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De Silva M, Dunn RC. Electric field-enhanced backscatter interferometry detection for capillary electrophoresis. Sci Rep 2024; 14:2110. [PMID: 38267528 PMCID: PMC10808210 DOI: 10.1038/s41598-024-52621-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
Backscatter interferometry (BSI) is a refractive index (RI) detection method that is easily integrated with capillary electrophoresis (CE) and is capable of detecting species ranging from inorganic ions to proteins without additional labels or contrast agents. The BSI signal changes linearly with the square of the separation voltage which has been used to quantify sample injection, but has not been explored as a potential signal enhancement mechanism in CE. Here we develop a mathematical model that predicts a signal enhancement at high field strengths, where the BSI signal is dominated by the voltage dependent mechanism. This is confirmed in both simulation and experiment, which show that the analyte peak area grows linearly with separation voltage at high field strengths. This effect can be exploited by adjusting the background electrolyte (BGE) to increase the conductivity difference between the BGE and analyte zones, which is shown to improve BSI performance. We also show that this approach has utility in small bore capillaries where larger separation fields can be applied before excess Joule heating degrades the separation. Unlike other optical detection methods that generally degrade as the optical pathlength is reduced, the BSI signal-to-noise can improve in small bore capillaries as the larger separation fields enhance the signal.
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Affiliation(s)
- Miyuru De Silva
- Department of Chemistry, University of Kansas, Lawrence, KS, 66047, USA
| | - Robert C Dunn
- Department of Chemistry, University of Kansas, Lawrence, KS, 66047, USA.
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2
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Abstract
We describe a system for horizontal 1D or 2D PAGE comprising an apparatus and microgels. There is no buffer outside the gel, making handling and sample loading easy. Specially designed electrodes on all four sides allow 2D electrophoresis without gel rotation. Electrophoresis is completed within 20 min and sensitivity is in the subnanogram range. The system is temperature controlled for speed, denaturation of nucleic acid molecules and maintaining molecules single-stranded. The system allows characterization of structure, conformation and damage in complex nucleic acid preparations. Besides quick 1D PAGE, 2D applications include characterization of efficiency of complex molecular procedures, checking quality of biosamples and detecting DNA damage in cells and body fluids. The system should also run protein gels.
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Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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4
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Zhang X, McGown LB. Sequence-based separation of single-stranded DNA using nucleotides in capillary electrophoresis: focus on phosphate. Electrophoresis 2013; 34:1778-86. [PMID: 23576075 PMCID: PMC3906628 DOI: 10.1002/elps.201200683] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/03/2013] [Accepted: 03/07/2013] [Indexed: 11/06/2022]
Abstract
DNA analysis has widespread applicability in biology, medicine, biotechnology, and forensics. DNA separation by length is readily achieved using sieving gels in electrophoresis. Separation by sequence is less simple, generally requiring adequate differences in native or induced conformation or differences in thermal or chemical stability of the strands that are hybridized prior to measurement. We previously demonstrated separation of four single-stranded DNA 76-mers that differ by only a few A-G substitutions based solely on sequence using guanosine-5'-monophosphate (GMP) in the running buffer. We attributed separation to the unique self-assembly of GMP to form higher order structures. Here, we examine an expanded set of 76-mers designed to probe the mechanism of the separation and effects of experimental conditions. We were surprised to find that other ribonucleotides achieved the similar separation to GMP, and that some separation was achieved using sodium phosphate instead of GMP. Potassium phosphate achieved almost as good separations as the ribonucleotides. This suggests that the separation medium provides a physicochemical environment for the DNA that effects strand migration in a sequence-selective manner. Further investigation is needed to determine whether the mechanism involves specific interactions between the phosphates and the DNA strands or is a result of other properties of the separation medium. Phosphate generally has been avoided in DNA separations by capillary gel electrophoresis because its high ionic strength exacerbates Joule heating. Our results suggest that phosphate compounds should be examined for separation of DNA based on sequence.
