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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] [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.
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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] [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.
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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] [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.
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Shaposhnikov S, Collins A. Twelve-Gel Comet Assay Format for Quick Examination of DNA Damage and Repair. Methods Mol Biol 2017; 1644:181-186. [PMID: 28710764 DOI: 10.1007/978-1-4939-7187-9_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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.
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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] [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.
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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. GENETICS AND MOLECULAR RESEARCH 2010; 9:259-65. [PMID: 20198581 DOI: 10.4238/vol9-1gmr714] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [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.
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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.
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Volpi N, Maccari F. Capillary blotting of glycosaminoglycans on nitrocellulose membranes after agarose-gel electrophoresis separation. Methods Mol Biol 2009; 536:95-102. [PMID: 19378049 DOI: 10.1007/978-1-59745-542-8_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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.
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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] [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.
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Raymer DM, Smith DE. A simple system for staining protein and nucleic acid electrophoresis gels. Electrophoresis 2007; 28:746-8. [PMID: 17265540 DOI: 10.1002/elps.200600325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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.
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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] [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.
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Porch TG, Erpelding JE. Low-cost conversion of the Polaroid MD-4 land camera to a digital gel documentation system. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL 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] [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.
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Hagedorn R, Schnelle T, Müller T, Scholz I, Lange K, Reh M. Electrophoresis in gel channels. Electrophoresis 2005; 26:2495-502. [PMID: 15948218 DOI: 10.1002/elps.200410389] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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.
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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] [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.
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Hodge R. Preparation of RNA gel blots. Methods Mol Biol 2003; 28:49-54. [PMID: 7509698 DOI: 10.1385/0-89603-254-x:49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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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] [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.
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Bossuyt X, Lissoir B, Mariën G, Maisin D, Vunckx J, Blanckaert N, Wallemacq P. Automated serum protein electrophoresis by Capillarys. Clin Chem Lab Med 2003; 41:704-10. [PMID: 12812271 DOI: 10.1515/cclm.2003.107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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.
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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] [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.
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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] [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.
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Spielmann T. Southern blotting of parasite DNA. METHODS IN MOLECULAR MEDICINE 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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ugaz VM, Lin R, Srivastava N, Burke DT, Burns MA. A versatile microfabricated platform for electrophoresis of double- and single-stranded DNA. Electrophoresis 2003; 24:151-7. [PMID: 12652585 DOI: 10.1002/elps.200390007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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.
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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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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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] [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.
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San Antonio JD, Lander AD. Affinity coelectrophoresis of proteoglycan-protein complexes. Methods Mol Biol 2002; 171:401-14. [PMID: 11450254 DOI: 10.1385/1-59259-209-0:401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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