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Shin G, Kim DK, Doh J, Lee D, Lee NK, Jung GY. High-resolution pluronic-filled microchip CE-SSCP analysis system via channel width control. Electrophoresis 2015; 37:676-9. [DOI: 10.1002/elps.201500427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Giyoung Shin
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
| | - Dong-Kyun Kim
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
| | - Junsang Doh
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
- Department of Mechanical Engineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering; University of Pennsylvania; Philadelphia PA USA
| | - Nam Ki Lee
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
- Department of Physics; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
- Department of Chemical Engineering; Pohang University of Science and Technology; Pohang Gyeongbuk Korea
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2
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Hwang HS, Shin GW, Jung GY, Jung GY. A simple and precise diagnostic method for spinal muscular atrophy using a quantitative SNP analysis system. Electrophoresis 2014; 35:3402-7. [PMID: 25113913 DOI: 10.1002/elps.201400207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/21/2014] [Accepted: 08/04/2014] [Indexed: 11/06/2022]
Abstract
A simple and precise diagnostic method for spinal muscular atrophy (SMA) using high-resolution CE-based single-strand conformation polymorphism (CE-SSCP) was developed in this study. SMA is a common genetic disorder caused by an abnormality in the relative copy numbers of SMN1 and its centromeric copy SMN2, which differ only in two nucleotides, namely at exons 7 and 8. Therefore, the precise discrimination of the differences in sequence as well as their relative quantities is crucial for the diagnosis of SMA. Multiplex ligation-dependent probe amplification and sequence-sensitive DNA separation using hydroxyethyl cellulose and hydroxypropyl cellulose blended polymer matrix are currently the available methods used in the diagnosis of SMA. However, these methods are limited by their extended hybridization step and low resolution. In this study, the simultaneous discrimination of SMN exons 7 and 8 was successfully demonstrated using high-resolution CE-SSCP. Unlike the previously reported alternative method, single base differing amplicons were baseline-separated because of its extraordinary resolution, thus providing accurate and precise quantification of each paralog.
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Affiliation(s)
- Hee Sung Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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Hwang HS, Shin GW, Park HJ, Ryu CY, Jung GY. Effect of temperature gradients on single-strand conformation polymorphism analysis in a capillary electrophoresis system using Pluronic polymer matrix. Anal Chim Acta 2013; 793:114-8. [DOI: 10.1016/j.aca.2013.07.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 11/30/2022]
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Hwang HS, Shin GW, Park HJ, Ryu CY, Jung GY. Micellar ordered structure effects on high-resolution CE-SSCP using Pluronic triblock copolymer blends. Electrophoresis 2013; 34:518-23. [DOI: 10.1002/elps.201200520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/24/2012] [Accepted: 10/11/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Hee Sung Hwang
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang; Gyeongbuk; Republic of Korea
| | - Gi Won Shin
- Institute of Environmental and Energy Technology; Pohang University of Science and Technology; Pohang; Gyeongbuk; Republic of Korea
| | - Han Jin Park
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; Troy; NY; USA
| | - Chang Yeol Ryu
- Department of Chemistry and Chemical Biology; Rensselaer Polytechnic Institute; Troy; NY; USA
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5
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Shin GW, Hwang HS, Seo SW, Oh MH, Ryu CY, Salvo CJ, Feldman S, Doh J, Jung GY. A novel pathogen detection system based on high-resolution CE-SSCP using a triblock copolymer matrix. J Sep Sci 2010; 33:1639-43. [PMID: 20405485 DOI: 10.1002/jssc.200900871] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although CE-SSCP analysis combined with 16S ribosomal RNA gene-specific PCR has enormous potential as a simple and versatile pathogen detection technique, low resolution of CE-SSCP causes the limited application. Among the experimental conditions affecting the resolution, the polymer matrix is considered to be most critical to improve the resolution of CE-SSCP analysis. However, due to the peak broadening caused by the interaction between hydrophobic moiety of polymer matrices and DNA, conventional polymer matrices are not ideal for CE-SSCP analysis. A poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) (PEO-PPO-PEO) triblock copolymer, with dynamic coating ability and a propensity to form micelles to minimize exposure of hydrophobic PPO block to DNA, can be an alternative matrix. In this study, we examined the resolution of CE-SSCP analysis using the PEO-PPO-PEO triblock copolymer as the polymer matrix and four same-sized DNA fragments of similar sequence content. Among 48 commercially available PEO-PPO-PEO triblock copolymers, three were selected due to their transparency in the operable range of viscosity and PEO(137)PPO(43)PEO(137) exhibited the most effective separation. Significant improvement in resolution allowed discrimination of the similar sequences, thus greatly facilitated CE-SSCP analysis compared to the conventional polymer matrix. The results indicate that PEO-PPO-PEO triblock copolymer may serve as an ideal matrix for high-resolution CE-SSCP analysis.