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Affiliation(s)
- Xueru Zhang
- Department of Chemistry and Chemical Biology, 321 Cogswell Laboratory, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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6
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Oh E, Hasan MN, Jamshed M, Park SH, Hong HM, Song EJ, Yoo YS. Growing trend of CE at the omics level: The frontier of systems biology. Electrophoresis 2010; 31:74-92. [DOI: 10.1002/elps.200900410] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Liu DN, Wang J, Guo YG, Yuan RJ, Wang HF, Bao JJ. Separation of aromatic acids by wide-bore electrophoresis with nanoparticles prepared by electrospray as pseudostationary phase. Electrophoresis 2008; 29:863-70. [DOI: 10.1002/elps.200700472] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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9
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Chen H, Wu YH, Song DY, Zhang W, Dong XY, Li PW, Lu CM. On-line pre-concentration and UV determination of DNA fragments by dynamic coating capillary electrophoresis and its application to detection of genetically modified oilseed rape based on PCR. Microchem J 2007. [DOI: 10.1016/j.microc.2006.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Masson C, Luong JHT, Nguyen AL. Analyses of Uric Acid in Urine and Reconstituted Serum by Capillary Electrophoresis. ANAL LETT 2006. [DOI: 10.1080/00032719108052913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Barron AE, Blanch HW. DNA Separations by Slab Gel, and Capillary Electrophoresis: Theory and Practice. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/03602549508014343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Sciacchitano CJ. Analysis of Polymerase Chain Reaction-Amplified DNA Fragments of Clostridium Botulinum Type E Neurotoxin Gene by High Performance Capillary Electrophoresis. J LIQ CHROMATOGR R T 2006. [DOI: 10.1080/10826079608017149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Carl J. Sciacchitano
- a U.S. Food and Drug Administration Northeast Regional Laboratory , Brooklyn, New York, 11232
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13
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Palma F, Potenza L, Amicucci A, Fiorani M, Labella D, Di Biase S, Stocchi V. HPLC and CE Analysis of PCR Products: A Comparative Study. J LIQ CHROMATOGR R T 2006. [DOI: 10.1080/10826079808000532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- F. Palma
- a Istituto di Chimica Biologica “Giorgio Fornaini” Università di Urbino , 61029, Urbino, Italy
| | - L. Potenza
- a Istituto di Chimica Biologica “Giorgio Fornaini” Università di Urbino , 61029, Urbino, Italy
| | - A. Amicucci
- a Istituto di Chimica Biologica “Giorgio Fornaini” Università di Urbino , 61029, Urbino, Italy
| | - M. Fiorani
- a Istituto di Chimica Biologica “Giorgio Fornaini” Università di Urbino , 61029, Urbino, Italy
| | - D. Labella
- b GeneDia Laboratorio di Ricerca e Sviluppo Napoli , Italy
| | - S. Di Biase
- b GeneDia Laboratorio di Ricerca e Sviluppo Napoli , Italy
| | - V. Stocchi
- a Istituto di Chimica Biologica “Giorgio Fornaini” Università di Urbino , 61029, Urbino, Italy
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14
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Gödde R, Akkad DA, Arning L, Dekomien G, Herchenbach J, Kunstmann E, Meins M, Wieczorek S, Epplen JT, Hoffjan S. Electrophoresis of DNA in human genetic diagnostics – state-of-the-art, alternatives and future prospects. Electrophoresis 2006; 27:939-46. [PMID: 16470775 DOI: 10.1002/elps.200500675] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electrophoretic separation of nucleic acids according to their molecular weights has dominated the methods' spectrum in molecular genetics for nearly half a century. We review the current methodological basis and evaluate its impact with special reference to new developments in the microarray technology. Although electrophoresis may be made redundant for many applications in DNA diagnostics within a few years, a number of electrophoretic vestiges will remain irreplaceable in the foreseeable future.
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Affiliation(s)
- René Gödde
- Department of Human Genetics, Ruhr-University, Bochum, Germany.
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15
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Endo Y, Zhang L, Katashima R, Itakura M, Doherty EAS, Barron AE, Baba Y. Effect of polymer matrix and glycerol on rapid single-strand conformation polymorphism analysis by capillary and microchip electrophoresis for detection of mutations in K-ras gene. Electrophoresis 2005; 26:3380-6. [PMID: 16097023 DOI: 10.1002/elps.200500142] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present the rapid single-strand conformation polymorphism (SSCP) analysis by capillary and microchip electrophoresis to detect the mutations in K-ras gene. Parameters that might affect the analysis of mutation in K-ras gene, such as the polymer and the additive in the sieving matrix, have been studied systematically. Under the optimal conditions, the analysis of seven mutants of K-ras gene could be finished within 10 min by capillary electrophoresis (CE). Furthermore, with the wild-type gene as the inner standard, the analysis accuracy of mutations could be improved. In addition, by studying the properties of polymer solutions, the matrix suitable for microchip electrophoresis was found, and the detection of mutations in K-ras gene could be further shortened to 1 min.
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Affiliation(s)
- Yuki Endo
- Department of Molecular and Pharmaceutical Biotechnology, Graduate School of Pharmaceutical Sciences, The University of Tokushima, Tokushima, Japan
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16
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Xu F, Jabasini M, Baba Y. Screening of mixed poly(ethylene oxide) solutions for microchip separation of double-stranded DNA using an orthogonal design approach. Electrophoresis 2005; 26:3013-20. [PMID: 16007697 DOI: 10.1002/elps.200410434] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a quick and systematic optimization of molecular weights (MWs) and concentrations of a series of mixed poly(ethylene oxide) (PEO) matrices for separating specific double-stranded DNA fragments on polymethylmethacrylate-based microchips by using an orthogonal design (ORD) approach. The mixed matrices are composed of PEOs in four MW ranges (M(w) 8 x 10(6), 1 x 10(6), 4 x 10(5), and 1 x 10(5)) with varying concentration ratios. In the mixed solutions, PEO with an intermediate MW of 4 x 10(5) is found to be a dominant factor for separating small DNA fragment pairs (e.g., 82 and 88 bp), while PEO with a high MW of 8 x 10(6) plays an important role in separating intermediate and large fragments (e.g., 271 and 281 bp, 506 and 517 bp, 7 and 10 kbp). High-concentration PEO mixtures give better resolution for short fragments, while dilute PEO mixtures show better resolution for long fragments. The optimized matrices are suitable for high-resolution separation of multiplex polymerase chain reaction-amplified products and restriction digest fragments ranging in size from 20 bp to 40 kbp within 4 min at a constant field strength of 177 V/cm. The experimental results indicate the robustness and speediness of the ORD to screen the contribution of PEO MWs and to tune optimally the PEO concentration ratio of different MWs with reference to the performance of specific DNA fragments separated.
