1
|
Cunha EN, de Souza MFB, Lanza DCF, Lima JPMS. A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum. PLoS One 2020; 15:e0240536. [PMID: 33057447 PMCID: PMC7561130 DOI: 10.1371/journal.pone.0240536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid detection by electrophoresis is still a quick and accessible technique for many diagnosis methods, primarily at research laboratories or at the point of care units. Standard protocols detect DNA/RNA molecules through specific bound chemical dyes using a UV-transilluminator or UV-photo documentation system. However, the acquisition costs and availability of these devices, mainly the ones with photography and internet connection capabilities, can be prohibitive, especially in developing countries public health units. Also, ultraviolet radiation is a common additional risk factor to professionals that use electrophoresis-based nucleic acid detection. With that in mind, this work describes the development of a low-cost DNA/RNA detection smart system capable of obtaining qualitative and semi-quantitative data from gel analysis. The proposed device explores the visible light absorption range of commonly used DNA/RNA dyes using readily available parts, and simple manufacturing processes, such as light-emitting diodes (LEDs) and 3D impression. By applying IoT techniques, our system covers a wide range of color spectrum in order to detect bands from various commercially used dyes, using Bluetooth communication and a smartphone for hardware control, image capturing, and sharing. The project also enables process scalability and has low manufacturing and maintenance costs. The use of LEDs at the visible spectrum can achieve very reproducible images, providing a high potential for rapid and point-of-care diagnostics as well as applications in several fields such as healthcare, agriculture, and aquaculture.
Collapse
Affiliation(s)
- Eduardo Nogueira Cunha
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
| | - Maria Fernanda Bezerra de Souza
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - Daniel Carlos Ferreira Lanza
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - João Paulo Matos Santos Lima
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Natal, Brazil
- * E-mail:
| |
Collapse
|
2
|
Professor Volodymyr Oleksiiovych Shlyakhovenko (on the 80th birth anniversary). Exp Oncol 2018; 40:345. [PMID: 30593753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In September 2018, Professor Volodymyr Oleksiiovych Shlyakhovenko, well-known Ukrainian scientist in the field of cancer biochemistry, celebrated his 80th anniversary.
Collapse
|
3
|
Montague TG, Almansoori A, Gleason EJ, Copeland DS, Foley K, Kraves S, Alvarez Saavedra E. Gene expression studies using a miniaturized thermal cycler system on board the International Space Station. PLoS One 2018; 13:e0205852. [PMID: 30379894 PMCID: PMC6209215 DOI: 10.1371/journal.pone.0205852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/02/2018] [Indexed: 02/02/2023] Open
Abstract
The distance and duration of human spaceflight missions is set to markedly increase over the coming decade as we prepare to send astronauts to Mars. However, the health impact of long-term exposure to cosmic radiation and microgravity is not fully understood. In order to identify the molecular mechanisms underpinning the effects of space travel on human health, we must develop the capacity to monitor changes in gene expression and DNA integrity in space. Here, we report successful implementation of three molecular biology procedures on board the International Space Station (ISS) using a miniaturized thermal cycler system and C. elegans as a model organism: first, DNA extraction–the initial step for any type of DNA analysis; second, reverse transcription of RNA to generate complementary DNA (cDNA); and third, the subsequent semi-quantitative PCR amplification of cDNA to analyze gene expression changes in space. These molecular procedures represent a significant expansion of the budding molecular biology capabilities of the ISS and will permit more complex analyses of space-induced genetic changes during spaceflight missions aboard the ISS and beyond.
Collapse
Affiliation(s)
- Tessa G. Montague
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | | | | | - Kevin Foley
- Boeing, Houston, TX, United States of America
| | | | | |
Collapse
|
4
|
Abstract
The comet assay (single cell gel electrophoresis) is a sensitive, versatile method for detecting DNA damage in eukaryotic cells. The traditional comet assay format has 1 or 2 gels on a microscope slide, 1 sample per slide, and there is a limit of 40 gels per experiment given the size of a typical electrophoresis tank. To increase throughput, we have designed and tested a system with 12 minigels on one slide, allowing analysis of up to 12 times more samples in one electrophoresis run. The novel comet assay format compares well with the traditional technology. The various steps are suitable for further automation, and the formats can be adapted to fully automated scoring. The new procedures save time at all stages as fewer slides are handled, and the amounts of reagents needed are reduced significantly. This format is particularly useful for testing of numerous genotoxic agents and nanomaterials at different concentrations and on different types of cells; simultaneous analysis of different lesions using a range of enzymes; and analysis of cell extracts for DNA repair activity.
Collapse
Affiliation(s)
| | - Andrew Collins
- NorGenoTech AS, Totenvegen 2049, 2848, Skreia, Norway
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
5
|
Fomina TV, Ostrovskiĭ OV, Verovskiĭ VE. [The comparative analysis of electrophoretic fractionating of blood serum proteins in diagnostics of multiple plasma cell myeloma]. Klin Lab Diagn 2012:16-18. [PMID: 22624456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The choice of technology of electrophoretic fractionating of blood serum proteins is determined, besides the analytical characteristics, by its economic component. The electrophoresis technologies developed by the R&D production facility "Astra" (Russia) and the firm "PZ Cormay S.A." (Poland) are compared from a viewpoint of applicability in routine laboratory, practice and diagnostics of multiple plasma cell myeloma in particular. It is established that under the comparable economic, "consumer" and analytic characteristics of technologies in the diagnostic process the application of the technology in agarose gel ("PZ Cormay S.A.") is more preferable.
