G-H. Capillary electrophoresis-based methodology for screening of oligonucleotide aptamers. Biomed Chromatogr. 2021;35:e5109.
Riley KR, Sims CM, Wood IT, Vanderah DJ, Walker ML. Short-chained oligo(ethylene oxide)-functionalized gold nanoparticles: realization of significant protein resistance. Anal Bioanal Chem. 2018;410:145-54.
Lou C, Ye X, Chen G, Zhu J, Kang J. Screening inhibitors for blocking UHRF1-methylated DNA interaction with capillary electrophoresis. J Chromatogr A. 2021;1636:461790.
Sun J, He B, Liu Q, Ruan T, Jiang G. Characterization of interactions between organotin compounds and human serum albumin by capillary electrophoresis coupled with inductively coupled plasma mass spectrometry. Talanta. 2012;93:239-44.
Beneito-Cambra M, Herrero-Martínez JM, Ramis-Ramos G. Characterization and determination of poly(vinylpyrrolidone) by complexation with an anionic azo-dye and nonequilibrium capillary electrophoresis. J Chromatogr A. 2009;1216:9014-21.
Carrasco-Correa EJ, Beneito-Cambra M, Herrero-Martínez JM, Ramis-Ramos G. Evaluation of molecular mass and tacticity of polyvinyl alcohol by non-equilibrium capillary electrophoresis of equilibrium mixtures of a polymer and a dye. J Chromatogr A. 2011;1218:2334-41.
Yang P, Ma Y, Lee A, Kennedy R. Measurement of dissociation rate of biomolecular complexes using CE. Electrophoresis. 2009;30:457-64.
Kanoatov M, Krylov SN. Analysis of DNA in phosphate buffered saline using kinetic capillary electrophoresis. Anal Chem. 2016;88:7421-8.
Bao J, Krylov SN. Volatile kinetic capillary electrophoresis for studies of protein-small molecule interactions. Anal Chem. 2012;84:6944-7.
Bao J, Krylova SM, Reinstein O, Johnson PE, Krylov SN. Label-free solution-based kinetic study of aptamer-small molecule interactions by kinetic capillary electrophoresis with UV detection revealing how kinetics control equilibrium. Anal Chem. 2011;83:8387-90.
Zhu C, Li L, Yang G, Fang S, Liu M, Ghulam M, et al. Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection. Anal Chim Acta. 2019;1070:112-22.
Dietz MS, Wehrheim SS, Harwardt M-LIE, Niemann HH, Heilemann M. Competitive binding study revealing the influence of fluorophore labels on biomolecular interactions. Nano Lett. 2019;19:8245-9.
Yin L, Wang W, Wang S, Zhang F, Zhang S, Tao N. How does fluorescent labeling affect the binding kinetics of proteins with intact cells? Biosens Bioelectron. 2015;66:412-6.
Nesbitt CA, Zhang H, Yeung KK-C. Recent applications of capillary electrophoresis-mass spectrometry (CE-MS): CE performing functions beyond separation. Anal Chim Acta. 2008;627:3-24.
Olivares JA, Nguyen NT, Yonker CR, Smith RD. On-line mass spectrometric detection for capillary zone electrophoresis. Anal Chem. 1987;59:1230-2.
Berezovski MV, Mironov GG. Utility of kinetic capillary electrophoresis-mass spectrometry to study protein dynamics and affinity interactions. Expert Rev Proteomics. 2012;9:477-9.
Bao J, Krylova SM, Wilson DJ, Reinstein O, Johnson PE, Krylov SN. Kinetic capillary electrophoresis with mass-spectrometry detection (KCE-MS) facilitates label-free solution-based kinetic analysis of protein small molecule binding. ChemBioChem. 2011;12:2551-4.
Mironov GG, Okhonin V, Khan N, Clouthier CM, Berezovski MV. Conformational dynamics of DNA G-Quadruplex in solution studied by kinetic capillary electrophoresis coupled on-line with mass spectrometry. ChemistryOpen. 2014;3:58-64.
Mironov GG, Clouthier CM, Akbar A, Keillor JW, Berezovski MV. Simultaneous analysis of enzyme structure and activity by kinetic capillary electrophoresis-MS. Nat Chem Biol. 2016;12:918-22.
Kanoatov M, Krylov SN. DNA adsorption to the reservoir walls causing irreproducibility in studies of protein-DNA interactions by methods of kinetic capillary electrophoresis. Anal Chem. 2011;83:8041-5.
de Jong S, Krylov SN. Pressure-based approach for the analysis of protein adsorption in capillary electrophoresis. Anal Chem. 2012;84:453-8.
Cherney LT, Petrov AP, Krylov SN. One-dimensional approach to study kinetics of reversible binding of protein on capillary walls. Anal Chem. 2015;87:1219-25.
de Jong S, Epelbaum N, Liyanage R, Krylov SN. A semipermanent coating for preventing protein adsorption at physiological pH in kinetic capillary electrophoresis. Electrophoresis. 2012;33:2584-90.
Liyanage R, Krylova SM, Krylov SN. Minimizing adsorption of histidine-tagged proteins for the study of protein-deoxyribonucleic acid interactions by kinetic capillary electrophoresis. J Chromatogr A. 2013;1322:90-6.

Keywords: aptamer; ligand; molecular interactions; nonequilibrium capillary electrophoresis of equilibrium mixtures; target

0 (Proteins)
0 (Oligonucleotides)
0 (Aptamers, Nucleotide)

Date Created: 20230825 Date Completed: 20231113 Latest Revision: 20231114

20231215

10.1002/elps.202300166

37621032