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Neaga I, Bodoki E, Hambye S, Blankert B, Oprean R. Study of nucleic acid–ligand interactions by capillary electrophoretic techniques: A review. Talanta 2016; 148:247-56. [DOI: 10.1016/j.talanta.2015.10.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 10/22/2022]
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Electromigration behavior of nucleic acids in capillary electrophoresis under pulsed-field conditions. J Chromatogr A 2014; 1331:100-7. [PMID: 24472841 DOI: 10.1016/j.chroma.2014.01.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 11/11/2013] [Accepted: 01/10/2014] [Indexed: 11/22/2022]
Abstract
We have presented a study focused on the migration pattern of double-stranded DNA (dsDNA) and RNA under pulsed field conditions. By calculating the dependence of nucleic acid mobility on its molecular size in a double logarithm plot, we found that (I) dsDNA molecules proceeded by a sigmoidal migration regime which was probably related to Ogston sieving, transition regime, and reptation model. Furthermore, the transition regime disappeared if DNA was resolved in a higher molecular mass HEC. (II) The migration pattern of RNA was relevant to the denaturant used for separation. When RNA was denatured by acetic acid, its mobility parabolically declined with its molecular size. The mobility was linearly decreased with the molecular size if urea was employed as denaturant. (III) RNA may migrate by Ogston, reptation without orientation mechanism when denatured by urea, whereas these two models were not suitable for RNA if denatured by acetic acid. Even though the electrophoretic conditions of PFCE were varied, the sigmoidal, linear, parabolic migration patterns could still be observed. (IV) Under certain modulation depth, the migration time (Tm) of acetic acid decreased with the increase of average separation voltage (Va), and when RNA denatured in 4.0M urea, Tm showed a linear correlation with Va. (V) The mobility of nucleic acids increased with the growth of artificial temperature in the capillary volume due to the decrease in the viscosity of the polymer. This is the first systematic and comparative research of high molecular mass nucleic acids in PFCE, which provides us deep insight into RNA and DNA migration behavior under pulsed electric field conditions.
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Sun Z, Ling X, Zhang Y, Tian L, Wang Y. Interactions of Peptides from Secreted Human CKLF1 and the N-Terminal Extracellular Tail of CCR4 Analyzed by CZE. Chromatographia 2009. [DOI: 10.1365/s10337-009-1151-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Liu Y, Zhang S, Ling X, Li Y, Zhang Y, Han W, Wang Y. Analysis of the interactions between the peptides from secreted human CKLF1 and heparin using capillary zone electrophoresis. J Pept Sci 2008; 14:984-8. [PMID: 18338323 DOI: 10.1002/psc.1028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Chemokine-like factor 1 (CKLF1) is a novel human cytokine and exhibits chemotactic activities on leukocytes. Two peptides named CKLF1-C27 and CKLF1-C19, were obtained from secreted CKLF1. In this study, a selective high-performance analytical method based on capillary zone electrophoresis (CZE) to investigate interactions between heparin and CKLF1-C27/CKLF1-C19 was developed. Samples containing CKLF1-C27/CKLF1-C19 and heparin at various ratios were incubated at room temperature and then separated by CZE with Tris-acetate buffer at pH 7.2. Both qualitative and quantitative characterizations of the binding were determined. The binding constants of the interactions between CKLF1-C27/CKLF1-C19 and heparin were calculated as (3.38 +/- 0.49) x 10(5) M(-1) and (1.10 +/- 0.02) x 10(5) M(-1) by Scatchard analysis. To study structural requirements, CKLF1-C19pm and CKLF1-C19km have been synthesized, and their interactions with heparin have been studied by CZE. We found that the Pro or Lys to Ala substitution within the residues of CKLF1-C19 (CKLF1-C19pm or CKLF1-C19km) strongly decreased or abolished its interaction with heparin, suggesting that the residues of Pro affect the affinity of CKLF1-C19 for heparin, and the residues of Lys of CKLF1-C19 play the important role for the interaction of CKLF1-C19 and heparin, respectively. The methodology presented should be generally applicable to study peptides and heparin interactions quantitatively and qualitatively.