Collapse
|
6
|
Arif IA, Khan HA, Shobrak M, Al Homaidan AA, Al Sadoon M, Al Farhan AH, Bahkali AH. Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx. Genet Mol Res 2010; 9:259-65. [PMID: 20198581 DOI: 10.4238/vol9-1gmr714] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx. All the alleles of different loci exhibited good peak resolutions and hence were clearly identified. Moreover, none of the stutter peaks impaired the recognition or differentiation between homozygote and heterozygote. Our findings suggest that correct identification of alleles in the presence of co-amplified nonspecific fragments is important for reliable interpretation of microsatellite data.
Collapse
Affiliation(s)
- I A Arif
- Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair for Environment and Wildlife, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
Agarose gel electrophoresis is by far the most widely used method for characterizing the topological state of DNA molecules. Although this technique has been used for more than 30 years, the physical mechanism underlying the resolution of topological states remains poorly understood. However, electrophoretic methods remain the most robust and precise techniques for determining the local unwinding of DNA induced by the binding of proteins and small-molecule ligands, analyzing conformational transitions in duplex DNA, measuring changes in helical repeat that accompany shifts in environmental conditions, and characterizing knotting and linking in duplex DNA.
Collapse
Affiliation(s)
- Stephen D Levene
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Dallas, TX, USA
| |
Collapse
|
8
|
Abstract
A method for the blotting and immobilizing of several nonsulfated and sulfated complex polysaccharides on membranes made hydrophilic and positively charged by cationic detergent after their separation by conventional agarose gel electrophoresis is illustrated. This new approach to the study of glycosaminoglycans (GAGs) utilizes the capacity of agarose gel electrophoresis to separate single species of polysaccharides from mixtures and the membrane technology for further preparative and analytical uses.Nitrocellulose membranes are derivatized with the cationic detergent cetylpyridinium chloride and mixtures of GAGs are capillary blotted after their separation in agarose gel electrophoresis. Single purified species of variously sulfated polysaccharides are transferred on derivatized membranes with an efficiency of 100% and stained with alcian blue (irreversible staining) and toluidine blue (reversible staining). This enables a lower amount limit of detection of 0.1 microg. Nonsulfated polyanions, for example hyaluronic acid, may also be transferred to membranes with a limit of detection of approximately 0.1-0.5 microg after irreversible or reversible staining. The membranes may be stained with reversible staining and the same lanes are used for immunological detection or other applications.
Collapse
Affiliation(s)
- Nicola Volpi
- Department of Biologia Animale, University of Modena and Reggio Emilia, Via Campi 213/d, 41100, Modena, Italy.
| | | |
Collapse
|
9
|
Larsson A, Hansson LO. Comparison between a second generation automated multicapillary electrophoresis system with an automated agarose gel electrophoresis system for the detection of M-components. Ups J Med Sci 2008; 113:65-72. [PMID: 18521800 DOI: 10.3109/2000-1967-219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the last decade, capillary electrophoresis (CE) has emerged as an interesting alternative to traditional analysis of serum, plasma and urine proteins by agarose gel electrophoresis. Initially there was a considerable difference in resolution between the two methods but the quality of CE has improved significantly. We thus wanted to evaluate a second generation of automated multicapillary instruments (Capillarys, Sebia, Paris, France) and the high resolution (HR) buffer for serum or plasma protein analysis with an automated agarose gel electrophoresis system for the detection of M-components. The comparison between the two systems was performed with patients samples with and without M-components. The comparison included 76 serum samples with M-components > 1 g/L. There was a total agreement between the two methods for detection of these M-components. When studying samples containing oligoclonal bands/small M-components, there were differences between the two systems. The capillary electrophoresis system detected a slightly higher number of samples with oligoclonal bands but the two systems found oligoclonal bands in different samples. When looking at resolution, the agarose gel electrophoresis system yielded a slightly better resolution in the alpha and beta regions, but it required an experienced interpreter to be able to benefit from the increased resolution. The capillary electrophoresis has shorter turn-around times and bar-code reader that allows positive sample identification. The Capillarys in combination with HR buffer gives better resolution of the alpha and beta regions than the same instrument with the beta1-beta2+ buffer or the Paragon CZE2000 (Beckman) which was the first generation of capillary electrophoresis systems.
Collapse
Affiliation(s)
- Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, University Hospital, Uppsala, Sweden.
| | | |
Collapse
|
10
|
Abstract
Researchers in molecular biology spend a significant amount of time tending to the staining and destaining of electrophoresis gels. Here we describe a simple system, costing approximately $100 and taking approximately 1 h to assemble, that automates standard nucleic acid and protein gel staining protocols. Staining is done in a tray or, with DNA gels, in the electrophoresis chamber itself following automatic detection of the voltage drop. Miniature pumps controlled by a microcontroller chip exchange the necessary solutions at programmed time intervals. We demonstrate efficient and highly reproducible ethidium bromide and methylene blue staining of DNA in agarose gels and Coomassie blue and silver staining of proteins in polyacrylamide gels.
