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Ward CL, Cornejo MA, Peli Thanthri SH, Linz TH. A review of electrophoretic separations in temperature-responsive Pluronic thermal gels. Anal Chim Acta 2023; 1276:341613. [PMID: 37573098 DOI: 10.1016/j.aca.2023.341613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 08/14/2023]
Abstract
Gel electrophoresis is a ubiquitous bioanalytical technique used in research laboratories to validate protein and nucleic acid samples. Polyacrylamide and agarose have been the gold standard gel materials for decades, but an alternative class of polymer has emerged with potentially superior performance. Pluronic thermal gels are water-soluble polymers that possess the unique ability to undergo a change in viscosity in response to changing temperature. Thermal gels can reversibly convert between low-viscosity liquids and high-viscosity solid gels using temperature as an adjustable parameter. The properties of thermal gels provide unmatched flexibility as a dynamic separations matrix to measure analytes ranging from small molecules to cells. This review article describes the physical and chemical properties of Pluronic thermal gels to provide a fundamental overview of polymer behavior. The performance of thermal gels is then reviewed to highlight their applications as a gel matrix for electrokinetic separations in capillary, microfluidic, and slab gel formats. The use of dynamic temperature-responsive gels in bioanalytical separations is an underexplored area of research but one that holds exciting potential to achieve performance unattainable with conventional static polymers.
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Affiliation(s)
- Cassandra L Ward
- Department of Chemistry, Wayne State University, Detroit, MI, USA; Lumigen Instrument Center, Wayne State University, Detroit, MI, USA.
| | - Mario A Cornejo
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Thomas H Linz
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
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2
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Nguyen VD, Nguyen HQ, Bui KH, Ko YS, Park BJ, Seo TS. A handheld-type total integrated capillary electrophoresis system for SARS-CoV-2 diagnostics: Power, fluorescence detection, and data analysis by smartphone. Biosens Bioelectron 2022; 195:113632. [PMID: 34571485 DOI: 10.1016/j.bios.2021.113632] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/23/2022]
Abstract
A micro-capillary electrophoresis (μCE) system is one of the widely adopted techniques in the molecular diagnostics and DNA sequencing due to the benefits of high resolution, rapid analysis, and low reagent consumption, but due to the requirements of bulky high-power suppliers and an expensive laser-induced fluorescence detector module, the conventional set-up of μCE system is not adequate for point-of-care (POC) molecular diagnostics. In this study, we constructed a miniaturized and integrated μCE system which can be manipulated by a smartphone. The smartphone not only powers two boost converters and an excited laser, but also controls the relay for the power switch. Moreover, the complementary metal-oxide-semiconductor (CMOS) camera of the smartphone was used for detecting the fluorescence signal of amplicons amplified with reverse transcription-polymerase chain reaction (RT-PCR). We also developed a web-based application so that the raw data of the recorded fluorescence intensity versus the running time can display typical capillary electropherograms on the smartphone. The total size of the hand-held μCE system was 9.6 cm [Width] × 22 cm [Length] × 15.5 cm [Height], and the weight was ∼1 kg, which is suitable for POC DNA testing. In the integrated smartphone-associated μCE system, we could accurately analyze two genes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), namely N gene and S gene along with two bracket ladders in 6 min to identify SARS-CoV-2. Such an advanced μCE platform can be applied for a variety of on-site molecular diagnostics fields with user-friendliness.
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Affiliation(s)
- Van Dan Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Huynh Quoc Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Khang Hoang Bui
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Young Soo Ko
- Department of Chemical Engineering and Department of Future Convergence Engineering, Kongju National University, Cheonan City, Chungcheongnam-do, Republic of Korea
| | - Bum Jun Park
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Tae Seok Seo
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea.
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3
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Lian DS, Zhao SJ. Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease. Clin Chem Lab Med 2017; 54:707-38. [PMID: 26352354 DOI: 10.1515/cclm-2015-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.
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4
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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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5
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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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6
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Chung M, Kim D, Herr AE. Polymer sieving matrices in microanalytical electrophoresis. Analyst 2014; 139:5635-54. [DOI: 10.1039/c4an01179a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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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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8
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Zhang RQ, Liu SL, Zhao W, Zhang WP, Yu X, Li Y, Li AJ, Pang DW, Zhang ZL. A Simple Point-of-Care Microfluidic Immunomagnetic Fluorescence Assay for Pathogens. Anal Chem 2013; 85:2645-51. [DOI: 10.1021/ac302903p] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Rui-Qiao Zhang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
| | - Shu-Lin Liu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Wei Zhao
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Wan-Po Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People’s
Republic of China
| | - Xu Yu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Yong Li
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - An-Jun Li
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Dai-Wen Pang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
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9
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Hwang HS, Shin GW, Chung B, Na J, Jung GY. Multiplex and quantitative pathogen detection with high-resolution capillary electrophoresis-based single-strand conformation polymorphism. Methods Mol Biol 2013; 919:155-163. [PMID: 22976099 DOI: 10.1007/978-1-62703-029-8_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Among the molecular diagnostic methods for bacteria-induced diseases, capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) combined with 16S rRNA gene-specific PCR has enormous potential because it can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S rRNA gene-specific markers into separate peaks. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this report, a protocol for the detection of 12 pathogenic bacteria is provided. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing the easy identification of the pathogens.
