1
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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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Jordan D, Mills D. Resolving human DNA mixtures with F-108 polymer and capillary electrophoresis single-strand conformational polymorphism analysis. J Sep Sci 2020; 43:3327-3332. [PMID: 32506742 DOI: 10.1002/jssc.202000194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/17/2020] [Accepted: 06/03/2020] [Indexed: 11/10/2022]
Abstract
Current technologies have increased the sensitivity for analyzing forensic DNA samples, especially those considered "touch samples." Because of this, there has been an increase in the number of forensic mixtures-two or more contributors within a single sample-submitted to the crime laboratories. Therefore, the need to resolve these mixtures has increased as well. Several technologies are currently utilized, but many of them are time consuming and do not resolve the entire profile. Therefore, CE-Single-Strand Conformational Polymorphisms coupled with the Pluronic F-108 polymer was assessed for its ability to resolve human forensic mixtures. This technique has been able to detect sequence variation, such as single nucleotide polymorphism in short tandem repeat loci, such as D7S820 and vWA. Samples were first analyzed with the Performance Optimized Polymer-7, and mixtures created from samples that shared alleles. These samples were sequenced to detect single base-pair mutations and evaluated with the F-108 and CE-Single Strand Conformational Polymorphism analysis. Results from this study indicated the method would serve as a valuable screening tool to detect base sequence variation between individuals when they share alleles in a mixture and before using Massive Parallel Sequencing technology to distinguish which bases differ.
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Affiliation(s)
- Deidra Jordan
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,International Forensic Research Institute, Florida International University, Miami, FL, USA
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3
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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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4
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Accurate and effective multidrug-resistant Mycobacterium tuberculosis detection method using gap-filling ligation coupled with high-resolution capillary electrophoresis-based single strand conformation polymorphism. Sci Rep 2017; 7:46090. [PMID: 28422112 PMCID: PMC5395819 DOI: 10.1038/srep46090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/09/2017] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) has severely threatened public health via emerging multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains. For effective TB treatment, rapid, accurate, and multiplex detection of drug resistance is extremely important. However, conventional methods for TB diagnosis are time consuming and have a limited effect on treatment. Nucleic acid-based molecular detection methods have been developed as an effective MDR/XDR-TB diagnosis technology. Among the nucleic acid-based methods, ligation-dependent methods are attractive as MDR/XDR-MTB detection technologies, but multiplex analysis is limited by the detection method. Although an electrophoresis-based method is considered for multiple target detection because it is free from the errors pertaining to hybridization-based systems, the procedure of multiplex analysis is quite complicated owing to the DNA size-based separation system. In this study, we report an accurate, rapid, and simple multiple MDR/XDR-MTB detection technology using gap-filling ligation reaction coupled with high-resolution capillary electrophoresis-based single-strand conformation polymorphism. Using this system, rapid and accurate MDR/XDR-MTB detection is feasible via similar length probes without the complicated step of probe design. We found that this method could accurately and effectively detect highly polymorphic regions in specific codons associated with drug resistance.
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5
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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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6
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Martin L, Damaso N, Mills D. Detection of single nucleotide polymorphisms (SNP) in equine coat color genes using SNaPshot
TM
multiplex kit or pluronic F‐108 tri‐block copolymer and capillary electrophoresis. Electrophoresis 2016; 37:2862-2866. [DOI: 10.1002/elps.201600245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Lauren Martin
- Department of Chemistry and Biochemistry Florida International University Miami FL USA
- International Forensic Research Institute Florida International University Miami FL USA
- Department of Biological Sciences Florida International University Miami FL USA
| | - Natalie Damaso
- Department of Chemistry and Biochemistry Florida International University Miami FL USA
- International Forensic Research Institute Florida International University Miami FL USA
- Department of Biological Sciences Florida International University Miami FL USA
| | - DeEtta Mills
- International Forensic Research Institute Florida International University Miami FL USA
- Department of Biological Sciences Florida International University Miami FL USA
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7
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Liu C, Yamaguchi Y, Sekine S, Ni Y, Li Z, Zhu X, Dou X. Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis. J Sep Sci 2015; 39:986-92. [PMID: 26648455 DOI: 10.1002/jssc.201501087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/09/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment.
