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Lim DW, Yoon TS, Han KH, Sajjad S, Shin HS, Kang S. Improved Separation in Horizontal Protein SDS-PAGE with Double-Deck Flat Electrodes and a Field Inversion Gel Electrophoresis Module. Methods Protoc 2023; 6:106. [PMID: 37987353 PMCID: PMC10660703 DOI: 10.3390/mps6060106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023] Open
Abstract
The horizontal flatbed electrophoresis method is employed to separate protein samples, providing greater flexibility for various electrophoretic applications and easier sample loading compared to its vertical counterpart. In the currently available equipment setup, cathode and anode electrodes are positioned on top of a gel at each end. Since an electric field enters the gel from the top, its strength gradually weakens from the top to the bottom of the gel. When examining the interior of gels following electrophoretic separation, the uneven electric field causes the protein bands to lie down forward in the direction of migration, leading to an increase in bandwidth. This issue has remained unaddressed for several decades. To address this problem, new clamp-shaped and double-deck electrodes were developed to apply an electric field simultaneously from both the top and bottom of the gel. Both of these new electrodes facilitated the formation of perpendicular protein band shapes and enhanced resolution at a comparable level. Due to their ease of use, double-deck electrodes are recommended. By combining these new electrodes with the field inversion gel electrophoresis (FIGE) technique, the protein bands could be focused and aligned nearly vertically, resulting in the highest level of electrophoretic resolution. Our electrodes are compatible with polyacrylamide gels of varying sizes, buffer systems, and sample well formats. They can be easily manufactured and seamlessly integrated into existing laboratory instruments for practical use.
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Affiliation(s)
- Dong Woo Lim
- T-MAC Co., Ltd., Yuseong-gu, Daejeon 34141, Republic of Korea; (D.W.L.); (H.-S.S.)
| | - Tae-Sung Yoon
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea; (T.-S.Y.); (S.S.)
| | - Kyung Ho Han
- Department of Biological Sciences and Biotechnology, Hannam University, Yuseong-gu, Daejeon 34054, Republic of Korea;
| | - Saba Sajjad
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea; (T.-S.Y.); (S.S.)
| | - Heung-Seon Shin
- T-MAC Co., Ltd., Yuseong-gu, Daejeon 34141, Republic of Korea; (D.W.L.); (H.-S.S.)
| | - Sunghyun Kang
- T-MAC Co., Ltd., Yuseong-gu, Daejeon 34141, Republic of Korea; (D.W.L.); (H.-S.S.)
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea; (T.-S.Y.); (S.S.)
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Dendani Chadi Z, Arcangioli MA. Pulsed-Field Gel Electrophoresis Analysis of Bovine Associated Staphylococcus aureus: A Review. Pathogens 2023; 12:966. [PMID: 37513813 PMCID: PMC10385338 DOI: 10.3390/pathogens12070966] [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: 06/09/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
For decades now, DNA fingerprinting by means of pulsed-field gel electrophoresis (PFGE) continues to be the most widely used to separate large DNA molecules and distinguish between different strains in alternating pulses. This is done by isolating intact chromosomal DNA and using restriction enzymes with specific restriction sites to generate less than 30 restriction fragments from 50 Kb to 10 Mbp. These results make clone-specific band profiles easy to compare. Specialized equipment is required for the optimization of DNA separation and resolution, among which a contour-clamped homogeneous electric field (CHEF) apparatus is the most commonly used. As a result, the PFGE analysis of a bacterial genome provides useful information in terms of epidemiological investigations of different bacterial pathogens. For Staphylococcus aureus subtyping, despite its limitations and the emergence of alternative methods, PFGE analysis has proven to be an adequate choice and the gold standard for determining genetic relatedness, especially in outbreak detection and short-term surveillance in the veterinary field.
