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Ethidium Bromide

Ethidium bromide is a fluorescent dye commonly used in molecular biology for visualizing nucleic acids, such as DNA and RNA, in gel electrophoresis.
It intercalates between base pairs, enhancing its fluorescence when bound to nucleic acids.
Researchers can use PubCompare.ai to easily locate the best ethidium bromide protocols from literature, preprints, and patents, optimizing their procedures for reproducible and accurate results.
This AI-driven tool empowers researchers to discover the most effective methods, achiecing reliable outcomes in their nucleic acid analysis.

Most cited protocols related to «Ethidium Bromide»

1
Detecting SINE200 Insertions Across Anopheles Genome
Genomic DNA was extracted with various standard procedures, and specimens were identified to species and molecular forms by PCR-RFLP [38 (link),39 (link)]. SINE200 elements were located in silico by BLASTN searches on the genome sequence of the A. gambiae PEST genome using the obtained SINE200 consensus sequence as a query. Thirteen SINE200 insertions lying within the A. gambiae molecular form speciation islands (sensu Turner [11 (link)]) on X, 2L and 2R chromosomes, and characterized by the presence of 500 bp flanking regions showing a single hit in the genome, were selected. Primers were designed to amplify across the element using Primer 3 software [40 (link)]. The selected loci were named 'S200' followed by the abbreviation of the chromosomal arm (2L, 2R, X), by a number/letter corresponding to the chromosomal location on the cytogenetic map [4 (link)] and by an additional number aimed to distinguish primer sets positioned on the same chromosome division. Genes annotated within a 20 Kb genome sequence including SINE200 insertions for each locus were retrieved from the PEST genome ver. Agam P3 Feb. 2006 (Table 2).
PCR reactions were carried out in a 25 μl reaction which contained 1 pmol of each primer, 0.2 mM of each dNTP, 1.5 mM MgCl2, 2.5 U Taq polymerase, and 0.5 μl of template DNA extracted from a single mosquito. Thermocycler conditions were 94°C for 10 min followed by thirty-five cycles of 94°C for 30 s, 54°C for 30 s and 72°C for 1 min., with a final elongation at 72°C for 10 min, and a 4°C hold. The resulting products were analysed on 1.5% agarose gels stained with ethidium bromide, with low and high molecular weight bands corresponding to fragments containing or lacking the targeted SINE200, respectively.
PCR products representing 'filled' and 'empty' sites of S200 X6.1 locus on X chromosome were sequenced on both strands using ABI Big Dye Terminator v.2 chemistry and an ABI Prism 3700 DNA Analyser. Multiple alignments were performed using ClustalX [37 (link)]. All sequences were deposited in GenBank under accession numbers EU881868–EU881887.
Indices of polymorphism (i.e. SINE200 insertion frequency and heterozygosity) and differentiation (Fst) at polymorphic loci were computed using Fstat 2.9.3.2 [41 ]. Significance was tested with Bonferroni-adjusted P-values, using the randomization approach implemented in Fstat.
Santolamazza F., Mancini E., Simard F., Qi Y., Tu Z, & della Torre A. (2008). Insertion polymorphisms of SINE200 retrotransposons within speciation islands of Anopheles gambiae molecular forms. Malaria Journal, 7, 163.
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Publication 2008
2-(2-(2-chloro-3-(2-(3,3-dimethyl-5-sulfo-1-(4-sulfo-butyl)-3H-indol-2-yl)-vinyl)-cyclohex-2-enylidene)-ethylidene)-3,3-dimethyl-1-(4-sulfo-butyl)-2,3-dihydro-1H-indole-5-carboxylic acid Chromosomes Chromosome Segregation Consensus Sequence Culicidae Ethidium Bromide Gels Genes Genetic Polymorphism Genome Heterozygote Magnesium Chloride Neutrophil Oligonucleotide Primers Plague prisma Restriction Fragment Length Polymorphism Sepharose Taq Polymerase X Chromosome
2
DNA Origami Scaffold Purification
Each sample was prepared by combining 20 nM scaffold (p7560 or p8064, derived from M13mp18), 100 nM of each staple oligonucleotide, buffer and salts including 5 mM Tris, 1 mM EDTA (pH 7.9 at 20°C), and 22 mM MgCl2, except for the 30-helix-per-x-raster block, which was folded with 15 mM MgCl2. Folding was carried out by rapid heat denaturation followed by slow cooling from 80 to 61°C over 80 min, then 60 to 24°C over 173 h. Samples were electrophoresed on 2% agarose gels (0.5× TBE, 11 mM MgCl2, 0.5 μg/ml ethidium bromide) at 70 V for 4 h in an ice-water bath. Leading monomer bands were visualized with ultraviolet light, physically excised, crushed with a pestle (17 (link)) and filtered through a cellulose-acetate spin column for 3 min at 15 000 × g, 4°C.
Douglas S.M., Marblestone A.H., Teerapittayanon S., Vazquez A., Church G.M, & Shih W.M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001-5006.
Publication 2009
acetylcellulose Bath Buffers Edetic Acid Ethidium Bromide Gels Helix (Snails) Magnesium Chloride Oligonucleotides Salts Sepharose Staple, Surgical Strains Tromethamine Ultraviolet Rays
3
Size Selection of cDNA Library
