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Multiplex quantitative analysis of microRNA expression via exponential isothermal amplification and conformation-sensitive DNA separation. Sci Rep 2017; 7:11396. [PMID: 28900270 PMCID: PMC5595994 DOI: 10.1038/s41598-017-11895-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/01/2017] [Indexed: 12/02/2022] Open
Abstract
Expression profiling of multiple microRNAs (miRNAs) generally provides valuable information for understanding various biological processes. Thus, it is necessary to develop a sensitive and accurate miRNA assay suitable for multiplexing. Isothermal exponential amplification reaction (EXPAR) has received significant interest as an miRNA analysis method because of high amplification efficiency. However, EXPAR cannot be used for a broader range of applications owing to limitations such as complexity of probe design and lack of proper detection method for multiplex analysis. Here, we developed a sensitive and accurate multiplex miRNA profiling method using modified isothermal EXPAR combined with high-resolution capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP). To increase target miRNA specificity, a stem-loop probe was introduced instead of a linear probe in isothermal EXPAR to allow specific amplification of multiple miRNAs with minimal background signals. CE-SSCP, a conformation-dependent separation method, was used for detection. Since CE-SSCP eliminates the need for probes to have different lengths, easier designing of probes with uniform amplification efficiency was possible. Eight small RNAs comprising six miRNAs involved in Caenorhabditis elegans development and two controls were analyzed. The expression patterns obtained using our method were concordant with those reported in previous studies, thereby supporting the proposed method’s robustness and utility.
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2
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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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3
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Hwang HS, Shin GW, Cohen A, Ryu CY, Jung GY. Sieving properties of end group-halogenated Pluronic polymer matrix in DNA separation under nondenaturing CE analysis. Electrophoresis 2014; 35:2946-50. [PMID: 25044023 DOI: 10.1002/elps.201400158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/03/2014] [Accepted: 07/04/2014] [Indexed: 11/10/2022]
Abstract
CE-SSCP analysis is a well-established DNA separation method that is based on variations in mobility caused by sequence-induced differences in the conformation of single-stranded DNA. The resolution of CE-SSCP analysis was improved by using a Pluronic polymer matrix, and it has been successfully applied in various genetic analyses. Because the Pluronic polymer forms a micellar cubic structure in the capillary, it provides a stable internal structure for high-resolution CE-SSCP analysis. We hypothesized that formation of micellar cubic structure is influenced by the end hydroxyl group of the Pluronic polymer, which affords structural stability through hydrogen bonding. To test this hypothesis, the hydroxyl group was halogenated to eliminate the hydrogen bonding without disturbing the polarity of polymer matrix. CE-SSCP resolution of two DNA fragments with a single base difference was significantly worse in the halogenated polymer matrices due to band broadening. The viscoelastic properties of control (which has hydroxyl group), chlorinated, and brominated F108 solution upon heating were also investigated by rheological experiments, and we found that gelation was significantly associated with resolution. In this series of experiments, the effect of the hydroxyl group in Pluronic polymer matrix on separation resolution of CE-SSCP analysis was demonstrated.
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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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4
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Chung B, Shin GW, Park CK, Choi W, Chung YJ, Yoon HK, Jung GY. Rapid and sensitive detection of lower respiratory tract infections by stuffer-free multiplex ligation-dependent probe amplification. Electrophoresis 2013; 35:511-4. [PMID: 24311198 DOI: 10.1002/elps.201300374] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/11/2013] [Accepted: 10/25/2013] [Indexed: 11/09/2022]
Abstract
Lower respiratory tract infection is one of the most common infectious diseases. However, conventional methods for detecting infectious pathogens are time-consuming, and generally have a limited impact on early therapeutic decisions. We previously reported a rapid and sensitive method for detecting such pathogens using stuffer-free multiplex ligation-dependent probe amplification coupled with high-resolution CE-SSCP. In this study, we report an application of this method to the detection of respiratory pathogens. As originally configured, this method was capable of simultaneously detecting seven bacterial species responsible for lower respiratory tract infections, but its detection limit and assay time were insufficient to provide useful information for early therapeutic decisions. To improve sensitivity and shorten assay time, we added a target-specific preamplification step, improving the detection limit from 50 pg of genomic DNA to 500 fg. We further decreased time requirements by optimizing the hybridization step, enabling the entire assay to be completed within 7 h while maintaining the same detection limit. Taken together, these improvements enable the rapid detection of infectious doses of pathogens (i.e. a few dozen cells), establishing the strong potential of the refined method, particularly for aiding early treatment decisions.