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Affiliation(s)
- Feng Xu
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, The 21st Century COE Program, The University of Tokushima, Japan.
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17
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Abstract
We present a mathematical model based on the models of Hubert et al. [Macromolecules 29 (1996) 1006] and Sunada and Blanch [Electrophoresis, 19 (1998) 3128] to describe the electrophoretic mobility of DNA by a transient entanglement coupling mechanism. The proposed model takes into account the interactions between molecules in the capillary and the cross-section of collision between DNA and polymer molecules. The results show that the calculated values agree remarkably well with our electrophoretic mobility data.
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Affiliation(s)
- Ho Jin Jung
- Division of Chemical Engineering and Molecular Thermodynamics Lab., Hanyang University, Seoul 133-791, South Korea
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18
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Végvári A, Hjertén S. Stable homogeneous gel for molecular-sieving of DNA fragments in capillary electrophoresis. J Chromatogr A 2002; 960:221-7. [PMID: 12150560 DOI: 10.1016/s0021-9673(01)01436-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A polyacrylamide gel crosslinked with allyl-beta-cyclodextrin can be used repeatedly for several weeks for the separation of DNA fragments, since bubbles are not generated during a run. Allyl-beta-cyclodextrin can easily be synthesized in one step from allylglycidylether and beta-cyclodextrin. The plate numbers for DNA fragments, up to about 1500 bp, are high: for the separation of pBR322/HaeIII fragments they were in the range 450,000-1,600,000 m(-1). The resolution was almost independent of the concentration of the crosslinker (allyl-beta-cyclodextrin)--in sharp contrast to gels crosslinked with N,N'-methylenebisacrylamide.
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Affiliation(s)
- Akos Végvári
- Department of Biochemistry, Biomedical Center, Uppsala University, Sweden
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19
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McIntosh SL, Deligeorgiev TG, Gadjev NI, McGown LB. Mono- and bis-intercalating dyes for multiplex fluorescence lifetime detection of DNA restriction fragments in capillary electrophoresis. Electrophoresis 2002; 23:1473-9. [PMID: 12116158 DOI: 10.1002/1522-2683(200205)23:10<1473::aid-elps1473>3.0.co;2-#] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of novel intercalating dyes as labels in DNA restriction fragment analysis by capillary electrophoresis with frequency-domain fluorescence lifetime detection is described. The dyes, including one mono-intercalating dye with three positive charges and three bis-intercalating, homodimeric dyes with four positive charges, were excited by the 488 nm line of an argon ion laser and exhibited lifetimes in the range of 1-3 ns. The separations were performed using a gel containing 1% high-molecular-weight (HMW) hydroxyethylcellulose (HEC) (90,000-105,000) and 0.3% low-molecular-weight (LMW) HEC (24,000-27,000) in Tris-borate-EDTA buffer (TBE). Multiplex lifetime detection of mixtures of dye-labeled DNA restriction fragment digests and size standard fragments was achieved. Compared to previous results obtained with several mono-intercalating dyes of lesser charge (McIntosh, S. L., Nunnally, B. K., Nesbit, A. R., Deligeorgiev, T. G., Gadjev, N. I., McGown, L. B., Anal. Chem. 2000, 72, 5444-5449), the present dyes provided a wider range of lifetimes and better lifetime discrimination in multiplex detection. There was no evidence of dye exchange during the capillary electrophoresis experiment.
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Affiliation(s)
- Sara L McIntosh
- Department of Chemistry, P. M. Gross Chemical Laboratory, Duke University, Durham, NC 27708, USA
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20
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Dai HJ, Parker CN, Bao JJ. Characterization and inhibition study of MurA enzyme by capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 766:123-32. [PMID: 11820287 DOI: 10.1016/s0378-4347(01)00461-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A capillary electrophoresis-based enzyme assay for UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is described. This method, based on UV detection, provides baseline separation of one of the reaction products, enolpyruvyluridine 5'-diphospho-N-acetylglucosamine (EP-UDP-GlcNAc), from substrates phosphoenolpyruvate (PEP) and uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) within 4 min. The other product, phosphate, is not detectable by UV at 200 nm. Quantitation of individual components, substrates or product, can be accomplished based on the separated peaks. This methodology was used to determine the Michaelis constant, Km, and product formation rate constant, Kcat, for MurA. Additionally, the CE method was used to evaluate the inhibition effects on MurA using one specific compound as an example. By following similar procedures, the apparent Km values in the presence of different inhibitor concentrations were determined. The inhibition constant, Ki, can be determined from these apparent Km values. In addition, this CE method can be used to study the inhibition mechanism. The principle of this approach is generally applicable to other enzyme studies.