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Affiliation(s)
- Gi Won Shin
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
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6
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Kim SJ, Shin GW, Choi SJ, Hwang HS, Jung GY, Seo TS. Triblock copolymer matrix-based capillary electrophoretic microdevice for high-resolution multiplex pathogen detection. Electrophoresis 2010; 31:1108-15. [PMID: 20309929 DOI: 10.1002/elps.200900651] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Rapid and simple analysis for the multiple target pathogens is critical for patient management. CE-SSCP analysis on a microchip provides high speed, high sensitivity, and a portable genetic analysis platform in molecular diagnostic fields. The capability of separating ssDNA molecules in a capillary electrophoretic microchannel with high resolution is a critical issue to perform the precise interpretation in the electropherogram. In this study, we explored the potential of poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) (PEO-PPO-PEO) triblock copolymer as a sieving matrix for CE-SSCP analysis on a microdevice. To demonstrate the superior resolving power of PEO-PPO-PEO copolymers, 255-bp PCR amplicons obtained from 16S ribosomal RNA genes of four bacterial species, namely Proteus mirabilis, Haemophilus ducreyi, Pseudomonas aeruginosa, and Neisseria meningitidis, were analyzed in the PEO-PPO-PEO matrix in comparison with 5% linear polyacrylamide and commercial GeneScan gel. Due to enhanced dynamic coating and sieving ability, PEO-PPO-PEO copolymer displayed fourfold enhancement of resolving power in the CE-SSCP to separate same-sized DNA molecules. Fivefold input of genomic DNA of P. aeruginosa and/or N. meningitidis produced proportionally increased corresponding amplicon peaks, enabling correct quantitative analysis in the pathogen detection. Besides the high-resolution sieving capability, a facile loading and replenishment of gel in the microchannel due to thermally reversible gelation property makes PEO-PPO-PEO triblock copolymer an excellent matrix in the CE-SSCP analysis on the microdevice.
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Affiliation(s)
- Se Jin Kim
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, KAIST, Gwahangno, Yuseong-Gu, Daejeon, Republic of Korea
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Jia ZP, Wang R, Chen QY, Xie H, Ma J, Liu YY, Wang J. CE of Small DNA Fragments Using Linear Polyacrylamide Matrices. Chromatographia 2009. [DOI: 10.1365/s10337-009-1280-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Wang CC, Chang JG, Ferrance J, Chen HY, You CY, Chang YF, Jong YJ, Wu SM, Yeh CH. Quantification of SMN1 and SMN2 genes by capillary electrophoresis for diagnosis of spinal muscular atrophy. Electrophoresis 2008; 29:2904-11. [DOI: 10.1002/elps.200700799] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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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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Sniehotta M, Schiffer E, Zürbig P, Novak J, Mischak H. CE – a multifunctional application for clinical diagnosis. Electrophoresis 2007; 28:1407-17. [PMID: 17427258 DOI: 10.1002/elps.200600581] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
CE has been used widely as an analytical tool with high separation power taking advantage of size, charge-to-size ratio, or isoelectric point of various analytes. In combination with detection methods, such as UV absorption, electrochemical detection, fluorescence, or mass spectrometry (MS), it allows the separation and detection of inorganic and organic ions, as well as complex compounds, such as polypeptides, nucleic acids, including PCR amplicons from viruses or bacteria. Recent interest in identification of biomarkers of diseases using body fluids leads to development of CE-MS techniques. These applications allowed identification of new potential biomarkers for clinical diagnosis and monitoring of therapeutic interventions. In this report, we present a technical overview of various CE techniques and discuss their applications in clinical medicine.