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Affiliation(s)
- Boram Chung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea
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5
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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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6
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Na J, Shin GW, Jung GY, Jung GY. A robust and simple-to-design multiplex DNA methylation assay based on MS-MLPA-CE-SSCP. Analyst 2013; 138:6969-76. [DOI: 10.1039/c3an01178j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Chung B, Shin GW, Choi W, Hwang HS, Oh MH, Jung GY. An accurate multiplex antibiotic susceptibility test using a high-resolution CE-SSCP-based stuffer-free multiplex ligation-dependent probe amplification system. Electrophoresis 2012; 34:284-8. [DOI: 10.1002/elps.201200372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/04/2012] [Accepted: 09/08/2012] [Indexed: 02/05/2023]
Affiliation(s)
- Boram Chung
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang; Gyeongbuk; Korea
| | - Gi Won Shin
- Institute of Environmental and Energy Technology; Pohang University of Science and Technology; Pohang; Gyeongbuk; Korea
| | - Woong Choi
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang; Gyeongbuk; Korea
| | - Hee Sung Hwang
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang; Gyeongbuk; Korea
| | - Mi-Hwa Oh
- National Institute of Animal Science; Rural Development Administration; Suwon; Gyeonggi; Korea
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Nai YH, Zemb O, Gutierrez-Zamora ML, Manefield M, Powell SM, Breadmore MC. Capillary electrophoresis ribosomal RNA single-stranded conformation polymorphism: a new approach for characterization of low-diversity microbial communities. Anal Bioanal Chem 2012; 404:1897-906. [PMID: 22865007 DOI: 10.1007/s00216-012-6268-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 11/28/2022]
Abstract
Capillary electrophoresis (CE) has been the principle system for nucleic acid analysis since the early 1990s due to its inherent advantages such as fast analysis time, high resolution and efficiency, minimal sample requirement, high detection sensitivity, and automation. In the past few decades, microbial community fingerprinting methods such as terminal restriction fragment length polymorphism and single-stranded conformation polymorphism (SSCP) have migrated to CE to utilize its advantages over conventional slab gel electrophoresis. Recently, a gel-based direct rRNA fingerprint method was demonstrated. Different from other existing microbial community characterization approaches, this novel approach is polymerase chain reaction free and capable of providing information on the relative abundance of rRNA from individual phylotypes in low-diversity samples. As a gel-based method, it has a long analysis time and relatively large reagent and sample requirements. Here, we addressed these limitations by transferring the RNA fingerprint approach to the CE platform. Analysis time significantly improved from 24 h to 60 min, and the use of a fluorescently labeled hybridization probe as the detection strategy decreased the sample requirement by ten-fold. The combination of fast analysis time, low sample requirement, and sensitive fluorescence detection makes CE-RNA-SSCP an appealing new approach for characterizing low-diversity microbial communities.
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Affiliation(s)
- Yi H Nai
- Australian Centre for Research on Separation Science (ACROSS), School of Chemistry, University of Tasmania, Hobart, TAS, Australia
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Zhang W, Yie S, Yue B, Zhou J, An R, Yang J, Chen W, Wang C, Zhang L, Shen F, Yang G, Hou R, Zhang Z. Determination of Baylisascaris schroederi infection in wild giant pandas by an accurate and sensitive PCR/CE-SSCP method. PLoS One 2012; 7:e41995. [PMID: 22911871 PMCID: PMC3416865 DOI: 10.1371/journal.pone.0041995] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/28/2012] [Indexed: 11/28/2022] Open
Abstract
It has been recognized that other than habitat loss, degradation and fragmentation, the infection of the roundworm Baylisascaris schroederi (B. schroederi) is one of the major causes of death in wild giant pandas. However, the prevalence and intensity of the parasite infection has been inconsistently reported through a method that uses sedimentation-floatation followed by a microscope examination. This method fails to accurately determine infection because there are many bamboo residues and/or few B. schroederi eggs in the examined fecal samples. In the present study, we adopted a method that uses PCR and capillary electrophoresis combined with a single-strand conformation polymorphism analysis (PCR/CE-SSCP) to detect B. schroederi infection in wild giant pandas at a nature reserve, and compared it to the traditional microscope approach. The PCR specifically amplified a single band of 279-bp from both fecal samples and positive controls, which was confirmed by sequence analysis to correspond to the mitochondrial COII gene of B. schroederi. Moreover, it was demonstrated that the amount of genomic DNA was linearly correlated with the peak area of the CE-SSCP analysis. Thus, our adopted method can reliably detect the infectious prevalence and intensity of B. schroederi in wild giant pandas. The prevalence of B. schroederi was found to be 54% in the 91 fecal samples examined, and 48% in the fecal samples of 31 identified individual giant pandas. Infectious intensities of the 91 fecal samples were detected to range from 2.8 to 959.2 units/gram, and from 4.8 to 959.2 units/gram in the fecal samples of the 31 identified giant pandas. For comparison, by using the traditional microscope method, the prevalence of B. schroederi was found to be only 33% in the 91 fecal samples, 32% in the fecal samples of the 31 identified giant pandas, and no reliable infectious intensity was observed.