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Affiliation(s)
- Hee Sung Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea
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10
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Shin GW, Kim YT, Heo HY, Chung B, Seo TS, Jung GY. Triblock copolymer-based microchip device for rapid analysis of stuffer-free multiplex ligation-dependent probe amplification products. Electrophoresis 2012; 33:3574-8. [PMID: 23135832 DOI: 10.1002/elps.201200436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/01/2012] [Accepted: 09/08/2012] [Indexed: 11/06/2022]
Abstract
Recent improvements in the multiplex ligation-dependent probe amplification (MLPA) method promise successful multiplex analysis of various genetic markers. In particular, it has been demonstrated that elimination of the stuffer sequence included in MLPA probes for length-dependent analysis substantially simplifies the probe design process and improves the accuracy of the analysis. As is the case for other CE-based methods, MLPA could be further developed on a microchip platform. However, high-resolution analysis of short MLPA probes requires careful microchip operation. In this study, we developed a microchip device for the multiplex analysis of five food-borne pathogens using a stuffer-free probe set. Microchip channel design and electrophoresis operating conditions were first optimized for reproducible analysis, after which two sieving matrices were tested. Finally, the method was validated using DNA samples isolated from intentionally infected milk.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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11
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Mnif S, Bru-Adan V, Godon JJ, Sayadi S, Chamkha M. Characterization of the microbial diversity in production waters of mesothermic and geothermic Tunisian oilfields. J Basic Microbiol 2012; 53:45-61. [DOI: 10.1002/jobm.201100528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 12/03/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Sami Mnif
- Laboratory of Environmental Bioprocesses, Regional Pole of Excellence AUF (PER-LBPE) - Centre of Biotechnology of Sfax; University of Sfax; Sfax; Tunisia
| | - Valérie Bru-Adan
- INRA, UR50; Laboratory of Environmental Biotechnology; Avenue des Etangs, Narbonne; France
| | - Jean-Jacques Godon
- INRA, UR50; Laboratory of Environmental Biotechnology; Avenue des Etangs, Narbonne; France
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, Regional Pole of Excellence AUF (PER-LBPE) - Centre of Biotechnology of Sfax; University of Sfax; Sfax; Tunisia
| | - Mohamed Chamkha
- Laboratory of Environmental Bioprocesses, Regional Pole of Excellence AUF (PER-LBPE) - Centre of Biotechnology of Sfax; University of Sfax; Sfax; Tunisia
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12
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Jung JH, Choi SJ, Park BH, Choi YK, Seo TS. Ultrafast rotary PCR system for multiple influenza viral RNA detection. LAB ON A CHIP 2012; 12:1598-1600. [PMID: 22437437 DOI: 10.1039/c2lc21269b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We presented a novel platform for an ultrafast PCR system, called the Rotary PCR Genetic Analyzer, which incorporates a thermal block and resistive temperature detector (RTD) for thermal cycling control, a disposable PCR microchip, and a stepper motor. The influenza viral RNAs from H3N2, H5N1, and H1N1 were simultaneously identified with high sensitivity and speed.
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Affiliation(s)
- Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon, South Korea
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13
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Integrated microdevice of reverse transcription-polymerase chain reaction with colorimetric immunochromatographic detection for rapid gene expression analysis of influenza A H1N1 virus. Biosens Bioelectron 2012; 33:88-94. [PMID: 22265877 PMCID: PMC7126693 DOI: 10.1016/j.bios.2011.12.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 11/29/2011] [Accepted: 12/14/2011] [Indexed: 11/26/2022]
Abstract
An integrated microdevice of a reverse transcription-polymerase chain reaction (RT-PCR) reactor and an immunochromatographic strip was constructed for colorimetric detection of gene expression of influenza A virus subtype H1N1. An RT-PCR cocktail, which included Texas Red-labeled primers, dNTP including biotin-labeled dUTP, and RNA templates of influenza A H1N1 virus, was filled in the PCR chamber through the micropump, and the RT-PCR was performed to amplify the target H1 gene (102 bp). The resultant amplicons bearing biotin moieties and Texas Red haptens were subsequently eluted to the immunochromatographic strip, in which they were first conjugated with the gold nanoparticle labeled anti-hapten antibody in the conjugation pad, and then captured on the streptavidin coated test line through the biotin–streptavidin interaction. By observing a violet color in the test line which was derived from the gold nanoparticle, we confirmed the H1N1 target virus. The entire process on the integrated microdevice consisting of a micropump, a 2 μL PCR chamber, and an immunochromatographic strip was carried out on the portable genetic analyzer within 2.5 h, enabling on-site colorimetric pathogen identification with detection sensitivity of 14.1 pg RNA templates.