Collapse
Affiliation(s)
- Dorian M Raymer
- Department of Physics, University of California, La Jolla, CA 92093, USA
| | | |
Collapse
|
11
|
Brüchert W, Helfrich A, Zinn N, Klimach T, Breckheimer M, Chen H, Lai S, Hoffmann T, Bettmer J. Gel Electrophoresis Coupled to Inductively Coupled Plasma−Mass Spectrometry Using Species-Specific Isotope Dilution for Iodide and Iodate Determination in Aerosols. Anal Chem 2007; 79:1714-9. [PMID: 17297978 DOI: 10.1021/ac061767y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we present an online coupling of gel electrophoresis (GE) and inductively coupled plasma-mass spectrometry (ICP-MS) for the determination of iodine species (iodide and iodate) in liquid (seawater) and aerosol samples. For the first time, this approach is applied to the analysis of small molecules, and initial systematic investigations revealed that the migration behavior as well as the detection sensitivity strongly depends on the matrix (e.g., high concentrations of chloride). These effects could consequently affect the accuracy of analytical results, so that they need to be considered for the analysis of real samples. The technique used for quantification is species-specific isotope dilution analysis (ssIDA), which is a matrix-independent calibration method under certain conditions. We demonstrate that the use of 129I-enriched iodide and iodate allows the correction of the impact of the matrix on both, the electrophoretic migration and the detection sensitivity of the ICP-MS. After optimization, this coupling offers a novel and alternative method in the analysis of iodine compounds in various matrices. Here, we demonstrate the analytical capability of the technique for the chemical characterization of marine aerosols. The results show the presence of iodide and iodate at the ng m(-3) and sub-ng m(-3) level in the investigated aerosol samples, which were taken at the coastal research station in Mace Head, Ireland. These results are in good agreement with other recent studies, which demonstrated that the iodine chemistry in the marine atmosphere is only poorly understood. In addition to iodide and iodate, another iodine compound could be separated and detected in certain samples with high total iodine concentrations and was identified as elemental iodine, probably in form of triiodide, by peak matching. However, it may arise from an artifact during sample preparation.
Collapse
Affiliation(s)
- Wolfram Brüchert
- University of Mainz, Institute of Inorganic Chemistry and Analytical Chemistry, Duesbergweg 10-14, D-55099 Mainz, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Porch TG, Erpelding JE. Low-cost conversion of the Polaroid MD-4 land camera to a digital gel documentation system. J Biochem Biophys Methods 2006; 67:1-5. [PMID: 16472866 DOI: 10.1016/j.jbbm.2005.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 11/15/2005] [Accepted: 12/15/2005] [Indexed: 11/15/2022]
Abstract
A simple, inexpensive design is presented for the rapid conversion of the popular MD-4 Polaroid land camera to a high quality digital gel documentation system. Images of ethidium bromide stained DNA gels captured using the digital system were compared to images captured on Polaroid instant film. Resolution and sensitivity were enhanced using the digital system. In addition to the low cost and superior image quality of the digital system, there is also the added convenience of real-time image viewing through the swivel LCD of the digital camera, wide flexibility of gel sizes, accurate automatic focusing, variable image resolution, and consistent ease of use and quality. Images can be directly imported to a computer by using the USB port on the digital camera, further enhancing the potential of the digital system for documentation, analysis, and archiving. The system is appropriate for use as a start-up gel documentation system and for routine gel analysis.
Collapse
Affiliation(s)
- Timothy G Porch
- USDA, Agricultural Research Service, Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Ave., Suite 201, Mayaguez, Puerto Rico, 00680-5470.
| | | |
Collapse
|
13
|
Abstract
We describe a novel approach to generate dynamic pH gradients suited to fractionate or purify samples of biomolecules or particles such as proteins and viruses in tiny volumes. The method combines diffusion and electromigration between micro-scaled channels embedded in hydrogel. For the used geometry and in accordance with numerical calculations the gel-channel system reaches a tuneable, steady-state pH gradient after a few minutes. For quantification of experimentally generated pH-profiles, the concentration independent extinction ratio of phenol red at two wavelengths is used. The proposed electrophoretic flow-cell is simple and flexible since no Immobilines are required to establish the pH gradient.
Collapse
Affiliation(s)
- Rolf Hagedorn
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.
| | | | | | | | | | | |
Collapse
|
14
|
Brody JR, Calhoun ES, Gallmeier E, Creavalle TD, Kern SE. Ultra-fast high-resolution agarose electrophoresis of DNA and RNA using low-molarity conductive media. Biotechniques 2005; 37:598, 600, 602. [PMID: 15517972 DOI: 10.2144/04374st04] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Current DNA electrophoretic solutions employ high ionic concentrations and require long electrophoretic run times. Here we demonstrate that high and low molecular weight double-stranded DNA, single-stranded DNA (ssDNA), and RNA can be separated rapidly in agarose-based low-molarity conductive media. Separation of small DNA fragments was optimized by substituting 1-mM solutions of alkali metals or a nonbiological amine that distributed voltage with a minute current. These ultra-dilute solutions can separate DNA at least 15-fold faster Low-molarity media at 5-10 mM adequately separated RNA and larger DNA fragments as well. These novel media reduce the Joule heating of the electrophoretic system and allow for easy-to-use, ultra-fast separation of DNA fragments.
Collapse
Affiliation(s)
- Jonathan R Brody
- The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
| | | | | | | | | |
Collapse
|
15
|
Affiliation(s)
- R Hodge
- Department of Botany, University of Leicester, UK
| |
Collapse
|
16
|
Cole KD. An apparatus for electrophoretic capture and recovery of circular DNA in thin layers. Biotechnol Appl Biochem 2003; 37:251-7. [PMID: 12670301 DOI: 10.1042/ba20030003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2003] [Revised: 03/28/2003] [Accepted: 04/01/2003] [Indexed: 11/17/2022]
Abstract
An apparatus was designed for the electrophoretic capture and recovery of circular DNA in thin layers (membranes). Rapid separations were done by the use of a low-conductivity buffer and high electric field strengths. Two methods that specifically retain circular DNA in the membranes were demonstrated using the supercoiled and open circular forms of two plasmids with sizes of 4.4 and 13 kbp. Electrophoretic trapping (by an impalement mechanism) in agarose-gel-filled membranes used electric field strength to immobilize circular DNA in the membranes. The other method of capture utilized the greatly reduced electrophoretic mobility of circular DNA in membranes composed of agarose and the linear polymer hydroxyethylcellulose. The reduction in electrophoretic mobility was not dependent upon the electric field strength, distinguishing it from electrophoretic trapping. Trapping of circular DNA in the membranes followed by size analysis using agarose-gel electrophoresis could be used as a two-dimensional separation tool for the analysis of complex mixtures. Captured DNA was recovered by two methods: (i). centrifugation of membranes made with low-melting-point agarose resulted in a gel slurry that could be heated to release the DNA; (ii). electroelution of the membranes. Electroelution was done by using an electrode that was isolated from the DNA by a 'barrier' membrane. A non-trapping electric field was used to reverse the DNA out of the membrane into a small volume of buffer above the membrane.