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Affiliation(s)
- Zoubida Dendani Chadi
- Laboratory of Biodiversity and Pollution of Ecosystems, Department of Veterinary Medicine, Faculty of Natural Science and Life, University of Chadli Bendjedid, El Tarf 36000, Algeria
| | - Marie-Anne Arcangioli
- VetAgro Sup, Université de Lyon, UMR Mycoplasmoses Animales, 69280 Marcy l'Etoile, France
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Lewnard JA, Whittles LK, Rick AM, Martin JM. Naturally Acquired Protection Against Upper Respiratory Symptoms Involving Group A Streptococcus in a Longitudinal Cohort Study. Clin Infect Dis 2021; 71:e244-e254. [PMID: 31955205 DOI: 10.1093/cid/ciaa044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/15/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pharyngitis due to group A Streptococcus (GAS) represents a major cause of outpatient visits and antibiotic use in the United States. A leading vaccine candidate targets 30 of the > 200 emm types of GAS. We aimed to assess natural protection conferred by GAS against respiratory symptoms. METHODS In a 5-year study among school-aged children in Pittsburgh, Pennsylvania, pharyngeal cultures were obtained from children at 2-week intervals, and active surveillance was conducted for respiratory illnesses. We assessed protection via the relative odds of previous detection of homologous strains (defined by field-inversion gel electrophoresis banding pattern), emm types, and emm clusters at visits where GAS was detected with symptoms, vs visits where GAS was detected without symptoms. We used a cluster bootstrap of children to adjust estimates for repeated sampling. RESULTS At visits where previously detected GAS emm types were identified, we estimated 81.8% (95% confidence interval [CI], 67.1%-91.7%) protection against typical pharyngitis symptoms among children reacquiring the same strain, and 94.5% (95% CI, 83.5%-98.6%) protection among children acquiring a distinct strain. We estimated 77.1% (95% CI, 33.7%-96.3%) protection against typical symptoms among children acquiring partially heterologous emm types belonging to a previously detected emm cluster. Protection was evident after both symptomatic and asymptomatic detections of GAS. We did not identify strong evidence of protection against atypical respiratory symptoms. CONCLUSIONS Within a 5-year longitudinal study, previous detection of GAS emm types was associated with protection against typical symptoms when homologous strains were subsequently detected. Naturally acquired protection against partially heterologous types suggests that emm type-based vaccines may have broader strain coverage than what has been previously assumed.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, California, USA.,Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA.,Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Lilith K Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.,Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Modelling Methodology, School of Public Health, Imperial College London, London, United Kingdom
| | - Anne-Marie Rick
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Judith M Martin
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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4
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Monitoring of DNA Replication and DNA Double-Strand Breaks in Saccharomyces cerevisiae by Pulsed-Field Gel Electrophoresis (PFGE). Methods Mol Biol 2020. [PMID: 31989520 DOI: 10.1007/978-1-0716-0323-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Separating DNA fragments using standard agarose gel electrophoresis is based on the capacity of negatively charged DNA molecules to move through the agarose gel matrix toward the positive electrode. Pulsed-field gel electrophoresis (PFGE) is an agarose gel electrophoresis technique that enables the separation of DNA molecules at a megabase scale, making the direct genomic analysis of large DNA molecules possible. For instance, 16 chromosomes (size range; 0.2-2.2 Mb) in Saccharomyces cerevisiae, whose karyotype cannot be easily observed with a microscope, can be directly separated on agarose gel. PFGE is also a powerful analytical tool for chromosomal mapping and genome structure analysis in bacterial and mammalian cells. In this chapter, we will describe the preparation of intact yeast chromosomal DNA for PFGE and general PFGE procedures and will introduce a PFGE method to monitor the DNA replication fork progression and DNA double-strand breaks (DSBs).
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6
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El Maaiden E, El Kharrassi Y, Essamadi AK, Moustaid K, Nasser B. Improved Method for DNA Extraction and Purification from Tetrahymena pyriformis. Methods Protoc 2019; 2:E40. [PMID: 31164619 PMCID: PMC6632170 DOI: 10.3390/mps2020040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/17/2022] Open
Abstract
Tetrahymena pyriformis (protozoa) is intensely investigated as a model organism, offering numerous advantages in comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is a vital step of any molecular experiment, here a new mixed surfactant (Sodium dodecyl sulfate (SDS) 20%/Triton X-100) was adopted for effective DNA extraction from Tetrahymena pyriformis under an easy, fast protocol. The efficiency of this technique was then compared with three widely-used alternative techniques, namely the Chelex 100 matrix, Ammonium pyrrolidine dithiocarbamate (APD) complex and SDS-chloroform methods. DNA extraction was analyzed by pulsed-field gel electrophoresis, spectral measurement, fluorometry (Qubit), restriction enzyme digestion, and polymerase chain reaction. Data analysis revealed that the quantity and quality of the recovered DNA varied depending on the applied DNA extraction method. The new method (SDS 20%/Triton X-100) was the most efficient for extracting DNA from Tetrahymena pyriformis with high integrity and purity, affordable cost, less time, and suitability for molecular applications.
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Affiliation(s)
- Ezzouhra El Maaiden
- Laboratory of Biochemistry and Neurosciences, Department of Biology, University Hassan I, BP 577, 26000 Settat, Morocco.
- Laboratory of Applied Chemistry and Environment, Department of Chemistry, University Hassan I, BP 577, 26000 Settat, Morocco.
| | - Youssef El Kharrassi
- Laboratory of Biochemistry and Neurosciences, Department of Biology, University Hassan I, BP 577, 26000 Settat, Morocco.
| | - Abdel Khalid Essamadi
- Laboratory of Biochemistry and Neurosciences, Department of Biology, University Hassan I, BP 577, 26000 Settat, Morocco.
| | - Khadija Moustaid
- Laboratory of Applied Chemistry and Environment, Department of Chemistry, University Hassan I, BP 577, 26000 Settat, Morocco.
| | - Boubker Nasser
- Laboratory of Biochemistry and Neurosciences, Department of Biology, University Hassan I, BP 577, 26000 Settat, Morocco.
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7
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Advances in Molecular Epidemiology of Infectious Diseases: Definitions, Approaches, and Scope of the Field. Microbiol Spectr 2019; 6. [PMID: 30387413 DOI: 10.1128/microbiolspec.ame-0001-2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Molecular epidemiology is a discipline that uses molecular microbiology tools to study the distribution and determinants of diseases in human populations and veterinary animals. Our understanding of epidemiology of infectious diseases has evolved with technological advancements made in molecular biology that refine our perception of the identity and dynamics of microorganisms. This review is an introduction to the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases that will discuss how these advancements have contributed to investigations of infectious disease outbreaks/epidemics, surveillance, transmission dynamics, risk factor identification, pathogenesis, and etiologic attribution of bacterial, viral, protozoan, and helminthic pathogens to a disease. Here we define "molecular epidemiology" and distinguish it from other disciplines that use many of the same molecular biology tools-taxonomy, phylogenetics, and molecular evolution of microorganisms. The Curated Collection will be spread throughout multiple issues of Microbiology Spectrum and will be divided into four general sections: (i) laboratory methods used to strain type microbial pathogens, (ii) methods used to analyze genotyping data, (iii) examples of molecular epidemiologic investigations of bacterial, viral, and parasitic diseases, and (iv) applications of molecular epidemiology to address new research questions in communicable and noncommunicable diseases. The major theme of this Curated Collection is to address the following question frequently asked by clinicians, clinical microbiologists, and public health professionals: what is the advantage or unique contribution of molecular epidemiology in solving infectious disease problems in the clinical and public health arenas? *This article is part of a curated collection.