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14
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Jung JH, Kim GY, Seo TS. An integrated passive micromixer-magnetic separation-capillary electrophoresis microdevice for rapid and multiplex pathogen detection at the single-cell level. LAB ON A CHIP 2011; 11:3465-70. [PMID: 21870015 DOI: 10.1039/c1lc20350a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Here we report an integrated microdevice consisting of an efficient passive mixer, a magnetic separation chamber, and a capillary electrophoretic microchannel in which DNA barcode assay, target pathogen separation, and barcode DNA capillary electrophoretic analysis were performed sequentially within 30 min for multiplex pathogen detection at the single-cell level. The intestine-shaped serpentine 3D micromixer provides a high mixing rate to generate magnetic particle-pathogenic bacteria-DNA barcode labelled AuNP complexes quantitatively. After magnetic separation and purification of those complexes, the barcode DNA strands were released and analyzed by the microfluidic capillary electrophoresis within 5 min. The size of the barcode DNA strand was controlled depending on the target bacteria (Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella typhimurium), and the different elution time of the barcode DNA peak in the electropherogram allows us to recognize the target pathogen with ease in the monoplex as well as in the multiplex analysis. In addition, the quantity of the DNA barcode strand (∼10(4)) per AuNP is enough to be observed in the laser-induced confocal fluorescence detector, thereby making single-cell analysis possible. This novel integrated microdevice enables us to perform rapid, sensitive, and multiplex pathogen detection with sample-in-answer-out capability to be applied for biosafety testing, environmental screening, and clinical trials.
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Affiliation(s)
- Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering (BK21 program), Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon, South Korea
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15
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Chen Y, Seo TS. PCR-free digital minisatellite tandem repeat genotyping. Electrophoresis 2011; 32:1456-64. [PMID: 21626523 DOI: 10.1002/elps.201100073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/03/2011] [Accepted: 03/03/2011] [Indexed: 11/11/2022]
Abstract
We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.
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Affiliation(s)
- Yuchao Chen
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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16
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Chen Y, Choi JY, Choi SJ, Seo TS. Sample stacking capillary electrophoretic microdevice for highly sensitive mini Y short tandem repeat genotyping. Electrophoresis 2010; 31:2974-80. [PMID: 20715129 DOI: 10.1002/elps.201000270] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Lab-on-a-chip provides an ideal platform for short tandem repeat (STR) genotyping due to its intrinsic low sample consumption, rapid analysis, and high-throughput capability. One of the challenges, however, in the forensic human identification on the microdevice is the detection sensitivity derived from the nanoliter volume sample handling. To overcome such a sensitivity issue, here we developed a sample stacking CE microdevice for mini Y STR genotyping. The mini Y STR includes redesigned primer sequences to generate smaller-sized PCR amplicons to enhance the PCR efficiency and the success rate for a low copy number and degraded DNA. The mini Y STR amplicons occupied in the 5- and 10-mm stacking microchannels are preconcentrated efficiently in a defined narrow region through the optimized sample stacking CE scheme, resulting in more than tenfold improved fluorescence peak intensities compared with that of a conventional cross-injection microcapillary electrophoresis method. Such signal enhancement allows us to successfully analyze the Y STR typing with only 25 pg of male genomic DNA, with high background of female genomic DNA, and with highly degraded male genomic DNA. The combination of the mini Y STR system with the novel sample stacking CE microdevice provides the highly sensitive Y STR typing on a chip, making it promising to perform high-performance on-site forensic human identification.
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Affiliation(s)
- Yuchao Chen
- Department of Chemical and Biomolecular Engineering (BK21 program) KAIST, 335 Gwahangno, Yuseong-Gu, Daejeon, Republic of Korea
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17
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Shin GW, Hwang HS, Oh MH, Doh J, Jung GY. Simultaneous quantitative detection of 12 pathogens using high-resolution CE-SSCP. Electrophoresis 2010; 31:2405-10. [PMID: 20568262 DOI: 10.1002/elps.201000091] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Several methods based on screening for a 16S ribosomal RNA gene marker have been developed for rapid and sensitive detection of pathogenic microorganisms. One such method, CE-based SSCP (CE-SSCP), has enormous potential because the technique can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S ribosomal RNA gene-specific markers unless combined with additional modification steps. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this study, we developed a method based on a high-resolution CE-SSCP system using a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer that is capable of simultaneous and quantitative detection of 12 clinically important pathogens. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing easy identification of pathogens. A series of experiments using different amounts of genomic pathogen DNA showed that the method had a limit of detection of 0.31-1.56 pg and a dynamic range of approximately 10(2). These results indicate that high-resolution CE-SSCP systems have considerable potential in the clinical diagnosis of bacteria-induced diseases.
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Affiliation(s)
- Gi Won Shin
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
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