Collapse
Affiliation(s)
- Kenneth D Cole
- Bioprocess Engineering Group, Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| |
Collapse
|
17
|
Abstract
Capillary zone electrophoresis (CZE) of serum proteins is increasingly gaining impact in clinical laboratories. In this report, we evaluate automated capillary zone electrophoresis by Capillarys (Sebia, France). Within-run and between-run imprecision for the five electrophoretic fractions was <2% and <6%, respectively. Data obtained with Capillarys correlated with results obtained with agarose gel electrophoresis and Paragon CZE 2000 (Beckman Coulter, USA). Analysis of serum obtained from patients with inflammation, nephrotic syndrome, bisalbuminemia, and alpha1-antitrypsin deficiency revealed that Capillarys was able to detect these abnormalities. Two hundred thirty eight samples were analyzed by agarose gel electrophoresis, Capillarys, capillary electrophoresis using Paragon CZE 2000 system, and immunofixation. Sample selection was based on the presence of a disturbed morphology (e.g., spike) of the protein profile or hypogammaglobulinemia on agarose gel electrophoresis and/or Capillarys. Immunofixation revealed the presence of a monoclonal protein, oligoclonal bands, polyclonal pattern, and a normal profile in, respectively, 89, 66, 19, and 64 samples. With Capillarys, Paragon, and agarose gel electrophoresis, a spike and/or disturbed morphology of the profile was found in 222, 182, and 180 samples, respectively. In these samples, immunofixation was negative in 73 (33%), 46 (25%), and 39 (22%) samples, respectively. These data indicate that Capillarys has a lower specificity than agarose gel electrophoresis and Paragon 2000. Of the 89 samples with a monoclonal protein, Capillarys, Paragon, and agarose gel electrophoresis failed to detect, respectively, three, three, and one monoclonal protein(s). Interferences by radio-opaque agents, complement degradation products, fibrinogen, and triglycerides are described. In conclusion, automated capillary zone electrophoresis with Capillarys provides for reproducible, rapid, and reliable serum electrophoresis.
Collapse
Affiliation(s)
- Xavier Bossuyt
- Laboratory Medicine, Immunology, University Hospital Leuven, Leuven, Belgium.
| | | | | | | | | | | | | |
Collapse
|
18
|
Thompson J, Pugh T, Guggenheimer K, Safarpour A, Christie A, Pel J, Chow S, Marziali A. Facilitated loading of horizontal gels using a capillary comb loader. Biotechniques 2003; 34:814-8. [PMID: 12703306 DOI: 10.2144/03344rr03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Manual loading of samples into horizontal gels, such as the agarose gels commonly used for DNA fragment sizing and quantification, is laborious and prone to errors. Manual-loading times for highthroughput gels can reach 10 min/gel, and human error can result in incorrect identification of samples because of reverse loading or other errors in the loading process. To reduce gel-loading times and to improve reliability, a novel comb has been developed that uses glass capillaries and hydrostatic pressure to simplify sample loading from microplates. Accurate sample metering is ensured by the uniform length and volume of the capillaries. The loaded comb is placed in the gel boat over a pre-cast agarose gel, and buffer is added to a reservoir at the top of the comb. Once the buffer rises over the ends of the capillaries, the samples are pushed into the wells by hydrostatic pressure. This technique was successfully demonstrated for a 24-lane comb. This capillary comb loader reduces loading time, maintains well-to-well uniformity, and retains the same geometry and appearance of manually loaded bands, making this loading method compatible with existing downstream processes and software for subsequent analysis of the gel image.
Collapse
Affiliation(s)
- J Thompson
- University of British Columbia, Vancouver, BC, Canada
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Smejkal GB, Shainoff JR, Kottke-Marchant KM. Rapid high-resolution electrophoresis of multimeric von Willebrand Factor using a thermopiloted gel apparatus. Electrophoresis 2003; 24:582-7. [PMID: 12601725 DOI: 10.1002/elps.200390068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rapid and highly reproducible nonreducing agarose gel electrophoresis (NRAGE) of von Willebrand Factor (vWF) multimers was performed using a thermostated minigel apparatus that monitors and precisely controls internal gel temperature. The substitution of lithium dodecyl sulfate (LiDS) for sodium dodecyl sulfate (SDS) allowed electrophoresis to be performed below the 16 degrees C Krafft point of SDS and facilitated NRAGE of vWF over the entire range of 0-35 degrees C. Internal gel temperature was regulated by a thermocouple probe inserted directly into the gel during electrophoresis which interfaced with a thermopilot that continually measures and adjusts temperature to within +/- 0.5 degrees C. At 10 degrees C operative temperature, NRAGE at 1.5% agarose concentration was completed in 20 min at 250 V. Electrophoresis could be performed in only 10 min at 500 V, but at such high voltages, localized temperature fluctuations as much as 6 degrees C resulted in perturbation of banding patterns in those vicinities. In the optimized method, both high molecular weight multimers and proteolytic fragments of vWF were separable suggesting clinical applicability of this system for the diagnosis of von Willebrand Disease and thrombotic thrombocytopenic purpura.
