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Lian DS, Zeng HS. Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis. Compr Rev Food Sci Food Saf 2017; 16:1281-1295. [DOI: 10.1111/1541-4337.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
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2
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Study on association of HSP70_hom gene polymorphism with rheumatoid arthritis using capillary electrophoresis-laser induced fluorescence. Microchem J 2017. [DOI: 10.1016/j.microc.2017.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Çakir Ö, Meriç S, Meriç S, Ari Ş. GMO Analysis Methods for Food: From Today to Tomorrow. Food Saf (Tokyo) 2016. [DOI: 10.1002/9781119160588.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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4
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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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5
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Characterization and study of transgenic cultivars by capillary and microchip electrophoresis. Int J Mol Sci 2014; 15:23851-77. [PMID: 25535077 PMCID: PMC4284794 DOI: 10.3390/ijms151223851] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 01/11/2023] Open
Abstract
Advances in biotechnology have increased the demand for suitable analytical techniques for the analysis of genetically modified organisms. Study of the substantial equivalence, discrimination between transgenic and non-transgenic cultivars, study of the unintended effects caused by a genetic modification or their response to diverse situations or stress conditions (e.g., environmental, climatic, infections) are some of the concerns that need to be addressed. Capillary electrophoresis (CE) is emerging as an alternative to conventional techniques for the study and characterization of genetically modified organisms. This article reviews the most recent applications of CE for the analysis and characterization of transgenic cultivars in the last five years. Different strategies have been described depending on the level analyzed (DNA, proteins or metabolites). Capillary gel electrophoresis (CGE) has shown to be particularly useful for the analysis of DNA fragments amplified by PCR. Metabolites and proteins have been mainly separated using capillary zone electrophoresis (CZE) using UV and MS detection. Electrophoretic chips have also proven their ability in the analysis of transgenic cultivars and a section describing the new applications is also included.
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6
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Shin GW, Chung B, Jung GY, Jung GY. Multiplex ligase-based genotyping methods combined with CE. Electrophoresis 2013; 35:1004-16. [PMID: 24123070 DOI: 10.1002/elps.201300361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 12/30/2022]
Abstract
In this genomic era, the ability to assay multiple genomic hot spots that have strong clinical implications is greatly desired. Conventional PCR-based methods suffer from frequent false-positive detections, particularly when a multiplex analysis is desirable. As an alternative to the error-prone conventional methods, multiplex ligase-based genotyping methods combined with CE have a strong potential. In this review, both previously developed methods and emerging methods are described to reveal the specificity, sensitivity, and simplicity of the ligase-based methods. For each step (ligation, amplification, and separation), the principles of several alternative methods are discussed along with their applications to explore the future development of ligase-based diagnostic methods.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Sciences and Technology, Pohang, Gyeongbuk, Korea
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7
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Valdés A, García-Cañas V, Cifuentes A. CGE-laser induced fluorescence of double-stranded DNA fragments using GelGreen dye. Electrophoresis 2013; 34:1555-62. [PMID: 23417332 DOI: 10.1002/elps.201200624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/19/2012] [Accepted: 01/03/2013] [Indexed: 12/14/2022]
Abstract
Nowadays, new solutions focused on the replacement of reagents hazardous to human health are highly demanded in laboratories and Green Chemistry. In the present work, GelGreen, a new nonhazardous DNA staining reagent, has been assayed for the first time to analyze double-stranded DNA by CGE with LIF detection. The effect of GelGreen concentration on S/N ratio and migration time of a wide concentration range of standard DNA mixtures was evaluated. Under optimum GelGreen concentration in the sieving buffer efficient and sensitive separations of DNA fragments with sizes from 100-500 base pairs (bp) were obtained. A comparison in terms of resolution, time of analysis, LOD, LOQ, reproducibility, sizing performance, and cost of analysis was established between two optimized CGE-LIF protocols for DNA analysis, one based on the dye YOPRO-1 (typically used for CGE-LIF of DNA fragments) and another one using the new GelGreen. Analyses using YOPRO-1 were faster than those using GelGreen (ca. 31 min versus 34 min for the analysis of 100-500 bp DNA fragments). On the other side, sensitivity using GelGreen was twofold higher than that using YOPRO-1. The cost of analysis was significantly cheaper (ninefold) using GelGreen than with YOPRO-1. The resolution values and sizing performance were not significantly different between the two dyes (e.g. both dyes allowed the separation of fragments differing in only 2 bp in the 100-200 bp range). The usefulness of the separation method using GelGreen is demonstrated by the characterization of different amplicons obtained by PCR.