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Affiliation(s)
- Maike Sniehotta
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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Lin YW, Chang HT. Analysis of double-stranded DNA by capillary electrophoresis using poly(ethylene oxide) in the presence of hexadecyltrimethylammonium bromide. J Chromatogr A 2006; 1130:206-11. [PMID: 16597443 DOI: 10.1016/j.chroma.2006.03.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 03/01/2006] [Accepted: 03/17/2006] [Indexed: 01/23/2023]
Abstract
The impact of hexadecyltrimethylammonium bromide (CTAB) on the separation of ds-DNA by capillary electrophoresis in conjunction with laser-induced fluorescence (CE-LIF) detection using poly(ethylene oxide) (PEO) solution is described. The use of CTAB for improved separation reproducibility and efficiency of DNA has not been demonstrated although it is widely used for controlling the magnitude and direction of electroosmotic flow in CE. With increasing CTAB concentration, the interactions of DNA with ethidium bromide (EtBr) and with the capillary wall decrease. For the separation of DNA fragments with the sizes ranging from several base pairs (bp) to 2,176 bp, a polymer solution consisting of 0.75% poly(ethylene oxide), 100 mM TB buffer (pH 8.0), 25 microg/mL EtBr, and 0.36 microg/mL CTAB is proper. Using the PEO solution, we separated a mixture of DNA markers V (pBR 322/HaeIII digest) and VI (pBR 328/BglI digest and pBR 328/HinfI digest) within 8 min at -375 V/cm, with the limit of detection of 2.0 ng/mL based on the peak height for the 18-bp DNA fragment. The method is highly efficient (>10(6)plate/m), repeatable (RSD of the migration times <1.5%), and sensitive. In addition, it is convenient to fill a capillary (75 microm in diameter) with such a low-viscosity PEO solution by syringe pushing.
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Affiliation(s)
- Yang-Wei Lin
- Department of Chemistry, National Taiwan University, Section 4, Roosevelt Road, Taipei, Taiwan, ROC
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Single-Strand Conformation Polymorphism Analysis by Microchip Electrophoresis for the Rapid Detection of Point Mutation in Human Obesity Gene. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.9.1346] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Sonehara T, Kawazoe H, Sakai T, Ozawa S, Anazawa T, Irie T. Ultra-slim laminated capillary array for high-speed DNA separation. Electrophoresis 2006; 27:2910-6. [PMID: 16688699 DOI: 10.1002/elps.200500734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We developed a new kind of capillary array for electrophoresis by using the numerical-control (NC) wiring technique conventionally used to produce printed-circuit boards. Laminating two polyimide sheets after laying cylindrical capillaries between them according to designed geometries, we fabricated a 16-lane laminated capillary array (LCA) 9.9 cm long, 7.2 cm wide, and 0.5 mm thick in which the effective length of all capillaries was only 10.9 cm. This compact LCA thus had separation columns as short as those in capillary array electrophoresis chips fabricated by lithography techniques. Like conventional capillary arrays, it also enabled pipetting-less direct injection of analytes from sample preparation plates. Using the LCA with LIF detection and a replaceable fluid sieving matrix, we demonstrated high-speed ssDNA fragment separations. At an electric field strength of 316 V/cm, 15 fragments ranging from 50 to 500 bases were completely separated within 5.8 min in all lanes. The lane-to-lane CV of migration time was only 0.38%, and the fragment size for which the resolution per base was 0.59 was 258 +/- 15 bases (average +/-SD).
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Kraly J, Fazal MA, Schoenherr RM, Bonn R, Harwood MM, Turner E, Jones M, Dovichi NJ. Bioanalytical Applications of Capillary Electrophoresis. Anal Chem 2006; 78:4097-110. [PMID: 16771542 DOI: 10.1021/ac060704c] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James Kraly
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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Liu BF, Xu B, Zhang G, Du W, Luo Q. Micro-separation toward systems biology. J Chromatogr A 2005; 1106:19-28. [PMID: 16236294 DOI: 10.1016/j.chroma.2005.09.066] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 09/14/2005] [Accepted: 09/21/2005] [Indexed: 10/25/2022]
Abstract
Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.
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Affiliation(s)
- Bi-Feng Liu
- The Key Laboratory of Biomedical Photonics of MOE - Hubei Bioinformatics, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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