Collapse
Affiliation(s)
- Gary B Smejkal
- Cleveland Clinic Foundation, Department of Clinical Pathology, Cleveland, OH, USA.
| | | | | |
Collapse
|
20
|
Spielmann T. Southern blotting of parasite DNA. Methods Mol Med 2003; 72:165-75. [PMID: 12125114 DOI: 10.1385/1-59259-271-6:165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
21
|
Abstract
We demonstrate a versatile microfabricated electrophoresis platform, incorporating arrays of integrated on-chip electrodes, heaters, and temperature sensors. This design allows a range of different sieving gels to be used within the same device to perform separations involving both single- and double-stranded DNA over distances on the order of 1 cm. We use this device to compare linear and cross-linked polyacrylamide, agarose, and thermo-reversible Pluronic-F127 gels on the basis of gel casting ease, reusability, and overall separation performance using a 100 base pair double-stranded DNA ladder as a standard sample. While cross-linked polyacrylamide matrices provide consistently high-quality separations in our system over a wide range of DNA fragment sizes, Pluronic gels also offer compelling advantages in terms of the ability to remove and reload the gel. Agarose gels offer good separation performance, however, additional care must be exercised to ensure consistent gel properties as a consequence of the need for elevated gel loading temperatures. We also demonstrate the use of denaturing cross-linked polyacrylamide gels at concentrations up to 19% to separate single-stranded DNA fragments ranging in size from 18 to 400 bases in length. Primers differing by 4 bases at a read length of 30 bases can be separated with a resolution of 0.9-1.0 in under 20 min. This level of performance is sufficient to conduct a variety of genotyping assays including the rapid detection of single nucleotide polymorphisms (SNPs) in a microfabricated platform. The ability to use a single microelectrophoresis system to satisfy a wide range of separation applications offers molecular biologists an unprecedented level of flexibility in a portable and inexpensive format.
Collapse
Affiliation(s)
- Victor M Ugaz
- Department of Chemical Engineering, The University of Michigan, Ann Arbor, 48109-2136, USA
| | | | | | | | | |
Collapse
|
22
|
Affiliation(s)
- Heather E Lorimer
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, USA
| |
Collapse
|
23
|
Khandurina J, Legg E, Wang X, Guttman A. Automated agarose gel electrophoresis of dsDNA fragments on a commercial DNA sequencer. Biotechniques 2002; 33:1008, 1010, 1012 passim. [PMID: 12449376 DOI: 10.2144/02335bm08] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
24
|
Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu AL, Coope R, Marziali A, Schein J, Jones S, Marra M. Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer. Biotechniques 2002; 33:532-4, 536, 538-9. [PMID: 12238763 DOI: 10.2144/02333st03] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We are investigating approaches to increase DNA sequencing quality. Since a majorfactor in sequence generation is the cost of reagents and sample preparations, we have developed and optimized methods to sequence directly plasmid DNA isolated from alkaline lysis preparations. These methods remove the costly PCR and post-sequencing purification steps but can result in low sequence quality when using standard resuspension protocols on some sequencing platforms. This work outlines a simple, robust, and inexpensive resuspension protocol for DNA sequencing to correct this shortcoming. Resuspending the sequenced products in agarose before electrophoresis results in a substantial and reproducible increase in sequence quality and read length over resuspension in deionized water and has allowed us to use the aforementioned sample preparation methods to cut considerably the overall sequencing costs without sacrificing sequence quality. We demonstrate that resuspension of unpurified sequence products generated from template DNA isolated by a modified alkaline lysis technique in low concentrations of agarose yields a 384% improvement in sequence quality compared to resuspension in deionized water. Utilizing this protocol, we have produced more than 74,000 high-quality, long-read-length sequences from plasmid DNA template on the MegaBACET 1000 platform.
Collapse
Affiliation(s)
- G Vatcher
- Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Affiliation(s)
- J D San Antonio
- Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | | |
Collapse
|
26
|
Abstract
In this paper, micromachined pipette arrays (MPAs) and microcombs were studied as a means of enabling high lane density gel electrophoresis. The MPA provide a miniaturized format to interface sub-microliter volumes of samples between macroscale sample preparation formats and microscale biochemical analysis systems. The microcombs provide a means of creating sample loading wells in the gel material on the same center-to-center spacing as the MPAs. Together, the two micromachined instruments provide an alternative to current combs and pipetting technologies used for creating sample loading wells and sample delivery in gel electrophoresis systems. Using three designs for the microcomb-MPA pair, center-to-center spacings of 1.0 mm, 500 microm, and 250 microm are studied. The results demonstrate an approximate 10-fold increase in lane density and a 10-fold reduction in sample size from 5 microL to 500 pL. As a result, the number of theoretical plates has increased 2.5-fold, while system resolution has increased 1.5-fold over the conventional agarose gel systems. An examination of changes in resolution across the width of individual separation lanes in both systems revealed dependence in the case of the conventional gels and no dependence for the gels loaded with the micromachined instrumentation.
