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Tao C, Yang B, Li Z, Zhang D, Yamaguchi Y. Real-time Tracking of DNA Fragment Separation by Smartphone. J Vis Exp 2017. [PMID: 28605369 DOI: 10.3791/55926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.
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Affiliation(s)
- Chunxian Tao
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology
| | - Bo Yang
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology
| | - Zhenqing Li
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology;
| | - Dawei Zhang
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology
| | - Yoshinori Yamaguchi
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology; Department of Applied Physics, Graduate School of Engineering, Osaka University; East China University of Science and Technology, Department of Physics Faculty of Science
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2
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Tůma P, Opekar F, Samcová E. Very fast electrophoretic separation on commercial instruments using a combination of two capillaries with different internal diameters. Electrophoresis 2013; 34:552-6. [DOI: 10.1002/elps.201200524] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 10/12/2012] [Accepted: 10/12/2012] [Indexed: 12/16/2022]
Affiliation(s)
- Petr Tůma
- Institute of Biochemistry, Cell and Molecular Biology; Third Faculty of Medicine, Charles University in Prague; Prague; Czech Republic
| | - František Opekar
- Department of Analytical Chemistry; Faculty of Science, Charles University in Prague; Prague; Czech Republic
| | - Eva Samcová
- Institute of Biochemistry, Cell and Molecular Biology; Third Faculty of Medicine, Charles University in Prague; Prague; Czech Republic
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Wang H, Knobel G, Wilson WB, Calimag-Williams K, Campiglia AD. Gold nanoparticles deposited capillaries for in-capillary microextraction capillary zone electrophoresis of monohydroxy-polycyclic aromatic hydrocarbons. Electrophoresis 2011; 32:720-7. [DOI: 10.1002/elps.201000516] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 01/03/2011] [Accepted: 01/03/2011] [Indexed: 11/10/2022]
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4
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Kim YK, Kwon YJ. Separation and recovery of nucleic acids with improved biological activity by acid-degradable polyacrylamide gel electrophoresis. Electrophoresis 2010; 31:1656-61. [DOI: 10.1002/elps.200900783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Lien KY, Lee GB. Miniaturization of molecular biological techniques for gene assay. Analyst 2010; 135:1499-518. [PMID: 20390199 DOI: 10.1039/c000037j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted.
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Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, National Cheng Kung University, Tainan, 701, Taiwan
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6
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Opekar F, Coufal P, Štulík K. Rapid Capillary Zone Electrophoresis Along Short Separation Pathways and Its Use in Some Hyphenated Systems: A Critical Review. Chem Rev 2009; 109:4487-99. [DOI: 10.1021/cr900018r] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- František Opekar
- Charles University in Prague, Faculty of Science, Department of Analytical Chemistry, Albertov 2030, CZ-128 43 Prague 2, Czech Republic
| | - Pavel Coufal
- Charles University in Prague, Faculty of Science, Department of Analytical Chemistry, Albertov 2030, CZ-128 43 Prague 2, Czech Republic
| | - Karel Štulík
- Charles University in Prague, Faculty of Science, Department of Analytical Chemistry, Albertov 2030, CZ-128 43 Prague 2, Czech Republic
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Ohno KI, Tachikawa K, Manz A. Microfluidics: Applications for analytical purposes in chemistry and biochemistry. Electrophoresis 2008; 29:4443-53. [DOI: 10.1002/elps.200800121] [Citation(s) in RCA: 296] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Oliver G, Simpson C, Kerby MB, Tripathi A, Chauhan A. Electrophoretic migration of proteins in semidilute polymer solutions. Electrophoresis 2008; 29:1152-63. [PMID: 18246577 DOI: 10.1002/elps.200700756] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We present a systematic study of the electrophoretic migration of 10-200 kDa protein fragments in dilute-polymer solutions using microfluidic chips. The electrophoretic mobility and dispersion of protein samples were measured in a series of monodisperse polydimethylacrylamide (PDMA) polymers of different molecular masses (243, 443, and 764 kDa, polydispersivity index <2) of varying concentration. The polymer solutions were characterized using rheometry. Prior to loading onto the microchip, the polymer solution was mixed with known concentrations of SDS (SDS) surfactant and a staining dye. SDS-denatured protein samples were electrokinetically injected, separated, and detected in the microchip using electric fields ranging from 100 to 300 V/cm. Our results show that the electrophoretic mobility of protein fragments decreases exponentially with the concentration c of the polymer solution. The mobility was found to decrease logarithmically with the molecular weight of the protein fragment. In addition, the mobility was found to be independent of the electric field in the separation channel. The dispersion is relatively independent of polymer concentration and it first increases with protein size and then decreases with a maximum at about 45 kDa. The resolution power of the device decreases with concentration of the PDMA solution but it is always better than 10% of the protein size. The protein migration does not seem to correspond to the Ogston or the reptation models. A semiempirical expression for mobility given by van Winkle fits the data very well.