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Affiliation(s)
- Chenchen Liu
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, China.,Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China
| | - Yoshinori Yamaguchi
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China.,Department of Applied Physics, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Shinichi Sekine
- Division of Special Care Dentistry, Osaka University Dental Hospital, Osaka University, Osaka, Japan.,Department of Preventive Dentistry, Osaka University Graduate School of Dentistry Osaka University, Osaka, Japan
| | - Yi Ni
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China
| | - Zhenqing Li
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, China
| | - Xifang Zhu
- School of Optoelectronic Engineering, ChangZhou Institute of Technology, Changzhou, Jiangsu, China
| | - Xiaoming Dou
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, China.,School of Optoelectronic Engineering, ChangZhou Institute of Technology, Changzhou, Jiangsu, China
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8
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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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9
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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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10
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Damaso N, Martin L, Kushwaha P, Mills D. F-108 polymer and capillary electrophoresis easily resolves complex environmental DNA mixtures and SNPs. Electrophoresis 2014; 35:3208-11. [PMID: 25168595 DOI: 10.1002/elps.201400069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/08/2022]
Abstract
Ecological studies of microbial communities often use profiling methods but the true community diversity can be underestimated in methods that separate amplicons based on sequence length using performance optimized polymer 4. Taxonomically, unrelated organisms can produce the same length amplicon even though the amplicons have different sequences. F-108 polymer has previously been shown to resolve same length amplicons by sequence polymorphisms. In this study, we showed F-108 polymer, using the ABI Prism 310 Genetic Analyzer and CE, resolved four bacteria that produced the same length amplicon for the 16S rRNA domain V3 but have variable nucleotide content. Second, a microbial mat community profile was resolved and supported by NextGen sequencing where the number of peaks in the F-108 profile was in concordance with the confirmed species numbers in the mat. Third, equine DNA was analyzed for SNPs. The F-108 polymer was able to distinguish heterozygous and homozygous individuals for the melanocortin 1 receptor coat color gene. The method proved to be rapid, inexpensive, reproducible, and uses common CE instruments. The potential for F-108 to resolve DNA mixtures or SNPs can be applied to various sample types-from SNPs to forensic mixtures to ecological communities.
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Affiliation(s)
- Natalie Damaso
- Department of Biological Sciences, Florida International University, Miami, FL, USA; International Forensic Research Institute, Florida International University, Miami, FL, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
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11
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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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12
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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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13
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Choi W, Shin GW, Hwang HS, Pack SP, Jung GY, Jung GY. A multiplex single nucleotide polymorphism genotyping method using ligase-based mismatch discrimination and CE-SSCP. Electrophoresis 2014; 35:1196-203. [PMID: 24452927 DOI: 10.1002/elps.201300486] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/14/2013] [Accepted: 12/31/2013] [Indexed: 11/07/2022]
Abstract
Accuracy, simplicity, and cost-effectiveness are the most important criteria for a genotyping method for SNPs compatible with clinical use. One method developed for SNP genotyping, ligase-based discrimination, is considered the simplest for clinical diagnosis. However, multiplex assays using this method are limited by the detection method. Although CE has been introduced as an alternative to error prone microarray-based detection, the design process and multiplex assay procedure are complicated because of the DNA size-dependent separation principle. In this study, we developed a simple and accurate multiplex genotyping method using reaction condition-optimized ligation and high-resolution CE-based SSCP. With this high-resolution CE-SSCP system, we are able to use similar-sized probes, thereby eliminating the complex probe design step and simplifying the optimization process. We found that this method could accurately discriminate single-base mismatches in SNPs of the tp53 gene, used as targets for multiplex detection.