Collapse
Affiliation(s)
- I Papautsky
- Department of Electrical and Computer Engineering and Computer Science, University of Cincinnati, OH 45221, USA.
| | | | | | | |
Collapse
|
27
|
Deforce DL, Van den Eeckhout EG. Analysis of DNA damage using capillary zone electrophoresis and electrospray mass spectrometry. Methods Mol Biol 2001; 162:429-41. [PMID: 11217353 DOI: 10.1385/1-59259-055-1:429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
MESH Headings
- Animals
- Cattle
- Chromatography, High Pressure Liquid/instrumentation
- Chromatography, High Pressure Liquid/methods
- DNA/analysis
- DNA/drug effects
- DNA Damage
- Electrophoresis, Agar Gel/instrumentation
- Electrophoresis, Agar Gel/methods
- Electrophoresis, Capillary/instrumentation
- Electrophoresis, Capillary/methods
- Equipment Design
- Ethidium
- Indicators and Reagents
- Phenyl Ethers/analysis
- Phenyl Ethers/toxicity
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
Collapse
Affiliation(s)
- D L Deforce
- Laboratory for Pharmaceutical Biotechnology, University of Ghent, Ghent, Belgium
| | | |
Collapse
|
28
|
Karge WH, Schaefer EJ, Ordovas JM. Quantification of mRNA by polymerase chain reaction (PCR) using an internal standard and a nonradioactive detection method. Methods Mol Biol 2001; 110:43-61. [PMID: 9918038 DOI: 10.1385/1-59259-582-0:43] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- W H Karge
- US Army Natick Laboratories, Natick, MA, USA
| | | | | |
Collapse
|
29
|
Abstract
DNA damages that can be converted to single- or double strand breaks can be quantified by separating DNA by gel electrophoresis and obtaining a quantitative image of the resulting distribution of DNA in the gel. We review the theory of this method and discuss its implementation, including the charge-coupled device (CCD) camera systems we developed to acquire images of fluorophore labeled DNA.
Collapse
Affiliation(s)
- J C Sutherland
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
| | | | | | | | | |
Collapse
|
30
|
Caudie C, Allausen O, Bancel J. [Detection of oligoclonal IgG bands in in cerebrospinal fluid by immunofixation after electrophoretic migration in the automated Hydrasys sebia system]]. Ann Biol Clin (Paris) 2000; 58:376-9. [PMID: 10846245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- C Caudie
- Laboratoire d'Immunologie et de neuro-immunologie, Hôpital neurologique, 59, boulevard Pinel, 69003 Lyon
| | | | | |
Collapse
|
31
|
Abstract
A technique has been developed for high lane density loading of small-volume DNA samples in a horizontal agarose gel. This technique has been investigated with a simple hand-held tool that is made to couple to sample output from a new capillary-based sample automation system. The approach consists of piercing the gel with pressurized sample capillaries and relieving the pressure shortly before withdrawal. The pressurization prevents the capillary from aspirating the gel buffer and keeps the sample at the tip of the capillary, so that it may be sucked into the gel during withdrawal. This method is shown to be adequate for a wide range of DNA ladders and PCR-based screening. In addition to allowing smaller lanes and a higher lane density than is achievable with traditional well-forming techniques, it relaxes the need for well formation and the alignment of the sample loader with those wells, providing an easy, efficient means of loading agarose gels.
Collapse
Affiliation(s)
- H T Evensen
- University of Washington, Seattle 98195-2500, USA
| | | | | | | |
Collapse
|
32
|
Sutherland BM, Bennett PV, Sutherland JC. DNA damage quantitation by alkaline gel electrophoresis. Methods Mol Biol 1999; 113:183-202. [PMID: 10443421 DOI: 10.1385/1-59259-675-4:183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- B M Sutherland
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | | | | |
Collapse
|
33
|
Darzynkiewicz Z, Juan G. Selective extraction of fragmented DNA from apoptotic cells for analysis by gel electrophoresis and identification of apoptotic cells by flow cytometry. Methods Mol Biol 1999; 113:599-605. [PMID: 10443455 DOI: 10.1385/1-59259-675-4:599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- Z Darzynkiewicz
- Cancer Research Institute, New York Medical College, Elmsford, USA
| | | |
Collapse
|
34
|
Affiliation(s)
- G Speit
- Abteilung Medizinische Genetik, Universitat Ulm, Germany
| | | |
Collapse
|
35
|
Abstract
The effect of gelation conditions on the structure and resolving properties of agarose-based DNA sequencing gels were studied. Gels that were formed by rapid cooling gave separation patterns with sharp, well-defined bands, and resolved base repeats that were not separated on gels which were allowed to cool slowly. Analyses by electron microscopy indicated that the rapidly cooled gels have a homogeneous pore structure with a smaller average pore size than gels that were cooled slowly. The two types of gels also differ in optical clarity, and have significant differences in their melting characteristics as measured by differential scanning calorimetry.
Collapse
Affiliation(s)
- N Kusukawa
- FMC BioProducts, Rockland, ME 04841, USA.
| | | | | |
Collapse
|
36
|
Abstract
A method and apparatus for the detection and quantification of large fragments of unlabelled nucleic acids in agarose gels is presented. The technique is based on ultraviolet (UV) absorption by nucleotides. A deuterium source illuminates individual sample lanes of an electrophoresis gel via an array of optical fibres. As DNA bands pass through the illuminated region of the gel the amount of UV light transmitted is reduced because of absorption by the DNA. During electrophoresis the regions of DNA are detected on-line using a UV-sensitive charge coupled device (CCD). As the absorption coefficient is proportional to the mass of DNA the technique is inherently quantitative. The mass of DNA in a region of the gel is approximately proportional to the integrated signal in the corresponding section of the CCD image. This system currently has a detection limit of less than 1.25 ng compared with 2-10 ng for the most popular conventional technique, ethidium bromide (EtBr) staining. In addition the DNA sample remains in its native state. The removal of the carcinogenic dye from the detection procedure greatly reduces associated biological hazards.