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8
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Lopez-Canovas L, Martinez Benitez MB, Herrera Isidron JA, Flores Soto E. Pulsed Field Gel Electrophoresis: Past, present, and future. Anal Biochem 2019; 573:17-29. [PMID: 30826351 DOI: 10.1016/j.ab.2019.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/27/2022]
Abstract
Pulsed Field Gel Electrophoresis (PFGE) has been considered for many years the 'gold-standard' for characterizing many pathogenic organisms as well as for subtyping bacterial species causing infection outbreaks. This article reviews the basic principles of PFGE and it includes the main advantages and limitations of the different electrode configurations that have been used in PFGE equipment and their influence on the DNA electrophoretic separation. Remarkably, we summarize here the most relevant theoretical and practical aspects that we have learned for more than 20 years developing and using the miniaturized PFGE systems. We also discussed the theoretical aspects related to DNA migration in PFGE agarose gels. It served as the basis for simulating the DNA electrophoretic patterns in CHEF mini gels and mini-chambers during experimental design and optimization. A critical comparison between standard and miniaturized PFGE systems, as well as the enzymatic and non-enzymatic methods for intact immobilized DNA preparation, is provided throughout the review. The PFGE current applications, advantages, limitations and future challenges of the methodology are also discussed.
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Affiliation(s)
- Lilia Lopez-Canovas
- Postgraduate Program in Genomic Sciences, School of Science and Technology (CCyT), Autonomous University of Mexico City (UACM), Mexico City, Mexico.
| | - Maximo B Martinez Benitez
- Postgraduate Program in Genomic Sciences, School of Science and Technology (CCyT), Autonomous University of Mexico City (UACM), Mexico City, Mexico.
| | | | - Eduardo Flores Soto
- Academy of Biology, School of Sciences and Humanities, UACM, Mexico City, Mexico.
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9
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Increase in Local Protein Concentration by Field-Inversion Gel Electrophoresis. Methods Mol Biol 2018. [PMID: 30426420 DOI: 10.1007/978-1-4939-8793-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and nonspecific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein recovery efficiency. Here, we describe the enhancement of protein separation efficiency for up to twofold in conventional one-dimensional PAG electrophoresis (1D PAGE), two-dimensional (2D) PAGE, and native PAGE by implementing pulses of inverted electric field during gel electrophoresis.
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10
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Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:31/4/e00019-18. [PMID: 30158299 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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11
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Tooley PW, Carras MM, Beck R, Peterson G, Bonde MR. Separation of Tilletia indica chromosomes using CHEF gel electrophoresis. Mycologia 2018. [DOI: 10.1080/00275514.1995.12026503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- P. W. Tooley
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Bldg. 1301, Ft. Detrick, Frederick, Maryland 21702
| | - M. M. Carras
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Bldg. 1301, Ft. Detrick, Frederick, Maryland 21702
| | - R. Beck
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Bldg. 1301, Ft. Detrick, Frederick, Maryland 21702
| | - G. Peterson
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Bldg. 1301, Ft. Detrick, Frederick, Maryland 21702
| | - M. R. Bonde
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Bldg. 1301, Ft. Detrick, Frederick, Maryland 21702
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12
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Casey GP, Pringle AT, Erdmann PA. Evaluation of Recent Techniques Used to Identify Individual Strains ofSaccharomycesYeasts. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-48-0100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Gregory P. Casey
- Anheuser-Busch Companies, Corporate R&D, One Busch Place, St. Louis, MO 63118
| | - A. T. Pringle
- Anheuser-Busch Companies, Corporate R&D, One Busch Place, St. Louis, MO 63118
| | - P. A. Erdmann
- Anheuser-Busch Companies, Corporate R&D, One Busch Place, St. Louis, MO 63118
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13
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Oakley-Gutowski KM, Hawthorne DB, Kavanagh TE. Application of Chromosome Fingerprinting to the Differentiation of Brewing Yeasts. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-50-0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kerin M. Oakley-Gutowski
- Carlton and United Breweries Limited/ Foster's Brewing Group Limited, Carlton, Victoria 3053 Australia
| | - Donn B. Hawthorne
- Carlton and United Breweries Limited/ Foster's Brewing Group Limited, Carlton, Victoria 3053 Australia
| | - Terry E. Kavanagh
- Carlton and United Breweries Limited/ Foster's Brewing Group Limited, Carlton, Victoria 3053 Australia
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14
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Duan L, Cao Z, Yobas L. Continuous-Flow Electrophoresis of DNA and Proteins in a Two-Dimensional Capillary-Well Sieve. Anal Chem 2017; 89:10022-10028. [DOI: 10.1021/acs.analchem.7b02484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lian Duan
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Zhen Cao
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Levent Yobas
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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Affiliation(s)
- Søren A Ladefoged
- Department of Medical Microbiology and Immunology University of Aarhus, Denmark.,Department of Clinical Biochemistry University Hospital of Aarhus, Denmark
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16
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Gumuscu B, Bomer JG, de Boer HL, van den Berg A, Eijkel JCT. Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform. MICROSYSTEMS & NANOENGINEERING 2017; 3:17001. [PMID: 31057856 PMCID: PMC6444976 DOI: 10.1038/micronano.2017.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 12/02/2016] [Accepted: 12/12/2016] [Indexed: 06/07/2023]
Abstract
A new approach is presented for preparative, continuous flow fractionation of sub-10-kbp DNA fragments, which exploits the variation in the field-dependent mobility of the DNA molecules based on their length. Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2% agarose gel. Using this method, we demonstrate a high-resolution separation of 0.5, 1, 2, 5, and 10 kbp DNA fragments within 2 min. During the separation, DNA fragments are also purified from other ionic species. Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing. The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.