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Affiliation(s)
- H Jian Dai
- Procter & Gamble Pharmaceuticals, Mason, OH 45040, USA
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21
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Wei W, Yeung ES. DNA capillary electrophoresis in entangled dynamic polymers of surfactant molecules. Anal Chem 2001; 73:1776-83. [PMID: 11338591 DOI: 10.1021/ac0012997] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous solutions of monomeric nonionic surfactants, n-alkyl polyoxyethylene ethers (C16E6, C16E8, C14E6), can be used as sieving matrixes for the separation of DNA fragments by capillary electrophoresis. Unlike ordinary polymer solutions, these surfactant solutions behave as dynamic polymers. By combining the "reversible gel" theory of DNA electrophoresis and the static and dynamic properties of wormlike surfactant micelles, a model is developed for describing the migration behavior of DNA molecules in these solutions. According to the model, the separation limit can be extended at low surfactant concentrations. Surfactant solutions as a separation medium provide many advantages over ordinary polymers, such as ease of preparation, solution homogeneity, stable structure, low viscosity, and self-coating property for reducing electroosmotic flow. More importantly, the properties of wormlike micelles (micelle size, entanglement concentration) can be adjusted by simply changing the monomer concentration, denaturant, and temperature to allow the separation of different size ranges of DNA fragments. Fast separation is achieved for DNA fragments ranging from 10 bp to 5 kb by using bare fused-silica columns. DNA sequencing fragments of BigDye G-labeled M13 up to 600 bases were separated within 60 min.
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Affiliation(s)
- W Wei
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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22
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Vilenchik M, Benimetsky L, Kolbanovsky A, Miller P, Stein CA. Evidence for higher-order structure formation by the c-myb 18-mer phosphorothioate antisense (codons 2-7) oligodeoxynucleotide: potential relationship to antisense c-myb inhibition. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:87-97. [PMID: 11334144 DOI: 10.1089/108729001750171317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have demonstrated the formation of higher-order structures (presumably tetraplexes) by an 18-mer phosphorothioate antisense c-myb oligodeoxyribonucleotide that has been shown to have activity in the treatment of leukemia xenograft models. Although not observable by conventionally employed techniques, such as PAGE and dimethyl sulfate (DMS) protection, the formation of such higher-order structures by this oligonucleotide was revealed by several techniques. These included capillary gel electrophoresis (CGE), which demonstrated the presence of molecules with greatly increased retention time compared with the monomer; magnetic circular dichroism spectroscopy, which demonstrated a band at 290 nm, a characteristic of antiparallel tetraplexes; and fluorescence energy transfer measurements. For the last, the 18-mer phosphorothioate oligonucleotide was synthesized with a 5'-fluorescein group. Similar to the molecular beacon model, its fluorescence was quenched when combined in solution with tetraplex-forming oligomers that contained a 3'-Dabcyl moiety. 7-Deazaguanosine inhibits the formation of tetraplexes by eliminated Hoogsteen base pair interactions. The wild-type and 7-deazaguanosine-substituted antisense c-myb oligomers differentially downregulated the expression of the c-myb proto-oncogene in K562 and HL60 cells, with the wild-type oligomer being the least active. The 18-mer c-myb molecule can, therefore, form highly complex structures, whose analysis in solution cannot be limited to examination of slab gel electrophoresis results alone.
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Affiliation(s)
- M Vilenchik
- Department of Pharmacology, Columbia University, New York, NY 10032, USA
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23
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Davidson YY, Soper SA, Margolis S, Sander LC. Immobilization of the restriction enzymesHaeIII andHindIII on porous silica particles via a glutaraldehyde linkage for the micro-digestion of dsDNA with analysis by capillary electrophoresis. J Sep Sci 2001. [DOI: 10.1002/1615-9314(20010101)24:1<10::aid-jssc10>3.0.co;2-n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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McIntosh SL, Nunnally BK, Nesbit AR, Deligeorgiev TG, Gadjev NI, McGown LB. Fluorescence lifetime for on-the-fly multiplex detection of DNA restriction fragments in capillary electrophoresis. Anal Chem 2000; 72:5444-9. [PMID: 11080899 DOI: 10.1021/ac000235t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the first use of frequency-domain fluorescence lifetime for multiplex detection of DNA restriction fragments in capillary electrophoresis (CE). The fragments were labeled with monomeric intercalating dyes that can be excited by either the 488- or 514-nm line of an argon ion laser and have lifetimes in the range of 0.5-2.5 ns. We were able to achieve multiplex lifetime detection in the CE separation of a restriction fragment digest and a DNA size ladder in the same run, for fragments shorter than 700 bp. Different gel buffer systems, including a modified polyacrylamide gel and several tris-borate-EDTA/hydroxyethylcellulose (TBE/HEC) gels, were investigated for separation and detection of the dye-labeled DNA fragments. Best results for both electrophoretic resolution and lifetime detection were obtained using a gel containing 1% high molecular weight (90,000-105,000) HEC and 0.3% low molecular weight (24,000-27,000) HEC in TBE buffer.
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Affiliation(s)
- S L McIntosh
- Department of Chemistry, P. M. Gross Chemical Laboratory, Duke University, Durham, North Carolina 27708, USA
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25
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Abstract
The actual methods to evaluate total DNA methylation based on high performance liquid chromatography (HPLC) are long and tedious due to the specific running buffers required. In this work, a new open-tube capillary electrophoresis system has been applied to the separation of acid hydrolyzed genomic DNA and so, to the evaluation of genomic DNA methylation. Several running conditions were tested but separation of cytosine and 5-methyl-cytosine was only possible by sodium dodecyl sulfate (SDS) micelle system. The importance of sample dissolution preparation has also been demonstrated. The results of this study open up the possibility of quantification of the relative methylation degree of rapid genomic DNA by a simple method based on high performance capillary electrophoresis (HPCE).