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Affiliation(s)
- Wenping Zhang
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Shangmian Yie
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Bisong Yue
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, Chengdu, People’s Republic of China
- * E-mail: (ZHZ); (BSY)
| | - Jielong Zhou
- College of Life Sciences, Southwest Forestry University, Kunming, People’s Republic of China
| | - Renxiong An
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Jiangdong Yang
- College of Animal Science, Sichuan Agricultural University, Ya’an, People’s Republic of China
| | - Wangli Chen
- Tangjiahe National Nature Reserve, Guangyuan, People’s Republic of China
| | - Chengdong Wang
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Liang Zhang
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Fujun Shen
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Guangyou Yang
- College of Animal Science, Sichuan Agricultural University, Ya’an, People’s Republic of China
| | - Rong Hou
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
| | - Zhihe Zhang
- The Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, People’s Republic of China
- * E-mail: (ZHZ); (BSY)
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10
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Oh MH, Hwang HS, Chung BR, Paik HD, Han SH, Kang SM, Ham JS, Kim HW, Seol KH, Jang AR, Jung GY. Simultaneous Detection of 10 Foodborne Pathogens using Capillary Electrophoresis-Based Single Strand Conformation Polymorphism. Korean J Food Sci Anim Resour 2012. [DOI: 10.5851/kosfa.2012.32.2.241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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11
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Gulija TK, Ivancic-Jelecki J, Šantak M, Forcic D. Comparative analysis of CE-SSCP to standard RFLP-CE-FLA method in quantification of known viral variants within an RNA virus quasispecies. Electrophoresis 2011; 32:1852-9. [DOI: 10.1002/elps.201100010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Parallel analysis of 7 food-borne pathogens using capillary electrophoresis-based single-strand conformation polymorphism. Food Sci Biotechnol 2010. [DOI: 10.1007/s10068-010-0206-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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13
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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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14
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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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15
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Shin GW, Hwang HS, Chung B, Jung GY. Recent developments in CE-based detection methods for food-borne pathogens. Electrophoresis 2010; 31:2137-53. [DOI: 10.1002/elps.200900682] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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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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Shin GW, Hwang HS, Nam HG, Oh MH, Jung GY. Sensitive multiplex RNA quantification using capillary electrophoresis-based single-strand conformation polymorphism. Biotechnol Bioeng 2010; 106:167-72. [PMID: 20014441 DOI: 10.1002/bit.22646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantification of RNA provides information crucial for various biological studies, including analysis of mRNA expression and that of microRNAs. Reverse transcription (RT) coupled with real-time polymerase chain reaction (PCR) is known to be the most accurate method for quantifying nucleic acids, and thus represents the state-of-the-art for RNA quantification. However, the use of real-time PCR for RNA quantification is limited to a single target per analytical run because of reductions in quantification power and limitations of fluorescence dyes associated with multiplex applications. Here, we report a novel multiplex RNA quantification method that uses capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) coupled with modified RT and asymmetric PCR. The reverse transcripts of seven in vitro transcribed RNAs were modified with common sequence tags and amplified by asymmetric PCR using primers specific to the common tags. The resulting amplicons were separated and quantified by CE-SSCP. A series of experiments using different amounts of RNA demonstrated that the assay had a limit of detection of 2 amol and a dynamic range of approximately 10(5). These results clearly indicate the potential of this method to provide robust and precise multiplex RNA quantification.
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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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18
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Microchip-based capillary electrophoretic analysis of telomerase activity for cancer diagnostics. BIOCHIP JOURNAL 2010. [DOI: 10.1007/s13206-010-4107-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Shin GW, Cho YS, Hwang HS, Oh MH, Nam HG, Park JH, Jung GY. A new single-step quantitative pathogen detection system: template-tagging followed by multiplex asymmetric PCR using common primers and CE-SSCP. Electrophoresis 2009; 30:2728-36. [PMID: 19621380 DOI: 10.1002/elps.200900074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid diagnosis of bacterial infection is important for patient management and appropriate therapy during the early phase of bacteria-induced disease. Among the existing techniques for identifying microbial, CE-SSCP combined with 16S ribosomal RNA gene-specific PCR has the benefits of excellent sensitivity, resolution, and reproducibility. However, even though CE-SSCP can separate PCR products with high-resolution, multiplex detection and quantification are complicated by primer-dimer formation and non-specific amplification. Here, we describe a novel technique for multiplex detection and quantification of pathogens by template-tagging followed by multiplex asymmetric PCR and subsequent CE-SSCP. More specifically, we reverse transcribed 16S ribosomal RNAs from seven septicemia-inducing pathogens, tagged the templates with common end sequences, and amplified them using common primers. The resulting amplicons could be successfully separated by CE-SSCP and quantified by comparison to an internal standard. This method yielded results that illustrate the potential of this system for diagnosing infectious disease.
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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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