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Affiliation(s)
- Burcu Gumuscu
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Johan G. Bomer
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Hans L. de Boer
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Albert van den Berg
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Jan C. T. Eijkel
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
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17
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Electrode Materials in Microfluidic Systems for the Processing and Separation of DNA: A Mini Review. MICROMACHINES 2017. [PMCID: PMC6190325 DOI: 10.3390/mi8030076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the advent of genetic analysis, electrode materials have played an irreplaceable role due to the easily-exploitable negatively-charged backbone of the DNA structure. Initially, the employment of electrophoretic movement lay only in the separation of DNA fragments of differing length; however, the widening utility of electrokinetic phenomena at the microscale in areas such as fluid transportation and multistep integration led researchers to capitalize further when translating processes to microfluidic or “lab-on-chip” devices. Over the following three decades, the field witnessed a plethora of ways in which the necessary voltages could be transmitted to the sample and reagents with many successes; however, additional demands were then placed on those hoping to bring their microdevices to the market place. A greater emphasis on the cost of all constituent parts along with the increased importance that fluidics be contained hermetically at all times meant groups would become more imaginative when incorporating electrode materials. This review will aim to exactly describe the evolution of how those materials have been employed in DNA-based microfluidic devices. It will focus on how developers began to explore other emerging uses and also discuss how their tactics reflected the progressive demands of their chosen industry.
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18
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Coates BS, Abel CA, Perera OP. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools. Genome 2016; 60:310-324. [PMID: 28177843 DOI: 10.1139/gen-2016-0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50 = 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
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Affiliation(s)
- Brad S Coates
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.,b Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Craig A Abel
- a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Omaththage P Perera
- c USDA-ARS, Southern Insect Management Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA
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Mulligan ME, Arbeit RD. Epidemiologic and Clinical Utility of Typing Systems for Differentiating Among Strains of Methicillin-Resistant Staphylococcus aureus. Infect Control Hosp Epidemiol 2016. [DOI: 10.2307/30147085] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractTyping systems for differentiating among strains of methicillin-resistant Staphylococcus aureus (MRSA) can be valuable tools for the epidemiologist and the clinician. Specific criteria for evaluating such systems are typeability, reproducibility, and discriminatory power. An ideal typing system also would be rapid, inexpensive, technically simple, and readily available. Systems based on the detection of phenotypic variations include antimicrobial susceptibility testing, bacteriophage typing, multilocus enzyme electrophoresis, and electrophoretic methods such as protein eletrophoresis and immunoblotting. Systems that directly detect genotypic variations include plasmid profile analysis, restriction enzyme analysis of plasmid DNA, restriction enzyme analysis of chromosomal DNA, Southern blot analysis of specific restriction fragment length polymorphisms, and pulse field gel electrophoresis. in general, the more widely available typing systems based on phenotypic assays and plasmid analysis have limitations in typeability and/or discriminatory power.The chromosomal DNA-based techniques, although promising, are unproven approaches still under active investigation.
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Parizad EG, Parizad EG, Valizadeh A. The Application of Pulsed Field Gel Electrophoresis in Clinical Studies. J Clin Diagn Res 2016; 10:DE01-4. [PMID: 26894068 PMCID: PMC4740595 DOI: 10.7860/jcdr/2016/15718.7043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/24/2015] [Indexed: 01/07/2023]
Abstract
Pulsed-field gel electrophoresis is a method applied in separating large segments of deoxyribonucleotide using an alternating and cross field. In a uniform magnetic field, components larger than 50kb pass a route through the gel and since the movement of DNA (Deoxyribonucleic acid) molecules are in a Zigzag form, separation of DNAs as bands carried out better via gel. PFGE in microbiology is a standard method which is used for typing of bacteria. It is also a very useful tool in epidemiological studies and gene mapping in microbes and mammalian cell, also motivated development of large-insert cloning system such as bacterial and yeast artifical chromosomes. In this method, close and similar species in terms of genetic patterns show alike profiles regarding DNA separation, and those ones which don't have similarity or are less similar, reveal different separation profiles. So this feature can be used to determine the common species as the prevalence agent of a disease. PFGE can be utilized for monitoring and evaluating different micro-organisms in clinical samples and existing ones in soil and water. This method can also be a reliable and standard method in vaccine preparation. In recent decades, PFGE is highly regarded as a powerful tool in control, prevention and monitoring diseases in different populations.