Collapse
Affiliation(s)
- A R Mahon
- Joint Department of Physics, Royal Marsden Hospital and Institute of Cancer Reserarch, Sutton, Surrey, UK
| | | | | | | |
Collapse
|
37
|
Abstract
Continuous agarose beds (monoliths) were prepared by casting agarose emulsions designed to generate superporous agarose. The gel structures obtained were transected by superpores (diameters could be varied in the range 20-200 microns) through which liquids could be pumped. The pore structure and the basic properties of the continuous gel were investigated by microscopy and size exclusion chromatography. The chromatographic behaviour was approximately the same as for beds packed with homogeneous agarose beads with a particle diameter equivalent to the distance between the superpores. In one application, the superporous continuous agarose bed was derivatized with a NAD+ analogue and used in the affinity purification of bovine lactate dehydrogenase from a crude extract. In another application, a new superporous composite gel material was prepared by adding hydroxyapatite particles to the agarose phase. The composite bed was used to separate a protein mixture by hydroxyapatite chromatography. In a third application, the continuous superporous agarose material was used as an electrophoresis gel. Here, a water-immiscible organic liquid was pumped through the superpores to dissipate the joule heat evolved, thus allowing high current densities.
Collapse
Affiliation(s)
- P E Gustavsson
- Department of Pure and Applied Biochemistry, Lund University, Sweden
| | | |
Collapse
|
38
|
Affiliation(s)
- E Hurt-Camejo
- Wallenberg Laboratory for Cardiovascular Research, Sahlgrenska University Hospital, University of Gothenburg, Sweden
| | | | | |
Collapse
|
39
|
Affiliation(s)
- J M Ordovas
- Lipid Metabolism Laboratory, JM-USDA-Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| |
Collapse
|
40
|
Ogura M, Agata Y, Watanabe K, McCormick RM, Hamaguchi Y, Aso Y, Mitsuhashi M. RNA chip: quality assessment of RNA by microchannel linear gel electrophoresis in injection-molded plastic chips. Clin Chem 1998; 44:2249-55. [PMID: 9799750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Two major components of rRNA (18S and 28S rRNA) were separated by electrophoresis in injection-molded acrylic chips with a microchannel 100 microm in width, 40 microm in depth, and with 1 cm of separation distance. Microchannels were filled with 4 g/L hydroxypropylmethylcellulose as sieving polymer and 5 mg/L ethidium bromide for RNA staining. The fluorescent signals were detected by a fluorescent microscope equipped with a photometer and 590 nm emission filter. The assay is rapid (<3 min), reproducible, RNase-free, and requires only 1-2 microL of sample. The detection limit was approximately 10 mg/L (10 ng/microL), 100-fold lower than that for conventional agarose gel electrophoresis. Because only 0.1 nL of the loaded sample was used for electrophoresis, the detectable peaks of rRNA in the separation were derived from less RNA than in a single cell. Because the quality of RNA is critical for RNA-related diagnostic tests, disposable plastic chips will be useful for quality assessment of RNA.
Collapse
Affiliation(s)
- M Ogura
- Hitachi Chemical Research Center, Irvine, CA 92612, USA
| | | | | | | | | | | | | |
Collapse
|
41
|
Zakharov SF, Kwok SH, Sokoloff H, Chang HT, Radko SP, Chrambach A. The band areas of proteins determined by fluorescent scanning in the commercial automated gel electrophoresis apparatus. Electrophoresis 1998; 19:1625-30. [PMID: 9719537 DOI: 10.1002/elps.1150191018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An automated gel electrophoresis apparatus, recently available commercially, allows one to follow the band during electrophoresis in real time, and lends itself therefore to an evaluation of bandwidth as a function of migration time (the dispersion coefficient), resolution and band shape. These determinations assume the constancy of band area with migration time and at various gel concentrations. The purpose of the present study was to verify these assumptions. Representative proteins and sodium dodecyl sulfate (SDS)-proteins, either natively fluorescent or fluorescein carboxylate labeled, were found to exhibit band areas which approach constancy as a function of migration time in both agarose and polyacrylamide gel electrophoresis, provided that (i) the protein concentration under the band was low enough to obviate self-quenching of fluorescence; (ii) the separation of the protein of interest from contaminants had progressed sufficiently during the time at which band areas were measured; (iii) the baseline under the peak was sufficiently well defined. However, band areas decrease with increasing gel concentration. Protein peaks exhibited leading and trailing tails. The ratio of the combined tail area to total area appeared to be near-constant at varying migration times. However, that ratio increases with increasing gel concentration. The tail area does not appear to be an artifact of fluorometric detection since it is reproduced upon fluorimetric analysis of the protein eluted from gel slices after electrophoresis. However, it may be due to photochemical destruction under the conditions of repetitive fluorometric peak detection.