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8
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Samson MC, Gullí M, Marmiroli N. Multiplex real-time PCR assays for simultaneous detection of maize MON810 and GA21 in food samples. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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9
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Gavazzi F, Casazza AP, Depedro C, Mastromauro F, Breviario D. Technical improvement of the TBP (tubulin-based polymorphism) method for plant species detection, based on capillary electrophoresis. Electrophoresis 2013; 33:2840-51. [PMID: 23019101 DOI: 10.1002/elps.201200144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Nowadays, feed and food safety and traceability are of primary importance. Hence, a correct labeling of the different products is highly desirable in general, but mandatory for those people who are suffering from eating disorders and food allergies. Among the technologies that have been developed for feed and food analysis, the patented tubulin-based polymorphism (TBP) method emerges as an easy, versatile, and inexpensive diagnostic tool. Initially used to fingerprint different plant species and varieties, TBP was then successfully applied to trace species in mixtures of plant origin such as commercial feeds. TBP is a DNA-based molecular marker, that makes use of PCR for the selective amplification of plant β-tubulin introns. Amplified fragments are then separated by PAGE and visualized by silver staining. We have now developed an improved version of TBP. Based on capillary electrophoresis and fluorescence detection, it makes the method automatic, more sensible, reproducible, and faster. Compared to the classic TBP, this new version allows to obtain a better data resolution and an easier interpretation of the results, clearing the way to large-scale feed/food diagnostics.
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Affiliation(s)
- Floriana Gavazzi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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10
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Capillary electrophoretic profiling of tryptic digests of water soluble proteins from Bacillus thuringiensis-transgenic and non-transgenic maize species. Food Chem 2012; 134:1607-15. [DOI: 10.1016/j.foodchem.2012.02.220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 11/22/2022]
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11
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Ohnoutkova L, Zitka O, Mrizova K, Vaskova J, Galuszka P, Cernei N, Smedley MA, Harwood WA, Adam V, Kizek R. Electrophoretic and chromatographic evaluation of transgenic barley expressing a bacterial dihydrodipicolinate synthase. Electrophoresis 2012; 33:2365-73. [DOI: 10.1002/elps.201200033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Katarina Mrizova
- Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research; Palacky University; Olomouc; Czech Republic
| | - Jana Vaskova
- Institute of Experimental Botany; Academy of Sciences of the Czech Republic; Olomouc; Czech Republic
| | - Petr Galuszka
- Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research; Palacky University; Olomouc; Czech Republic
| | - Natalie Cernei
- Department of Chemistry and Biochemistry; Faculty of Agronomy, Mendel University in Brno; Brno; Czech Republic
| | - Mark A. Smedley
- Department of Crop Genetics, John Innes Centre; Norwich Research Park; United Kingdom
| | - Wendy A. Harwood
- Department of Crop Genetics, John Innes Centre; Norwich Research Park; United Kingdom
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12
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Global Foodomics strategy to investigate the health benefits of dietary constituents. J Chromatogr A 2012; 1248:139-53. [DOI: 10.1016/j.chroma.2012.06.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/29/2012] [Accepted: 06/01/2012] [Indexed: 12/21/2022]
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13
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Castro-Puyana M, García-Cañas V, Simó C, Cifuentes A. Recent advances in the application of capillary electromigration methods for food analysis and Foodomics. Electrophoresis 2011; 33:147-67. [DOI: 10.1002/elps.201100385] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 08/10/2011] [Accepted: 08/10/2011] [Indexed: 12/17/2022]
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14
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León C, García-Cañas V, González R, Morales P, Cifuentes A. Fast and sensitive detection of genetically modified yeasts in wine. J Chromatogr A 2011; 1218:7550-6. [DOI: 10.1016/j.chroma.2011.01.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/12/2011] [Accepted: 01/14/2011] [Indexed: 11/17/2022]
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15
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Piñero MY, Bauza R, Arce L. Thirty years of capillary electrophoresis in food analysis laboratories: potential applications. Electrophoresis 2011; 32:1379-93. [PMID: 21538397 DOI: 10.1002/elps.201000541] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 02/07/2011] [Accepted: 02/07/2011] [Indexed: 01/20/2023]
Abstract
CE has generated considerable interest in the research community since instruments were introduced by different trading companies in the 1990s. Nowadays, CE is popular due to its simplicity, speed, highly efficient separations and minimal solvent and reagent consumption; it can also be included as a useful technique in the nanotechnology field and it covers a wide range of specific applications in different fields (chemical, pharmaceutical, genetic, clinical, food and environmental). CE has been very well evaluated in research laboratories for several years, and different new approaches to improve sensitivity (one of the main drawbacks of CE) and robustness have been proposed. However, this technique is still not well accepted in routine laboratories for food analysis. Researching in data bases, it is easy to find several electrophoretic methods to determine different groups of analytes and sometimes they are compared in terms of sensitivity, selectivity, precision and applicability with other separation techniques. Although these papers frequently prove the potential of this methodology in spiked samples, it is not common to find a discussion of the well-known complexity of the matrices to extract analytes from the sample and/or to study the interferences in the target analytes. Summarizing, the majority of CE scientific papers focus primarily on the effects upon the separation of the analytes while ignoring their behavior if these analytes are presented in real samples.
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García-Cañas V, Mondello M, Cifuentes A. Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes. J Sep Sci 2011; 34:1011-9. [PMID: 21404441 DOI: 10.1002/jssc.201000826] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/24/2011] [Accepted: 02/01/2011] [Indexed: 11/12/2022]
Abstract
New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive detection of transgenic maize at percentages lower than 1%.
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