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Affiliation(s)
- Elaheh Gholami Parizad
- PhD Student, Department of Medical Microbiology, Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Eskandar Gholami Parizad
- Faculty, Member of Public Health School and Psychosocial Injuries Prevention Research Center, Ilam, Iran
| | - Azar Valizadeh
- PhD Student, Department of Medical Microbiology, Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
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21
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Hakenberg S, Hügle M, Meyer P, Behrmann O, Dame G, Urban G. Fenton fragmentation for faster electrophoretic on chip purification of amplifiable genomic DNA. Biosens Bioelectron 2015; 67:49-52. [DOI: 10.1016/j.bios.2014.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/22/2014] [Accepted: 06/01/2014] [Indexed: 12/01/2022]
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22
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Zhou P, Oyarzabal OA. Application of pulsed field gel electrophoresis to type Campylobacter jejuni. Methods Mol Biol 2015; 1301:139-156. [PMID: 25862055 DOI: 10.1007/978-1-4939-2599-5_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pulsed field gel electrophoresis (PFGE) is generally accepted as one of the most discriminatory methods available for genotyping Campylobacter jejuni. PFGE has been extensively used in epidemiological studies, including outbreak investigation, persistence of genotypes in a human population, environmental diversity of sporadic infection isolates, dissemination of antibiotic-resistant strains, and comparison of genotypes within and between hosts. The main purpose of this chapter is to present a working PFGE protocol for those interested in incorporating this technique in their laboratories.
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Affiliation(s)
- Ping Zhou
- Department of Neurology, University of Alabama at Birmingham, 1720 7th Avenue South, Birmingham, AL, 35233, USA
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23
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Golding GR, Campbell J, Spreitzer D, Chui L. Pulsed-field gel electrophoresis of Staphylococcus aureus. Methods Mol Biol 2015; 1301:85-93. [PMID: 25862050 DOI: 10.1007/978-1-4939-2599-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
For many bacterial pathogens, including Staphylococcus aureus, pulsed-field gel electrophoresis (PFGE) is a molecular typing method widely used in surveillance and epidemiological investigations. The general principle of PFGE involves creating large DNA fragments from intact bacterial chromosomes using rare cutting restriction endonucleases. These large DNA fragments are successfully separated in an agarose gel by alternating the direction of the electrical fields over a prolonged period of time. The resulting DNA banding patterns in the gel create a "DNA fingerprint," which can then be used to discriminate clonal relatedness of isolates based on set interpretation guidelines. Standardization of protocols has greatly enhanced the reproducibility of PFGE between labs, enabling national surveillance and further molecular epidemiological studies of S. aureus.
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Affiliation(s)
- George R Golding
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada,
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24
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Chui L, Li V. Technical and Software Advances in Bacterial Pathogen Typing. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Shi N, Ugaz VM. Noise-enhanced gel electrophoresis. Electrophoresis 2014; 35:1758-65. [PMID: 24740474 DOI: 10.1002/elps.201300644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/12/2014] [Accepted: 03/25/2014] [Indexed: 11/12/2022]
Abstract
Macromolecules confined within a nanoporous matrix experience entropic trapping when their dimensions approach the average pore size, leading to emergence of anomalous transport behavior that can be beneficial in separation applications. But the ability to exploit these effects in practical settings (e.g., electrophoretic separation of DNA) has been hindered by additional dispersion introduced as a consequence of the uncorrelated process by which the embedded macromolecules discretely hop from pore to pore. Here, we show how both the source and solution to these difficulties are intimately linked to the inherent dynamics of the underlying activated transport mechanism. By modulating the applied electric field at a frequency tuned to the characteristic activation timescale, a resonance condition can be established that synergistically combines accelerated mobility and reduced diffusion. This resonance effect can be precisely manipulated by adjusting the magnitude and period of the driving electric field, enabling enhanced separation performance and bi-directional transport of different-sized species to be achieved. Notably, these phenomena are readily accessible in ordinary hydrogels (as opposed to idealized nanomachined topologies) suggesting broad potential to apply them in a host of useful settings.
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Affiliation(s)
- Nan Shi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
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27
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Cao Z, Yobas L. Fast DNA Sieving through Submicrometer Cylindrical Glass Capillary Matrix. Anal Chem 2013; 86:737-43. [DOI: 10.1021/ac4031994] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen Cao
- Department of Electronic
and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Levent Yobas
- Department of Electronic
and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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29
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Panchal CJ, Bast L, Dowiianick T, Stewart GG. A RAPID, SIMPLE AND RELIABLE METHOD OF DIFFERENTIATING BREWING YEAST STRAINS BASED ON DNA RESTRICTION PATTERNS. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1987.tb04512.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Casey GP, Xiao W, Rank GH. APPLICATION OF PULSED FIELD CHROMOSOME ELECTROPHORESIS IN THE STUDY OF CHROMOSOMEXIIIAND THE ELECTROPHORETIC KARYOTYPE OF INDUSTRIAL STRAINS OFSACCHAROMYCESYEASTS. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1988.tb04579.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Meaden P. DNA FINGERPRINTING OF BREWERS' YEAST: CURRENT PERSPECTIVES. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1990.tb01027.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Abstract
The technique of gel electrophoresis is now firmly established as a routine laboratory method for analyzing DNA. Here, we describe the development of the methodology as well as a brief explanation of how the technique works. There is a short introduction to pulsed-field agarose gel electrophoresis, which represents a critical advancement in the method that facilitates the analysis of very large fragments of DNA. Finally, theoretical considerations are included.