The cDNA library was size-fractionated on a 2% TAE low melt agarose gel (Lonza catalog # 50080), with a 100 bp ladder (Roche catalog # 14703220) run in adjacent lanes. Prior to loading on the gel, the ligated cDNA library was taken over a G50 Sephadex column to remove excess salts that interfere with loading the sample in the wells. After post-staining the gel in ethidium bromide, a narrow slice (∼2mm) of the cDNA lane centered at the 300 bp marker was cut. The slice was extracted using the QiaEx II kit (Qiagen catalog # 20021), and the extract was filtered over a Microcon YM-100 microconcentrator (Millipore catalog # 42409) to remove DNA fragments shorter than 100 bps. Filtration was performed by pipeting the extract into the upper chamber of a microconcentrator, and adding ultra pure water (Gibco catalog # 10977) to a volume of 500 uLs. The filter was spun at 500 X g until only 50 uLs remained in the upper chamber (about 20 minutes per spin) and then the upper chamber volume was replenished to 500 uLs. This procedure was repeated 6 times. The filtered sample was then recovered from the filter chamber according to the manufacturer's protocol. Fragment length distributions obtained after size selection were estimated from the spike-in sequences and are show in Supplementary Fig. 1.
Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., van Baren M.J., Salzberg S.L., Wold B.J, & Pachter L. (2010). Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature biotechnology, 28(5), 511-515.
Publication 2010
cDNA Library DNA, Complementary Ethidium Bromide Filtration Salts sephadex Sepharose
4
Microarray Analysis of Differential Gene Expression
The two real datasets were performed using Qiagen-Operon's mus musculus version 1.1 70-mer oligonucleotide library, representing 13,664 annotated transcripts. The first dataset is a simple comparison of wildtype mouse embryo fibroblast (MEF) cells to Ahr-/- MEF cells. A similar microarray comparison performed with mouse smooth muscle cells has previously been published [16 (link)-18 (link)]. The second dataset has been published [19 (link)], but we summarize the methods below. RNA quality for both experiments was assessed by separation with a denaturing formaldehyde/agarose/ethidium bromide gel, and quantified by analysis with an Agilent Bioanalyzer (Quantum Analytics, Inc., Foster City, CA). To examine differential gene expression, a 70-mer oligonucleotide library, representing 13,443 mouse genes (Operon Biotechnologies, Inc., Huntsville, AL), was used by the Genomic and Microarray Laboratory, Center for Environmental Genetics, University of Cincinnati, was used to fabricate microarrays. The microarray hybridisations were carried out as described [16 (link),18 (link)]. For the AHR experiment, each biological replicate consisted of one mouse cell culture, and for the Ni-treatment experiment, each exposure group consisted of nine mice. RNA from three mice was pooled for each microarray, and three separate microarrays per exposure group were compared to non-exposed controls. Both experiments were performed using 20 μg total RNA per array. Each sample of mRNA was reverse transcribed and tagged with either fluorescent Cyanine 3 (Cy3) or Cyanine 5 (Cy5) (e.g., Cy3 forcontrol and Cy5 for72-h exposure). Cy3 and Cy5 samples were co-hybridized with the printed 70-mers. Following hybridization, slides were washed and scanned at 635 (Cy5) and 532 (Cy3) nm (GenePix 4000B, Axon Instruments, Inc., Union City, CA).
Sartor M.A., Tomlinson C.R., Wesselkamper S.C., Sivaganesan S., Leikauf G.D, & Medvedovic M. (2006). Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics, 7, 538.
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Publication 2006
Axon Biopharmaceuticals cDNA Library Cell Culture Techniques Crossbreeding DNA Replication Embryo Ethidium Bromide Fibroblasts Formaldehyde Gene Expression Genes Genome GPER protein, human Mice, House Microarray Analysis Mus Myocytes, Smooth Muscle Oligonucleotides Operon RNA, Messenger Sepharose Therapies, Investigational
5
Electrophoretic Separation and Blotting of RNA
All RNA samples were separated by electrophoresis using either 10 or 15% polyacrylamide (19:1) gels cast in 7 M urea and buffered with 20 mM MOPS/NaOH (pH 7) using a Protean II rig (Bio-Rad). Tris-based buffers were avoided as it was anticipated that these might interfere with the EDC-mediated cross-linking step. The electrophoresis buffer was 20 mM MOPS/NaOH (pH 7). RNA markers were 32γP-end-labelled Decade® RNA markers (Ambion) prepared according to the manufacturer's instructions. After gel electrophoresis, gels were stained with ethidium bromide (EtBr) or SybrGold® (Molecular Probes) and imaged on a FLA-5000 system (Fuji) with Aida Image Analyser software to visualize and record the amount and distribution of the RNA.
For blotting, gels were placed over a sheet of nylon hybridization membrane (Hybond-NX®, Amersham/Pharmacia) that had been pre-wetted in distilled water. This was then sandwiched between pieces of 3MM® Whatman filter paper (three layers on each side), also pre-wetted in distilled water and placed in a ‘semidry’ electroblotter (SciPlas). Excess liquid and air bubbles were squeezed from the sandwich by rolling the surface with a clean pipette. Electrophoretic transfer of RNA from the gel to the membrane was carried out at 20 V at 4°C for 30–60 min.
Pall G.S., Codony-Servat C., Byrne J., Ritchie L, & Hamilton A. (2007). Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Research, 35(8), e60.
Publication 2007
Buffers CD3EAP protein, human Crossbreeding Edema Electrophoresis Ethidium Bromide Molecular Probes morpholinopropane sulfonic acid Nylons polyacrylamide Tissue, Membrane Transfer RNA Urea