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Affiliation(s)
- M F Fraga
- Universidad de Oviedo, Departamento BOS, Spain
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26
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Hoagland DA, Arvanitidou E, Welch C. Capillary Electrophoresis Measurements of the Free Solution Mobility for Several Model Polyelectrolyte Systems. Macromolecules 1999. [DOI: 10.1021/ma9903761] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. A. Hoagland
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, Amherst, Massachusetts 01003
| | - E. Arvanitidou
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, Amherst, Massachusetts 01003
| | - C. Welch
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, Amherst, Massachusetts 01003
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27
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Liu Y, Kuhr WG. Separation of double- and single-stranded DNA restriction fragments: capillary electrophoresis with polymer solutions under alkaline conditions. Anal Chem 1999; 71:1668-73. [PMID: 10330903 DOI: 10.1021/ac9814492] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capillary electrophoresis in buffers containing hydroxyethyl cellulose (HEC) was used to separate double- and single-stranded DNA restriction fragments under neutral and alkaline conditions in epoxy-coated capillaries. It was found that better resolution was achieved using highly entangled HEC solutions for a narrow range of DNA fragment sizes, while lower resolution was obtained over a wide separation range using diluted HEC solutions. Optimal resolution of these DNA fragments was obtained using buffers containing 0.5% HEC at pH 11 with plate numbers exceeding 3 x 10(6) plates/m. It was also found that the diffusion coefficients and electrophoretic mobilities of DNA fragments decreased with increasing pH. This may indicate a more extended DNA conformation and, therefore, enhancement of transient entanglement coupling between DNA and HEC polymers under alkaline condition. At pH 12, ss-DNA were well separated in entangled HEC solutions; however, the resolution of ss-DNA was significantly decreased in diluted polymer solution.
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Affiliation(s)
- Y Liu
- Department of Chemistry, University of California, Riverside 92521, USA
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28
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Abstract
When investigating the use of different polymers for capillary electrophoresis we found that poly-N,N-dimethylacrylamide (pDMA) has a very low viscosity compared to other polymers of comparable molecular mass and resolving power. This makes it a potentially useful matrix for DNA separation in multi-capillary electrophoresis, where short cycle times or low pressure for matrix replacement are preferred. We have characterized this matrix by systematic studies on concentration, chain length and field strength dependence. It is shown that pDMA performs well for the separation of oligonucleotides and double-stranded DNA fragments. Together with the application of DNA sequencing, pDMA is a universal polymer for the separation of biological macromolecules.
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Affiliation(s)
- C Heller
- Abteilung Lehrach, Max-Planck-Institut für Molekulare Genetik, Berlin-Dahlem, Germany.
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29
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Abstract
We have investigated the viscosity of different commercially available polymers in solution and found that dextran has a low viscosity compared to other polymers of comparable molecular weight and resolving power. This makes it a potentially useful matrix for DNA separation in capillary electrophoresis, where either short time or low pressure are preferred for matrix replacement. We showed that dextran performs well for the separation of oligonucleotides and double-stranded DNA fragments. Together with the well-known application for protein separation, this makes dextran a universal polymer for the separation of biological macromolecules.
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Affiliation(s)
- C Heller
- Max-Planck-Institut für molekulare Genetik, Berlin-Dahlem, Germany.
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30
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Djordjevic NM, Houdiere F, Fowler P, Natt F. HPLC Separation of Oligonucleotides in Isocratic and Temperature-Programming Mode. Anal Chem 1998; 70:1921-5. [DOI: 10.1021/ac9711697] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nebojsa M. Djordjevic
- Pharma Discovery, Novartis Pharma Inc., Building 503/1106, Basle CH-4002, Switzerland
| | - Fabrice Houdiere
- Pharma Discovery, Novartis Pharma Inc., Building 503/1106, Basle CH-4002, Switzerland
| | - Patrick Fowler
- Pharma Discovery, Novartis Pharma Inc., Building 503/1106, Basle CH-4002, Switzerland
| | - Francois Natt
- Pharma Discovery, Novartis Pharma Inc., Building 503/1106, Basle CH-4002, Switzerland
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31
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Jenkins MA, Guerin MD. Capillary electrophoresis procedures for serum protein analysis: comparison with established techniques. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 699:257-68. [PMID: 9392378 DOI: 10.1016/s0378-4347(97)00180-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Methods using automated capillary electrophoresis (CE) instrumentation are available for serum protein electrophoresis with monoclonal band quantitation, isoelectric focusing and sodium dodecyl sulphate-polyacrylamide gel electrophoresis separations. The advantages of CE over previous gel methods relate to the time and labour saved by the automated instrumentation. High pI monoclonal bands and cryoglobulin specimens can be successfully analysed by CE. However, if the CE application uses a standard company supplied kit, then the cost savings are often negated by the high cost of the kit. Improvements such as the inclusion of both a UV-Vis as well as a fluorescence detector as standard within the one commercial instrument, the production of coated IEF capillaries with a useful life of at least 100 samples, and the introduction of a capillary array into all commercial instrumentation would ensure greater use of CE within both the clinical and other protein laboratories.