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33
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Kaneko S, Yoshida J, Ishikawa H, Takamatsu K. Single-cell pulsed-field gel electrophoresis to detect the early stage of DNA fragmentation in human sperm nuclei. PLoS One 2012; 7:e42257. [PMID: 22848752 PMCID: PMC3407096 DOI: 10.1371/journal.pone.0042257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/04/2012] [Indexed: 11/18/2022] Open
Abstract
Single-cell pulsed-field gel electrophoresis (SCPFGE) with dual electrode pairs was developed to detect the early stage of DNA fragmentation in human sperm. The motile sperm were purified by the commonly used density-gradient centrifugation technique and subsequent swim-up. The sperm were embedded in a thin film of agarose containing bovine trypsin (20 µg/mL) and were then lysed. Prior to SCPFGE, proteolysis of DNA-binding components, such as protamine and the nuclear matrix was essential to separate the long chain fibers from the fibrous and granular fragments derived from a single nucleus. The overall electrophoretic profiles elucidated the course of DNA fragmentation. A few large fibrous fragments were observed at the beginning of the process, however, as the fragmentation advanced, the long chain fibers decreased and shortened, and, conversely, the granular fragments increased until finally almost all the DNA was shredded. Although the ejaculate contained sperm with heterogeneous stages, the purified motile sperm exhibited several dozens of uniformly elongated fibers arising from the tangled DNA at the origin, whereas a part of these fibers gave rise to fibrous fragments beyond the tip of the elongated fibers, and their numbers and sizes varied among the sperm. Conventional intra-cytoplasmic sperm injection (ICSI) usually depends on intra-operative light microscopic observation to select a sperm for injection. The present results revealed that sperm motility could not give full assurance of DNA integrity. SCPFGE is likely to serve an important role in the preoperative differential diagnosis to determine the competence of the sperm population provided for injection.
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Affiliation(s)
- Satoru Kaneko
- Reproduction Center, Gynecology, Ichikawa General Hospital, Tokyo Dental College, Ichikawa, Chiba, Japan.
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Terranova GR, Mártin HO, Aldao CM. Separation of long linear polymers in gel electrophoresis with alternating electric fields: a theoretical study using the necklace model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061801. [PMID: 23005118 DOI: 10.1103/physreve.85.061801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Indexed: 06/01/2023]
Abstract
The necklace model, which mimics the reptation of a chain of N beads in a square lattice, is used to study the drift velocity of charged linear polymers in gels under an applied electric field that periodically changes its direction. The characteristics of the model allow us to determine the effects of the alternating electric field on the chains' dynamics. We explain why chains of different N can be made to move in opposite directions with a nonuniform electric field with certain values of intensity and frequency. The key point is that, when alternating electric fields are applied, longer chains spend more time out of the steady-state regime than lower chains. Numerical results are obtained by means of Monte Carlo simulations and they are qualitatively in agreement with experiments of DNA migration in gel electrophoresis.
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Affiliation(s)
- G R Terranova
- Instituto de Investigaciones Físicas de Mar del Plata (IFIMAR), Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata-CONICET Deán Funes 3350, B7602AYL Mar del Plata, Argentina
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35
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Increase in local protein concentration by field-inversion gel electrophoresis. Methods Mol Biol 2012. [PMID: 22585482 DOI: 10.1007/978-1-61779-821-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and nonspecific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein recovery efficiency. Here, we describe the enhancement of protein separation efficiency up to twofold in conventional one-dimensional PAG electrophoresis (1D PAGE), two-dimensional (2D) PAGE, and native PAGE by implementing pulses of inverted electric field during gel electrophoresis.
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36
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Sun M, Lin JS, Barron AE. Ultrafast, efficient separations of large-sized dsDNA in a blended polymer matrix by microfluidic chip electrophoresis: a design of experiments approach. Electrophoresis 2011; 32:3233-40. [PMID: 22009451 DOI: 10.1002/elps.201100260] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 05/06/2011] [Accepted: 06/09/2011] [Indexed: 01/23/2023]
Abstract
Double-stranded (ds) DNA fragments over a wide size range were successfully separated in blended polymer matrices by microfluidic chip electrophoresis. Novel blended polymer matrices composed of two types of polymers with three different molar masses were developed to provide improved separations of large dsDNA without negatively impacting the separation of small dsDNA. Hydroxyethyl celluloses with average molar masses of ∼27 kDa and ∼1 MDa were blended with a second class of polymer, high-molar mass (∼7 MDa) linear polyacrylamide. Fast and highly efficient separations of commercially available DNA ladders were achieved on a borosilicate glass microchip. A distinct separation of a 1-kb DNA extension ladder (200-40,000 bp) was completed in 2 min. An orthogonal design of experiments was used to optimize experimental parameters for DNA separations over a wide size range. We find that the two dominant factors are the applied electric field strength and the inclusion of a high concentration of low-molar mass polymer in the matrix solution. These two factors exerted different effects on the separations of small dsDNA fragments below 1 kbp, medium dsDNA fragments between 1 and 10 kbp, and large dsDNA fragments above 10 kbp.