Most recents protocols related to «Ethidium Bromide»

1
Disrupting Efflux Pump Function
Not available on PMC !

EXAMPLE 7

Efflux pumps draw energy from hydrolysis of ATP, ions, or protons. Therefore, disruption of these processes could lead to inhibition of efflux pumps. Ethidium bromide (EtBr), a fluorescent dye, is an efflux pumps' substrate and damages on the membrane directly or indirectly lead to the accumulation of EtBr. As shown in FIG. 12, a concentration-dependent fluorescence increase was observed from both OCG- and BDQ-treated cells. Considering that OCG does not cause physical membrane damage, the increased fluorescent signals could be an indirect result of impaired functions of the efflux pumps. The dissipation of the PMF caused by BDQ indirectly damaged the efflux pumps, resulting in the accumulation of EtBr.

US11857521B1. Anti-mycobacterial drugs (2024-01-02). None [US], None [US]. Inventors: Joong Ho Moon [US], Michelle Miranda [US].
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Patent 2024
Biological Assay Cells Ethidium Ethidium Bromide Fluorescence Fluorescent Dyes Hydrolysis Ions lead bromide Physical Examination Protons Psychological Inhibition Tissue, Membrane
2
Monitoring NDM-1 Monoculture Expression
Monocultures of cells expressing C26D, C26S, and wild-type NDM-1 were grown to an OD of 0.5 before induction following the protocol for monoculture growth assays. We then diluted to an approximate OD of 0.2 and added 1 mM IPTG to each flask. Monocultures were grown for 6 h with 10 ml of culture collected every hour for plasmid extraction. We diluted cultures back to an OD of 0.2 each hour to maintain an exponential growth phase while still having enough cells available at the next hour for plasmid extraction. The resulting DNA was submitted for Sanger sequencing and run on a 1% agarose gel containing ethidium bromide for imaging under UV light.
Mehlhoff J.D, & Ostermeier M. (2023). Genes Vary Greatly in Their Propensity for Collateral Fitness Effects of Mutations. Molecular Biology and Evolution, 40(3), msad038.
Publication 2023
Biological Assay Cells Ethidium Bromide Isopropyl Thiogalactoside Plasmids Sepharose Ultraviolet Rays
3
Monoculture Growth and Plasmid Isolation
We grew monocultures of uninduced and induced wild-type CAT-I along with induced monocultures of the S27M and Q30M mutants following the monoculture growth assay outlined previously. We utilized the Qiagen Large-Construct Kit following the protocol for high yields of large-construct DNA without the removal of genomic DNA. The traJ and traI genes were PCR amplified using 2X GoTaq Green MasterMix starting from 10 ng of template from each sample. PCR products were loaded on a 1% TAE gel containing ethidium bromide. Bands were visualized under UV light and imaged with Carestream Gel Logic 112.
Mehlhoff J.D, & Ostermeier M. (2023). Genes Vary Greatly in Their Propensity for Collateral Fitness Effects of Mutations. Molecular Biology and Evolution, 40(3), msad038.
Publication 2023
Biological Assay Chloramphenicol O-Acetyltransferase Ethidium Bromide Genes Genome Recombinant DNA Ultraviolet Rays
4
Quantifying ArcR Binding to katA Promoter