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Affiliation(s)
- M A Jenkins
- Division of Laboratory Medicine, Austin and Repatriation Medical Center, Heidelberg, Vic., Australia
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32
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Gibson TJ, Sepaniak MJ. Examination of band dispersion during size-selective capillary electrophoresis separations of DNA fragments. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 695:103-11. [PMID: 9271134 DOI: 10.1016/s0378-4347(97)00212-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Versatile capillary electrophoresis instrumentation that permits the rapid and precise translation of a laser fluorometric detection zone along the capillary wall has been used to examine the factors which cause band broadening during size-selective separations of DNA fragments. Separations are performed using capillaries containing entangled polymer solutions. The scanning capabilities of this instrumentation facilitates the determination of diffusion coefficients under static conditions without the need to discontinue and reapply an electric field. The ability to rapidly translate the detection zone along the column allows the monitoring of the separation at various points along the capillary which enables the examination of the sources of band dispersion under kinetic conditions. Results from experiments utilizing various concentrations of both high and low molecular mass methyl cellulose polymers as sieving media are presented. It is shown that axial diffusion, even when adjusted for kinetic conditions using the Einstein relationship, does not account for the total observed band variance. Possible explanations for this behavior are presented.
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Affiliation(s)
- T J Gibson
- Department of Chemistry, University of Tennessee, Knoxville 37996-1600, USA
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33
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34
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35
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Iki N, Kim Y, Yeung ES. Electrostatic and Hydrodynamic Separation of DNA Fragments in Capillary Tubes. Anal Chem 1996. [DOI: 10.1021/ac9605814] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nobuhiko Iki
- Ames LaboratoryUSDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Yongseong Kim
- Ames LaboratoryUSDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Edward S. Yeung
- Ames LaboratoryUSDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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36
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Jenkins MA, Guerin MD. Capillary electrophoresis as a clinical tool. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL APPLICATIONS 1996; 682:23-34. [PMID: 8832422 DOI: 10.1016/0378-4347(95)00552-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Clinical laboratories must produce accurate results for patients with a minimum turn-around time. Automated commercial capillary electrophoresis instrumentation has been available to the clinical laboratory for the past five years. Our laboratory has utilised capillary electrophoresis (CE) to automate serum protein electrophoresis. We have used the technique of CE to produce clinical results for nearly two years. CE methods are also available for the quantitation of haemoglobin variants, by both isoelectric focusing and free solution techniques. Micellar electrokinetic separations by CE have been developed for some specialised drug assays and for B-group vitamin analysis, while gel-filled capillaries have the capability to separate DNA fragments, such as PCR products. Isoenzyme analysis has shown possibilities by CE, but quantitative results are needed to be clinically useful. Analysis of amino acids for newborn screening programs and as an arterial clotting indicator are being developed. The next five years should see a proliferation of clinical laboratory methods using automated CE.
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Affiliation(s)
- M A Jenkins
- Repatriation Medical Centre, Victoria, Australia
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37
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Personett DA, Chouinard M, Sugaya K, McKinney M. Simplified RT/PCR quantitation of gene transcripts in cultured neuroblastoma (SN49) and microglial (BV-2) cells using capillary electrophoresis and laser-induced fluorescence. J Neurosci Methods 1996; 65:77-91. [PMID: 8815312 DOI: 10.1016/0165-0270(95)00150-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We developed a simplified protocol for sensitive quantitation of mRNA using polymerase chain reaction (PCR) amplification of cDNA made by reverse transcriptase (RT), as resolved with capillary electrophoresis (CE) and detected with laser-induced fluorescence (LIF). The conditions required for adequate accuracy of the simplified version of the RT/PCR quantitation, in which a single concentration of external standard and amplification to within or near the plateau phase are used, were established for assay of mRNAs expressed at high, moderate, and low abundance. The mRNAs for the cytosolic enzyme, glyceraldehyde phosphate dehydrogenase (GAPDH) and the growth-associated protein GAP-43 in cultured SN49 neuroblastoma cells were used as target genes for high and moderate levels of expression, respectively. Using cultured mouse microglial cells (BV-2), we demonstrated the utility of this RT/PCR/CE/LIF protocol to quantitate a low-abundance mRNA, encoding a form of nitric oxide synthase (i-NOS) induced by treatment with endotoxin. The appearance of i-NOS mRNA after endotoxin treatment of BV-2 cells was confirmed by Northern blot analysis and in situ hybridization histochemistry, and functional enzyme activity was followed by release of nitric oxide (as nitrite) into the medium. The many advantages of the 'single-point' RT/PCR/CE/LIF protocol for quantitating mRNAs of interest include: simplified protocol, elimination of the use of radiotracers, high sensitivity and precision, and semi-automation of the quantitation phase of analysis.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Brain Neoplasms/metabolism
- DNA, Complementary/analysis
- DNA, Complementary/metabolism
- Electrophoresis, Capillary
- In Situ Hybridization
- Lasers
- Mice
- Microglia/metabolism
- Molecular Sequence Data
- Neuroblastoma/metabolism
- Nitric Oxide Synthase/biosynthesis
- Nitric Oxide Synthase/genetics
- Polymerase Chain Reaction/instrumentation
- Polymerase Chain Reaction/methods
- RNA, Messenger/biosynthesis
- RNA, Messenger/isolation & purification
- Spectrometry, Fluorescence
- Templates, Genetic
- Transcription, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- D A Personett
- Mayo Clinic Jacksonville, Alzheimer Research Group, FL 32224, USA
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38
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Chapter 2 Column technologies for capillary electrophoresis. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1464-3456(96)80019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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39
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Belenky A, Smisek DL, Cohen AS. Sequencing of antisense DNA analogues by capillary gel electrophoresis with laser-induced fluorescence detection. J Chromatogr A 1995; 700:137-49. [PMID: 7767460 DOI: 10.1016/0021-9673(94)01092-s] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A method using capillary gel electrophoresis with laser-induced fluorescence detection is described which permits complete sequence determination of antisense DNA analogues of unknown sequence. This method, originally created as a tool to confirm the sequence of antisense oligonucleotides being developed as therapeutic drugs, utilizes data collected under a range of experimental conditions described by the Ogston model as applied to gel electrophoresis. A linear relationship independent of experimental conditions between the relative electrophoretic migration time and the oligonucleotide base number was observed and is shown to be consistent with a simplified version of this model and can be used to facilitate the sequence determination.