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Affiliation(s)
- Mingyun Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305-5444, USA
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37
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Liu KL, Hsu JP, Tseng S. Influence of membrane layer properties on the electrophoretic behavior of a soft particle. Electrophoresis 2011; 32:3053-61. [DOI: 10.1002/elps.201100193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 11/06/2022]
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38
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Borrelia burgdorferi linear plasmid 38 is dispensable for completion of the mouse-tick infectious cycle. Infect Immun 2011; 79:3510-7. [PMID: 21708994 DOI: 10.1128/iai.05014-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease, exists in a complex enzootic cycle, transiting between its vector, Ixodes ticks, and a diverse range of vertebrate hosts. B. burgdorferi linear plasmid 38 (lp38) contains several genes that are differentially regulated in response to conditions mimicking the tick or mouse environments, suggesting that these plasmid-borne genes may encode proteins important for the B. burgdorferi infectious cycle. Some of these genes encode potential virulence factors, including hypothetical lipoproteins as well as a putative membrane transport system. To characterize the role of lp38 in the B. burgdorferi infectious cycle, we constructed a shuttle vector to selectively displace lp38 from the B. burgdorferi genome and analyzed the resulting clones to confirm the loss of lp38. We found that, in vitro, clones lacking lp38 were similar to isogenic wild-type bacteria, both in growth rate and in antigenic protein production. We analyzed these strains in an experimental mouse-tick infectious cycle, and our results demonstrate that clones lacking lp38 are fully infectious in a mouse, can efficiently colonize the tick vector, and are readily transmitted to a naive host.
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39
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Loomans D, Blumen A. Evaluation of the tension on dna-segments in the lakes-straits model. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/masy.19940810112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Pulsed-Field Gel Electrophoresis: Laboratory and Epidemiologic Considerations for Interpretation of Data. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Rafferty B, Dolgilevich S, Kalachikov S, Morozova I, Ju J, Whittier S, Nowygrod R, Kozarov E. Cultivation of Enterobacter hormaechei from human atherosclerotic tissue. J Atheroscler Thromb 2010; 18:72-81. [PMID: 20972353 DOI: 10.5551/jat.5207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
AIM To determine whether culturable bacterial strains are present in human atheromatous tissue and to investigate their properties using culture, quantitative PCR, metagenomic screening, genomic and biochemical methods. METHODS We analyzed femoral atherosclerotic plaque and five pairs of diseased and healthy arterial tissue for the presence of culturable bacteria using cell cultures and genomic analysis. RESULTS Gram negative aerobic bacilli were cultivated from the plaque tissue. Ribosomal 16S DNA amplification and sequencing identified the isolates as Enterobacter hormaechei. The isolate was resistant to ampicillin, cefazolin, and erythromycin. A circular 10 kb plasmid was isolated from the strain. Antibiotic protection assays of the isolate demonstrated invasive ability in a human monocytic cell line. To extend the study, five matched pairs of diseased and healthy aortic tissue were analyzed via quantitative PCR. Eubacterial 16S rDNA was detected in all specimens, however, E. hormaechei DNA was detected in surprisingly high numbers in two of the diseased tissues only. CONCLUSIONS While it is well documented that inflammation is an important risk factor for vascular pathophysiology, the association of bacteria with atherosclerosis has not been clearly established, in large part due to the inability to isolate live bacteria from atheromatous tissue. This is the first study providing direct evidence of Enterobacter spp. associated with atheromatous tissues. The data suggest that chronic infection with bacteria may be an under-reported etiologic factor in vascular pathogenesis. Importantly, characterization of the clinical isolate supports a model of atherogenesis where systemic dissemination of bacteria to atherosclerotic sites may occur via internalization in phagocytic cells.
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Affiliation(s)
- Brian Rafferty
- Section of Oral and Diagnostic Sciences, College of Dental Medicine, Columbia University Medical Center, New York 10032, USA
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42
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Dubé A, Slater GW. Detrapping particles in gel electrophoresis: A numerical study of different pulsed field sequences. Electrophoresis 2010; 31:3233-46. [DOI: 10.1002/elps.201000158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Goering RV. Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease. INFECTION GENETICS AND EVOLUTION 2010; 10:866-75. [PMID: 20692376 DOI: 10.1016/j.meegid.2010.07.023] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 07/27/2010] [Accepted: 07/29/2010] [Indexed: 11/27/2022]
Abstract
Over the years, approaches to the epidemiological analysis of infectious disease have undergone a remarkable evolutionary transition moving from phenotypic to molecular in nature. As discussed here, the quest for a clearer comparison of genomic relatedness between bacterial clinical isolates has involved four generations of molecular iteration. First generation plasmid analysis gave way to a second generation use of restriction enzymes and probes. This was followed by third generation pulsed field gel electrophoresis (PFGE) and PCR-based methods with movement now to fourth-generation DNA sequence-based approaches. Remarkably, despite (or perhaps because of) its more than 20-year history as a typing method, PFGE has demonstrated exceptional staying power. The reasons for this endurance as well as the pros and cons of PFGE use are examined in this review. In broad context the history and technology behind PFGE are considered. Issues commonly influencing the quality of PFGE data and its analysis are discussed. Specifics regarding the mechanics of DNA preparation, restriction-enzyme digestion, and proper conditions for electrophoresis are detailed and, most importantly for any approach to epidemiological assessment, issues regarding the analysis and interpretation of PFGE data are explored.