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Affiliation(s)
- Woong Choi
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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14
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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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15
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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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16
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Shin GW, Na J, Seo M, Chung B, Nam HG, Lee SJ, Jung GY. Precise Expression Profiling by Stuffer-Free Multiplex Ligation-Dependent Probe Amplification. Anal Chem 2013; 85:9383-9. [DOI: 10.1021/ac402314h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gi Won Shin
- Institute of Environmental
and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Jeongkyeong Na
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Mihwa Seo
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Boram Chung
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Hong Gil Nam
- Department
of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873, Korea
| | - Seung-Jae Lee
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
- Department of
Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
- World Class University
Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang,Gyeongbuk 790-784, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
- Department
of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
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17
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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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18
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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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19
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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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20
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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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21
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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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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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23
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Shin GW, Jung SH, Yim SH, Chung B, Yeol Jung G, Chung YJ. Stuffer-free multiplex ligation-dependent probe amplification based on conformation-sensitive capillary electrophoresis: a novel technology for robust multiplex determination of copy number variation. Electrophoresis 2012; 33:3052-61. [PMID: 22965760 DOI: 10.1002/elps.201200334] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 07/18/2012] [Accepted: 07/23/2012] [Indexed: 01/12/2023]
Abstract
Developing diagnostic tools based on the application of known disease/phenotype-associated copy number variations (CNVs) requires the capacity to measure CNVs in a multiplex format with sufficient reliability and methodological simplicity. In this study, we developed a reliable and user-friendly multiplex CNV detection method, termed stuffer-free MLPA-CE-SSCP, that combines a variation of multiplex ligation-dependent probe amplification (MLPA) with CE-SSCP. In this variation, MLPA probes were designed without the conventionally required stuffer sequences. To separate the similar-sized stuffer-free MLPA products, we adopted CE-SSCP rather than length-dependent conventional CE analysis. An examination of the genomic DNA from five cell lines known to vary in X-chromosome copy number (1-5) revealed that copy number determinations using stuffer-free MLPA-CE-SSCP were more accurate than those of conventional MLPA, and the CV of the measured copy numbers was significantly lower. Applying our system to measure the CNVs on autosomes between two HapMap individuals, we found that all peaks for CNV targets showed the expected copy number changes. Taken together, our results indicate that this new strategy can overcome the limitations of conventional MLPA, which are mainly related to long probe length and difficulties of probe preparation.
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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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Chung B, Shin GW, Na J, Oh MH, Jung GY. Multiplex quantitative foodborne pathogen detection using high resolution CE-SSCP coupled stuffer-free multiplex ligation-dependent probe amplification. Electrophoresis 2012; 33:1477-81. [PMID: 22648818 DOI: 10.1002/elps.201100615] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sensitive multiplex detection methods for foodborne pathogens are important in controlling food safety, and detection of genetic markers is accepted to be one of the best tools for sensitive detection. Although CE technology offers great potential in terms of sensitive multiplex detection, the necessary amplification is confined to markers sharing common primers such as the 16S rRNA gene. For precise and sensitive detection, pathogen-specific genes are optimal markers. Although multiplex ligation-dependent probe amplification (MLPA) is appropriate for amplification of specific markers, the requirement for stuffers, to ensure length-dependent separation on CE, is a major obstacle in detection of foodborne pathogens. In the present study, we developed stuffer-free MLPA using high-resolution CE-SSCP to sensitively detect ten foodborne pathogens. The probe set for MLPA prior to CE-SSCP analysis was designed for species-specific detection. After careful optimization of each MLPA step, to ensure that CE-SSCP analysis was informative, we found that all ten pathogens could be reliably identified; the limits of detection were 0.5-5 pg of genomic DNA, and more than 100-fold increase could be quantitatively determined. Thus, MLPA-CE-SSCP is a sensitive and reliable technique for pathogen detection.
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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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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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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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