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Affiliation(s)
- A Belenky
- Hybridon Inc., Worcester, MA 01605, USA
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40
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Heller C. Capillary electrophoresis of proteins and nucleic acids in gels and entangled polymer solutions. J Chromatogr A 1995. [DOI: 10.1016/0021-9673(94)01169-f] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Ruberto MA, Grayeski ML. Investigation of acridinium labelling for chemiluminescence detection of peptides separated by capillary electrophoresis. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/mcs.1220060603] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Abstract
New trends in adulteration monitoring, favor the development of methods analyzing simultaneously as many compounds as possible. Capillary electrophoresis has been applied to the examination of a broad spectrum of citrus juice molecules that absorb in the UV and in the visible light. Depending on the conditions up to thirty compounds could be separated. The identified molecules included phenolic amines, amino acids, flavonoids, polyphenols and vitamin C. Samples can be analyzed without specific preparation and the best separations were obtained with diluted solutions due to a stacking effect. This method has been applied to the comparison of pure orange juice and pulpwash, a major adulterant of orange juice. Several significant quantitative differences were seen and it is hoped that this procedure will provide a more precise way of estimating pulpwash in orange juice.
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43
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Bae YC, Soane D. Polymeric separation media for electrophoresis: Cross-linked systems or entangled solutions. J Chromatogr A 1993. [DOI: 10.1016/0021-9673(93)80640-t] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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44
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Pulsed-laser fluorescence detection in capillary zone electrophoresis of some banned substances in sport. Anal Chim Acta 1993. [DOI: 10.1016/0003-2670(93)80133-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Chiesa C, Horváth C. Capillary zone electrophoresis of malto-oligosaccharides derivatized with 8-aminonaphthalene-1,3,6-trisulfonic acid. J Chromatogr A 1993; 645:337-52. [PMID: 8408418 DOI: 10.1016/0021-9673(93)83394-8] [Citation(s) in RCA: 146] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Malto-oligosaccharides were derivatized via their reducing end with 8-aminonaphthalene-1,3,6-trisulfonic acid by reductive amination, and the separation and electrophoretic migration behavior of the labelled sugars were investigated by capillary zone electrophoresis. Series of linear malto-oligosaccharides were found particularly suitable for both the study of the effect of the operating conditions on the separation and the investigation of the relationship between the electrophoretic mobility and the molecular size of the homologues. The electrophoretic mobility of the malto-oligosaccharide conjugates was found to be a linear function of the molecular mass to the negative two-thirds power. The sugar derivatives employed here carry three negative charges due to the presence of the dissociated sulfonic acid groups even at strongly acidic pH. Therefore, the analytes can migrate in the electric field without interference by electroendosmotic flow and/or wall adsorption in uncoated silica capillaries at low pH. As a result, the separation of these carbohydrate conjugates can be carried out under such conditions with high speed and efficiency in free solution, i.e., without an anticonvective medium such as a gel or a viscous polymer solution. Appropriate use of triethylammonium phosphate buffer, pH 2.5, as the background electrolyte improves not only the reproducibility, but also the efficiency and speed of the separation. The labelled sugars allow monitoring of the separation by UV detector or laser-induced fluorescence detector with concomitant enhancement of analytical sensitivity.
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Affiliation(s)
- C Chiesa
- Department of Chemical Engineering, Yale University, New Haven, CT 06520
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46
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Hebenbrock K, Schügerl K, Freitag R. Analysis of plasmid-DNA and cell protein of recombinant Escherichia coli using capillary gel electrophoresis. Electrophoresis 1993; 14:753-8. [PMID: 8404819 DOI: 10.1002/elps.11501401118] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Plasmid DNA prepared from cultivation samples of recombinant Escherichia coli was analyzed by capillary gel electrophoresis. We used this method to control the genetic stability during a fed-batch culture. The plasmid DNA and a standard DNA mixture with molecular weights in the size range of 3000-22,000 base pairs (bp) were analyzed in capillaries that were filled with solutions of non-cross-linked polyacrylamide. With this method the plasmid DNA from recombinant E. coli cultivation samples was analyzed within 30 min. Separation parameters such as gel concentration, capillary length and current were optimized for that purpose. The method was modified to allow the analysis of proteins. Crude cell lysate samples could be screened for the protein pattern within 15 min in sodium dodecyl sulfate-polyacrylamide filled capillaries. The method was also used to verify product purity after the down-stream process.