Collapse
Affiliation(s)
- S F Zakharov
- Section on Macromolecular Analysis, Laboratory of Cellular and Molecular Biophysics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | |
Collapse
|
42
|
Affiliation(s)
- J M Thomson
- Dept. of Poultry Science, University of Georgia, Athens 30602-2772, USA
| | | |
Collapse
|
43
|
Tormey WP. Low concentration monoclonal and oligoclonal bands in serum and urine using the Sebia Hydragel Protein Electrophoresis System. Clin Chem Lab Med 1998; 36:253-4. [PMID: 9638353 DOI: 10.1515/cclm.1998.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
44
|
Affiliation(s)
- C P Phillips
- Department of Haematology, St. Bartholomew's, Royal London School of Medicine and Dentistry, London, UK
| | | | | |
Collapse
|
45
|
Affiliation(s)
- D Fong
- C226 Nelson Biological Laboratories, Rutgers University, Piscataway, NJ 08855-1059, USA
| | | | | |
Collapse
|
46
|
Yarmola E, Chrambach A. Improved sensitivity of detection with the commercial automated gel electrophoresis (HPGE-1000) apparatus through modification of its optical system. Electrophoresis 1997; 18:1951-4. [PMID: 9420151 DOI: 10.1002/elps.1150181112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In a representative application to a fluorescently detectable protein of commercial automated gel electrophoresis apparatus (HPGE-1000, LabIntelligence, Belmont, CA) the sensitivity of detection by fluorescence was significantly increased by elimination of the mirror below the gel tray. That increase in detection sensitivity is due to a decrease of fluorescent background noise by nearly one order of magnitude, overcompensating a decrease in signal by a factor of two. The resulting increase in signal/noise ratio, i.e., detection sensitivity, should allow for lowered sample loads by which the band width is reduced with benefits to resolution.
Collapse
Affiliation(s)
- E Yarmola
- Laboratory of Cellular and Molecular Biophysics, NICHD, National Institutes of Health, Bethesda, MD 20892-1580, USA
| | | |
Collapse
|
47
|
Chen N, Chrambach A. Isolation of subcellular-sized particles separated by electrophoresis in dilute polymer solution, using commercial electrophoresis apparatus with intermittent scanning of fluorescence. Electrophoresis 1997; 18:781-3. [PMID: 9194606 DOI: 10.1002/elps.1150180520] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Resolution of subcellular-sized particles in electrophoresis employing semi-dilute polymer solutions as "sieving media" improves as the polymer concentration is decreased. Therefore, the previously reported conditions of preparative electrophoresis of microsomes, using concentrated (12%) polyvinylpyrrolidone (PVP) solutions, while solving the problem of non-entrance of large particles into "sieving media", do not provide adequate resolving capacity, as exemplified by failure of the microsome preparation used, to resolve in the manner of gels or dilute solutions. The present report provides the conditions under which the HPGE-1000 apparatus can be preparatively applied when the electrophoretic separation is effectively conducted in a dilute polymer solution. The isolation of three microsome components under those conditions constitutes the first application of "particle sieving", i.e., a separation due preponderantly to size and shape differences, at a preparative scale.
Collapse
Affiliation(s)
- N Chen
- Laboratory of Cellular and Molecular Biophysics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1583, USA
| | | |
Collapse
|
48
|
Hansen JC, Kreider JI, Demeler B, Fletcher TM. Analytical ultracentrifugation and agarose gel electrophoresis as tools for studying chromatin folding in solution. Methods 1997; 12:62-72. [PMID: 9169196 DOI: 10.1006/meth.1997.0448] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Analytical ultracentrifugation and agarose gel electrophoresis each can be used to accurately quantify changes in structure that accompany chromatin folding in solution. Analytical ultracentrifugation directly measures the extent of compaction of each species present in a chromatin sample under a wide range of solution conditions. Agarose gel electrophoresis yields information about changes in the average surface charge density, size and/or shape, and conformational flexibility during chromatin folding. When used together, these methodologies are particularly powerful. Protocols for the characterization of chromatin folding by analytical ultracentrifugation and agarose gel electrophoresis are described. Discussion focuses on analysis and interpretation of experimental chromatin folding data.
Collapse
Affiliation(s)
- J C Hansen
- Department of Biochemistry, University of Texas Health Science Center at San Antonio
| | | | | | | |
Collapse
|
49
|
Abstract
Incubation of human lymphocytes, neonatal fibroblasts, and Molt-4 cells (T-cell leukemia cell line) with sodium ascorbate for 1 h resulted in a concentration-dependent increase in DNA single-strand breaks as assayed by an alkaline microgel electrophoresis technique. Fibroblasts and Molt-4 cells were significantly more sensitive than lymphocytes to the induction of DNA single-strand breaks by 25, 50, and 100 microM concentrations of sodium ascorbate. Significant cell loss was observed in Molt-4, but not in lymphocyte and fibroblast cultures, after 4 h of incubation in 50 microM of sodium ascorbate, a concentration similar to the plasma level of ascorbic acid in humans.
Collapse
Affiliation(s)
- N P Singh
- Bioelectromagnetics Research Laboratory, College of Medicine, University of Washington, Seattle 98195, USA
| |
Collapse
|
50
|
Itoh M, Carninci P, Nagaoka S, Sasaki N, Okazaki Y, Ohsumi T, Muramatsu M, Hayashizaki Y. Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates. Nucleic Acids Res 1997; 25:1315-6. [PMID: 9092649 PMCID: PMC146577 DOI: 10.1093/nar/25.6.1315] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We developed a new simple high-throughput plasmid DNA extraction procedure, based on a modified alkaline lysis method, using only one 96-well microtiter glassfilter plate. In this method, cell harvesting, lysis by alkaline and plasmid purification are performed on only one microtiter glassfilter plate. After washing out RNAs or other contaminants, plasmid DNA is eluted by low-ion strength solution, although precipitated chromosomal DNA is not eluted. The plasmid prepared by this method can be applied to sequencing reactions or restriction enzyme cleavage.
Collapse
Affiliation(s)
- M Itoh
- Genome Science Laboratory, Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Koyadai 3-1-1, Tsukuba-city, Ibaraki 305, Japan
| | | | | | | | | | | | | | | |
Collapse
|