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Affiliation(s)
- Yi Liu
- Department of Pharmacy, Peking University People's Hospital, Beijing 100044, PR China
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Zhao P, Jin HW, Yang ZJ, Zhang LR, Zhang LH. Solid-phase synthesis and evaluation of TAR RNA targeted β-carboline–nucleoside conjugates. Org Biomol Chem 2008; 6:3741-50. [DOI: 10.1039/b809598a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Study of the interactions between fluoroquinolones and human serum albumin by affinity capillary electrophoresis and fluorescence method. Anal Chim Acta 2007; 603:101-10. [DOI: 10.1016/j.aca.2007.09.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 08/28/2007] [Accepted: 09/13/2007] [Indexed: 11/22/2022]
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Sun Z, Ling X, Sun W, Xiao J, Yin C, Wang Y. Studies on the interactions between lactam analogs and theN-terminal extracellular tail of CC chemokine receptor 4 by CZE. Electrophoresis 2007; 28:3064-9. [PMID: 17668450 DOI: 10.1002/elps.200700258] [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: 11/07/2022]
Abstract
CC chemokine receptor 4 (CCR4) is a kind of G-protein-coupled receptors with a characteristic seven-transmembrane structure and selectively expressed on Th2-type CD4+ T-cells, which play a pivotal role in allergic inflammation. In this study, the interactions between 2-(2-(2,4-dichloro-phenyl)-4-{[(2-methyl-3-chloro-phenyl)-1-ylmethyl]-carbamoyl}-methyl)-5-oxo-pyrrole-1-yl)-N-(3-piperidinyl-propyl)-acetamide (compound A), a known CCR4 antagonist, and ML40 were studied by CZE for the first time. Both qualitative and quantitative characterizations of the drug-peptide binding were determined. The binding constant of the interaction between the trans-diastereomer of compound A and ML40, calculated from the Scatchard plot by regression, was (1.06 +/- 0.11)x10(5)/M. Also, it was confirmed that the trans-diastereomer was more potent affinity with CCR4 than its cis-counterpart. The experimental results show that this reported method by CZE for the determination of the compound A and ML40 interactions is powerful, sensitive, and fast, requires less amounts of reagents, and further, it can be employed as one of the reliable screening methods to a series of lactam analogs in the drug discovery for allergic inflammation diseases.
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Affiliation(s)
- Zhe Sun
- Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences, Peking University, Beijing, PR China
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Østergaard J. Application of Retention Factors in Affinity Electrokinetic Chromatography and Capillary Electrophoresis. ANAL SCI 2007; 23:489-92. [PMID: 17420558 DOI: 10.2116/analsci.23.489] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Affinity capillary electrophoresis has become an established approach for performing interaction studies. In affinity electrokinetic chromatography the retention factor, as in liquid chromatography, is useful for describing the migration behavior of the analytes, and is instrumental for assessing the affinity of an analyte for the pseudo-stationary phase. Erroneous use of the retention factor concept in affinity capillary electrophoretic studies has appeared in a number of recent papers. The errors and their origin are pointed out, and the correct use of retention factors in affinity electrokinetic chromatography and capillary electrophoresis is summarized.
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Affiliation(s)
- Jesper Østergaard
- Department of Pharmaceutics and Analytical Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Denmark.