EMSA was performed as previously described with minor modifications (Hellman and Fried, 2007 (link)). We used NCTC8325 as the template to amplify katA promoter region DNA fragment. The 30 ng DNA fragment was incubated with 0, 100, 200, and 400 ng purified ArcR in binding buffer (25 mM HEPES, 1 mM dithiothreitol, 200 mM NaCl, and 10% glycerol, pH 7.8) at 37°C for 30 min. The 8% polyacrylamide gel was pre-electrophoresed in 1× Tris-borate-EDTA buffer (0.044 M Tris, 0.044 M boric acid, and 0.001 M EDTA, pH 8.0) for 1 h to remove impurities. After adding the sample, electrophoresis was performed for 1 h 40 min on ice. At the end of the electrophoresis, the glue was stained with 0.5 μg/ml ethidium bromide. Imaging was performed using a gel imager (Bio-Rad, Hercules, CA, USA).
Fu T., Fan Z., Li Y., Li Z., Du B., Liu S., Cui X., Zhang R., Zhao H., Feng Y., Xue G., Cui J., Yan C., Gan L., Feng J., Xu Z., Yu Z., Tian Z., Ding Z., Chen J., Chen Y, & Yuan J. (2023). ArcR contributes to tolerance to fluoroquinolone antibiotics by regulating katA in Staphylococcus aureus. Frontiers in Microbiology, 14, 1106340.
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Publication 2023
boric acid Buffers Dithiothreitol Edetic Acid Electrophoresis Electrophoretic Mobility Shift Assay Ethidium Bromide Glycerin HEPES polyacrylamide gels Sodium Chloride Tris-borate-EDTA buffer Tromethamine
5
Wheat DNA Extraction and SSR Genotyping
Total genomic DNA was isolated by a micro-extraction protocol (Prabhu et al., 1998 (link)). A polymerase chain reaction (PCR) was performed in a 10 μL total reaction volume containing 2–3 μL (60–70 ng/μL) DNA, 2.0 μL 109 buffer with 25 mM MgCl2, 0.5 μL dNTPs (10 mM) (Bangalore Genei, Bangalore, Karnataka, India), 1.0 μL each forward and reverse SSR primers (20 mM) (Sigma Inc., St. Louis, MO, United States), 0.3 μL Taq polymerase (3 U/μL) (Bangalore Genei, Bangalore, Karnataka, India), and 5.2 μL distilled water (sterile). Amplification of the template DNA was performed according to the annealing conditions for the wmc, gwm, barc, cfa, and cfd series of SSR markers used (Roder et al., 1998 (link); Pestsova et al., 2000 (link); Gupta et al., 2002 (link); Somers et al., 2004 (link); Quarrie et al., 2005 (link); Kumar et al., 2012 (link)). Amplified products were resolved on a 3.2% agarose gel (MetaPhor, Lonza, Rockland, ME, United States), along with a DNA ladder size standard (MBI, Fermentas), stained with 0.5 μg/mL ethidium bromide (Amresco, Solon, OH, United States), and documented with a gel documentation system (Bio-Rad, Hercules, CA, United States). The donor parent, C306, and recurrent parent, HD2733, were screened with 700 SSR markers, including markers associated with targeted traits.
Kumar P.K., Bellundagi A., Krishna H., Mallikarjuna M.G., Thimmappa R.K., Rai N., Shashikumara P., Sinha N., Jain N., Singh P.K., Singh G.P, & Prabhu K.V. (2023). Development of bread wheat (Triticum aestivum L) variety HD3411 following marker-assisted backcross breeding for drought tolerance. Frontiers in Genetics, 14, 1046624.
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Publication 2023
Buffers DNA, A-Form Ethidium Bromide Genome Magnesium Chloride Oligonucleotide Primers Parent Polymerase Chain Reaction Sepharose Solon Sterility, Reproductive Taq Polymerase Tissue Donors