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Affiliation(s)
- Richard V Goering
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA.
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44
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Dhindsa M, Heikenfeld J, Kwon S, Park J, Rack PD, Papautsky I. Virtual electrowetting channels: electronic liquid transport with continuous channel functionality. LAB ON A CHIP 2010; 10:832-836. [PMID: 20379566 DOI: 10.1039/b925278a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Reported is a new mechanism for electronic transport of liquid in virtual channels. These virtual channels are formed by application of voltage to an array of polymer posts. The posts are coated with a conducting electrode and hydrophobic dielectric, and thereby capable of electrowetting. Directional channel formation, as well as splitting and merging, is also demonstrated using specific arrangements of posts. The channel dimensions are approximately 20 microm in cross-section, are scalable, and at the threshold for channel formation the minimum transport speed is approximately 1 mm s(-1). The virtual electrowetting channels are further unique as they can retain any channel geometry even in the absence of voltage. With the addition of arrayed voltage controls, the virtual electrowetting channels have the potential to combine the advantages of programmable electrowetting and continuous channel functionality into a single lab-on-chip platform.
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Affiliation(s)
- Manjeet Dhindsa
- Novel Devices Laboratory, Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221, USA
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45
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Li A, Chen X, Ugaz VM. Miniaturized System for Rapid Field Inversion Gel Electrophoresis of DNA with Real-Time Whole-Gel Detection. Anal Chem 2010; 82:1831-7. [DOI: 10.1021/ac902490e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Airong Li
- College of Chemical Engineering, Sichuan University, Chengdu, PR China, and Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843-3122
| | - Xiaojia Chen
- College of Chemical Engineering, Sichuan University, Chengdu, PR China, and Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843-3122
| | - Victor M. Ugaz
- College of Chemical Engineering, Sichuan University, Chengdu, PR China, and Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843-3122
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46
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Wang X, Veerappan V, Cheng C, Jiang X, Allen RD, Dasgupta PK, Liu S. Free Solution Hydrodynamic Separation of DNA Fragments from 75 to 106 000 Base Pairs in A Single Run. J Am Chem Soc 2009; 132:40-1. [DOI: 10.1021/ja909233n] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiayan Wang
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
| | - Vijaykumar Veerappan
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
| | - Chang Cheng
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
| | - Xin Jiang
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
| | - Randy D. Allen
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
| | - Purnendu K. Dasgupta
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, Department of Biochemistry and Molecular Biology 246 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078, and Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019
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Forster RE, Hert DG, Chiesl TN, Fredlake CP, Barron AE. DNA migration mechanism analyses for applications in capillary and microchip electrophoresis. Electrophoresis 2009; 30:2014-24. [PMID: 19582705 DOI: 10.1002/elps.200900264] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In 2009, electrophoretically driven DNA separations in slab gels and capillaries have the sepia tones of an old-fashioned technology in the eyes of many, even while they remain ubiquitously used, fill a unique niche, and arguably have yet to reach their full potential. For comic relief, what is old becomes new again: agarose slab gel separations are used to prepare DNA samples for "next-gen" sequencing platforms (e.g. the Illumina and 454 machines) - dsDNA molecules within a certain size range are "cut out" of a gel and recovered for subsequent "massively parallel" pyrosequencing. In this review, we give a Barron lab perspective on how our comprehension of DNA migration mechanisms in electrophoresis has evolved, since the first reports of DNA separations by CE ( approximately 1989) until now, 20 years later. Fused-silica capillaries and borosilicate glass and plastic microchips quietly offer increasing capacities for fast (and even "ultra-fast"), efficient DNA separations. While the channel-by-channel scaling of both old and new electrophoresis platforms provides key flexibility, it requires each unique DNA sample to be prepared in its own micro or nanovolume. This Achilles' heel of electrophoresis technologies left an opening through which pooled sample, next-gen DNA sequencing technologies rushed. We shall see, over time, whether sharpening understanding of transitions in DNA migration modes in crosslinked gels, nanogel solutions, and uncrosslinked polymer solutions will allow electrophoretic DNA analysis technologies to flower again. Microchannel electrophoresis, after a quiet period of metamorphosis, may emerge sleeker and more powerful, to claim its own important niche applications.
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Affiliation(s)
- Ryan E Forster
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
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Hooberman AL, Westbrook CA. Molecular Diagnosis of the Philadelphia Chromosome in Acute Lymphoblastic Leukemia. Leuk Lymphoma 2009; 1:3-10. [DOI: 10.3109/10428198909042452] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Stellwagen NC, Stellwagen E. Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A 2009; 1216:1917-29. [PMID: 19100556 PMCID: PMC2643323 DOI: 10.1016/j.chroma.2008.11.090] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/24/2008] [Accepted: 11/27/2008] [Indexed: 11/18/2022]
Abstract
DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.
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Affiliation(s)
- Nancy C Stellwagen
- Department of Biochemistry, University of Iowa, 4403 Bowen Science Building, Iowa City, IA 52242, USA.
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Nassonova ES. Pulsed field gel electrophoresis: Theory, instruments and application. ACTA ACUST UNITED AC 2008. [DOI: 10.1134/s1990519x08060011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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