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Hernandez L, Rudolph M, Lammertink R, Kornfield J, Zurita C, Gomez FA. Determination of Binding Constants of Polyethylene Glycol Vancomycin Derivatives to Peptide Ligands Using Affinity Capillary Electrophoresis. Chromatographia 2006. [DOI: 10.1365/s10337-006-0148-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Liu Y, Lai X, Ling X, Zhao Y, Cui J. Interactions Between Thrombin with Flavonoids from Abelmoschus manihot (L.) Medicus by CZE. Chromatographia 2006. [DOI: 10.1365/s10337-006-0841-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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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
Systems biology depends on a comprehensive assignment and characterization of the interactions of proteins and polypeptides (functional proteomics) and of other classes of biomolecules in a given organism. High‐capacity screening methods are in place for ligand capture and interaction screening, but a detailed dynamic characterization of molecular interactions under physiological conditions in efficiently separated mixtures with minimal sample consumption is presently provided only by electrophoretic interaction analysis in capillaries, affinity CE (ACE). This has been realized in different fields of biology and analytical chemistry, and the resulting advances and uses of ACE during the last 2.5 years are covered in this review. Dealing with anything from small divalent metal ions to large supramolecular assemblies, the applications of ACE span from low‐affinity binding of broad specificity being exploited in optimizing selectivity, e.g., in enantiomer analysis to miniaturized affinity technologies, e.g., for fast processing immunoassay. Also, approaches that provide detailed quantitative characterization of analyte–ligand interaction for drug, immunoassay, and aptamer development are increasingly important, but various approaches to ACE are more and more generally applied in biological research. In addition, the present overview emphasizes that distinct challenges regarding sensitivity, parallel processing, information‐rich detection, interfacing with MS, analyte recovery, and preparative capabilities remain. This will be addressed by future technological improvements that will ensure continuing new applications of ACE in the years to come.
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Affiliation(s)
- Christian Schou
- Department of Autoimmunology, Statens Serum Institute, Copenhagen, Denmark
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Liu S, Zhang LW, Zhang XX. Interaction between Fluoroquinolones and Bovine Serum Albumin Studied by Affinity Capillary Electrophoresis. ANAL SCI 2006; 22:1515-8. [PMID: 17159308 DOI: 10.2116/analsci.22.1515] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The interactions between eight fluoroquinolone antibiotics (ciprofloxacin, enoxacin, fleroxacin, levofloxacin, lomefloxacin, norfloxacin, ofloxacin, pefloxacin) and bovine serum albumin (BSA) were studied by affinity capillary electrophoresis (ACE). The binding constants were estimated by the change of migration times of the analytes through the change of concentration of BSA in the buffer solution. The yield binding constants were between 3.19 x 10(4) and 1.21 x 10(5) M(-1). These were related with the structures of fluoroquinolones, and agreed with the results obtained by other techniques. The obtained binding constants may help us in gaining some insights on possible drug/protein interactions and in early evaluation of the drugs' pharmacokinetic profiles during drug discovery.
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Affiliation(s)
- Shiwang Liu
- Department of Biology, Huanggang Normal University, Hubei, China
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Ding L, Zhang XX, Wei P, Fan K, Lai L. The interaction between severe acute respiratory syndrome coronavirus 3C-like proteinase and a dimeric inhibitor by capillary electrophoresis. Anal Biochem 2005; 343:159-65. [PMID: 15935325 PMCID: PMC7094366 DOI: 10.1016/j.ab.2005.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 04/12/2005] [Accepted: 04/18/2005] [Indexed: 01/28/2023]
Abstract
3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been demonstrated to be a key target for drug design against SARS. The interaction between SARS coronavirus 3C-like (3CL) proteinase and an octapeptide interface inhibitor was studied by affinity capillary electrophoresis (ACE). The binding constants were estimated by the change of migration time of the analytes in the buffer solution containing different concentrations of SARS 3CL proteinase. The results showed that SARS 3CL proteinase was able to complex with the octapeptide competitively, with binding constants of 2.44 x 10(4) M(-1) at 20 degrees C and 2.11 x 10(4)M(-1) at 37 degrees C. In addition, the thermodynamic parameters deduced reveal that hydrophobic interaction might play major roles, along with electrostatic force, in the binding process. The ACE method used here could be developed to be an effective and simple way of applying large-scale drug screening and evaluation.
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Affiliation(s)
- Li Ding
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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