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Affiliation(s)
- Gloria Oliver
- Division of Engineering and Medical Science, Brown University, Providence, RI 02912, USA
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Atha DH. High-throughput DNA diagnostic measurements using capillary electrophoresis: p53, fragile X and telomerase. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2008; 2:91-100. [PMID: 23485119 DOI: 10.1517/17530059.2.1.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Capillary electrophoresis (CE) has become recognized as a powerful tool for the characterization of DNA. It has numerous advantages over slab-gel electrophoresis in that it is fast, highly reproducible and easy to automate. It is well known for its contribution to success in sequencing the human genome, but it is equally important in a wide range of forensic and pharmaceutical applications. Of these applications, CE plays a large and important role in mutation scanning and DNA sizing. From the author's laboratory, three previously published examples are given of clinical applications in this area that have benefited from the use of capillary electrophoresis: the detection of p53 mutations by single strand conformational polymorphism, the analysis of fragile X syndrome and the measurement of telomerase activity. There are many examples from other laboratories where CE has played an important role in this field. For acceptance by the medical community, there must be a clear demonstration that capillary electrophoresis can replace and improve previous slab-gel methods. In this regard, the examples given in this review help to demonstrate that CE can replace previous slab-gel methods and show that CE can improve a wide range of applications in the medical field.
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Affiliation(s)
- Donald H Atha
- National Institute of Standards and Technology, Biochemical Science Division, 100 Bureau Drive, MS 8311, Gaithersburg, MD 20899, USA +1 301 975 3092 ; +1 301 975 8505 ;
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Tempels FWA, Underberg WJM, Somsen GW, de Jong GJ. Design and applications of coupled SPE-CE. Electrophoresis 2008; 29:108-28. [DOI: 10.1002/elps.200700149] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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11
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Luo Y, Zhang Q, Qin J, Lin B. Further improvement of hydrostatic pressure sample injection for microchip electrophoresis. Electrophoresis 2007; 28:4769-71. [DOI: 10.1002/elps.200700330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Hung CC, Chien SC, Lin CY, Chang CH, Chang YF, Jong YJ, Hsieh ST, Hsieh WS, Liu MS, Lin WL, Lee CN, Su YN. Use of multiplex PCR and CE for gene dosage quantification and its biomedical applications for SMN, PMP22, and alpha-globin genes. Electrophoresis 2007; 28:2826-34. [PMID: 17640091 DOI: 10.1002/elps.200600647] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many genetic diseases are caused by the presence of point mutations, small insertions, and deletions in respective genes, and the number of diseases known to be caused by deletions and duplications involving large DNA genomes is increasing. These changes lead to underexpression or overexpression of the gene, according to changes in gene dosage. The methods for the detection of point mutations, small insertions, and deletions are well established, but the detection of larger genomic deletions or duplications is more difficult. Due to the lack of efficient and technically feasible protocols for gene dosage quantification, we describe a diagnostic protocol employing a combination of available methods. The efficient and accurate gene dosage quantification platform is combined with multiplex PCR and CE, and applied to detect dosages of several genes, including SMN, PMP22, and alpha-globin genes. The reliability of this novel methodology shows that it is a relatively speedy and low-cost procedure and a significant tool for genetic diagnosis. Its sensitivity and specificity for identifying deletion and duplication genotypes approach 100%. Moreover, once we establish this powerful system, we will further apply this technique to the rapid detection of trisomy syndromes and microdeletion syndromes, including trisomy 13, Down syndrome, DiGeorge syndrome, and others.
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Affiliation(s)
- Chia-Cheng Hung
- Institute of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
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Kim YH, Yang I, Park SR. Well-Less Capillary Array Electrophoresis Chip Using Hydrophilic Sample Bridges. Anal Chem 2007; 79:9205-10. [DOI: 10.1021/ac071115p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young Ho Kim
- Health Metrology Group, Korea Research Institute of Standards and Science, Daejeon, Korea
| | - Inchul Yang
- Health Metrology Group, Korea Research Institute of Standards and Science, Daejeon, Korea
| | - Sang-Ryoul Park
- Health Metrology Group, Korea Research Institute of Standards and Science, Daejeon, Korea
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Lin MT, Rich RG, Shipley RF, Hafez MJ, Tseng LH, Murphy KM, Gocke CD, Eshleman JR. A molecular fraction collecting tool for the ABI 310 automated sequencer. J Mol Diagn 2007; 9:598-603. [PMID: 17916601 DOI: 10.2353/jmoldx.2007.070022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several methods exist to retrieve and purify DNA fragments after agarose or polyacrylamide gel electrophoresis for subsequent analyses. However, molecules present in low concentration and molecules similar in size to their neighbors are difficult to purify. Capillary electrophoresis has become popular in molecular diagnostic laboratories because of its automation, excellent resolution, and high sensitivity. In the current study, the ABI Prism 310 Genetic Analyzer was reconfigured into a fraction collector by adapting the standard gel block to accommodate a collection tube at the distal end of capillary. The time to collect the desired peaks was estimated by extrapolating from standard capillary electrophoresis using the original gel block. Fraction collection from a mixture of DNA fragments amplified from wild type and several internal tandem duplication mutations of the FMS-like tyrosine kinase 3 (Flt3) gene yielded highly purified DNA fragments containing internal tandem duplication mutations and predictable electrokinetics using the reconstructed gel block. The reconfigured instrument could successfully isolate DNA amplicons from extremely low-amplitude peaks (110 relative fluorescent units), which were undetectable using polyacrylamide gel electrophoresis. In addition, we successfully isolated bands that were only three bases apart that comigrated on polyacrylamide gel electrophoresis. DNA sequencing was used to confirm that the correct peaks were recovered at sufficient purity.
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Affiliation(s)
- Ming-Tseh Lin
- The Sol Goldman Pancreatic Cancer Research Center, Departments of Pathology and Oncology, Johns Hopkins School of Medicine, 1550 Orleans Street, Baltimore, MD 21231, USA
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