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Affiliation(s)
- K Hebenbrock
- Institut für Technische Chemie, Universität Hannover, Germany
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47
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Clark BK, Sepaniak MJ. Evaluation of on-column labeling with intercalating dyes for fluorescence detection of DNA fragments separated by capillary electrophoresis. ACTA ACUST UNITED AC 1993. [DOI: 10.1002/mcs.1220050312] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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48
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Huber CG, Oefner PJ, Preuss E, Bonn GK. High-resolution liquid chromatography of DNA fragments on non-porous poly(styrene-divinylbenzene) particles. Nucleic Acids Res 1993; 21:1061-6. [PMID: 8503958 PMCID: PMC309263 DOI: 10.1093/nar/21.5.1061] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
DNA restriction fragments and PCR products were separated by means of ion-pair reversed-phase high-performance liquid chromatography on alkylated non-porous poly(styrene-divinylbenzene) particles with a mean diameter of 2.1 microns. Optimum resolution was obtained by using an acetonitrile gradient in 100 mM of triethylammonium acetate and a column temperature of 50 degrees C. This allowed the separation of DNA fragments differing in chain length by 1-5% up to a size of 500 base pairs. PCR products could be analyzed directly in less than two minutes with a concentration sensitivity of at least 300 ng/ml. Compared with anion-exchange chromatography or gel electrophoresis no desaltation of the purified DNA molecules is required because the volatile buffer system can be readily evaporated. Subsequently, the method was used for the semiquantitative evaluation of the expression of multidrug resistance genes in mononuclear white blood cells.
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Affiliation(s)
- C G Huber
- Institute of Radiochemistry, Leopold-Franzens-University, Innsbruck, Austria
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49
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Chiari M, Nesi M, Fazio M, Righetti PG. Capillary electrophoresis of macromolecules in 'syrupy' solutions: facts and misfacts. Electrophoresis 1992; 13:690-7. [PMID: 1459094 DOI: 10.1002/elps.11501301147] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
'Syrupy' solutions of liquid linear polyacrylamide (> or = 10%T, 0%C) appear to be excellent for fractionation of oligonucleotides and, potentially, for DNA sequencing. For such analyses, the silica wall must be coated by covalently bound strings of polyacrylamide; otherwise, the electroosmotic flow will slowly pump out the viscous electrolyte solution. Due to the enormous viscosity (100 Pa s for an 8% T solution) the polymer strings must be prepared in situ, by filling the capillary with the appropriate monomer solution. The reaction, however, cannot be driven to better than 80-85% conversion: in 10%T, the concentration of unreacted monomers will thus be 200-300 mM. This will give a substantial background absorbance (even at 254 nm) and leave a huge amount of potentially harmful reacting species in the background electrolyte. A chemical scavenging method is proposed here: after polymerization, a 100 mM solution of cysteine is driven in from the cathode and allowed to react for up to 10 h. At the end of the reaction period, the excess cysteine and its acrylamido adduct are driven out electrophoretically and the column is reconstituted with its normal background electrolyte. Columns thus preconditioned have been found to perform extremely well and to last as long as the inner coating (and the linear polymer filling) will last. No 'carry over' from run to run was experienced.
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Affiliation(s)
- M Chiari
- Department of Biomedical Sciences and Technologies, University of Milano, Italy
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50
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Landers JP, Schuchard MD, Subramaniam M, Sismelich TP, Spelsberg TC. High-performance capillary electrophoretic analysis of chloramphenicol acetyl transferase activity. J Chromatogr A 1992; 603:247-57. [PMID: 1644882 DOI: 10.1016/0021-9673(92)85368-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This study highlights the potential utility of high-performance capillary electrophoresis (HPCE) for monitoring enzyme activity. Free-zone capillary electrophoresis is used to rapidly and reproducibly analyze the activity of the bacterial enzyme chloramphenicol acetyl transferase (CAT) which converts the substrates acetyl coenzyme A (CoA) and chloramphenicol to acetyl chloramphenicol and CoA. The results of this study indicate that HPCE may be an excellent tool for studying enzyme activities since it has several advantages over standard single parameters assays, most notably, the ability to monitor both loss of substrate and appearance of products simultaneously. Conditions have been identified for optimal separation of the substrate (chloramphenicol) from the products (acetylated derivatives). This presents a unique potential of HPCE for the analysis of enzymatic reactions that may be applied to areas of analytical research presently utilizing enzymatic reactions. One such analytical method is the CAT assay used for analysis of gene promoter activity. In this study, HPCE is shown to yield similar quantitative results with nonradiolabelled substrate in a fraction of the time. HPCE has several advantages over standard techniques including speed of analysis, no need for radiolabelled substrate, small sample volumes, high sensitivity/resolution and excellent quantitative capabilities.
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Affiliation(s)
- J P Landers
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
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