Top products related to «Ethidium Bromide»

1
Trizol reagent by Thermo Fisher Scientific
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
2
Ethidium bromide by Merck Group
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Ethidium bromide is a fluorescent dye commonly used in molecular biology laboratories. It is used to visualize and detect the presence of nucleic acids, such as DNA and RNA, in agarose gel electrophoresis.
3
Rneasy mini kit by Qiagen
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TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
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Ethidium bromide by Thermo Fisher Scientific
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Ethidium bromide is a fluorescent dye commonly used in molecular biology to detect and visualize nucleic acids, such as DNA and RNA, in gel electrophoresis. It intercalates between the base pairs of nucleic acids, allowing for the visualization of DNA or RNA bands under ultraviolet light.
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GoTaq Green Master Mix is a pre-mixed solution used for performing polymerase chain reaction (PCR) amplification of DNA samples. It contains Taq DNA polymerase, dNTPs, MgCl2, and a green dye for visualization of PCR products during gel electrophoresis.
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The QIAquick PCR Purification Kit is a lab equipment product designed for the rapid purification of PCR (Polymerase Chain Reaction) amplicons. It utilizes a silica-membrane technology to efficiently capture and purify DNA fragments from PCR reactions, removing unwanted primers, nucleotides, and enzymes.
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Acridine orange by Merck Group
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Acridine orange is a fluorescent dye used in various laboratory applications. It is a metachromatic dye that can detect and differentiate between DNA and RNA within cells. Acridine orange is commonly used in microscopy techniques, cell biology studies, and nucleic acid staining.

More about "Ethidium Bromide"

Ethidium Bromide (EB) is a widely used fluorescent dye in molecular biology applications, particularly for visualizing nucleic acids like DNA and RNA in gel electrophoresis.
This intercalating agent binds between DNA/RNA base pairs, enhancing its fluorescence when bound to nucleic acids.
Researchers can leverage tools like PubCompare.ai to easily locate the best EB protocols from literature, preprints, and patents, optimizing their procedures for reproducible and accurate results.
This AI-driven platform empowers scientists to discover the most effective methods, achieving reliable outcomes in their nucleic acid analysis.
EB is often used in conjunction with other common molecular biology reagents and techniques.
TRIzol, for example, is a popular reagent for total RNA extraction, while the RNeasy Mini Kit provides a convenient way to purify RNA.
Taq DNA polymerase is a widely used enzyme for PCR amplification, and the QIAamp DNA Mini Kit allows for efficient DNA extraction.
GoTaq Green Master Mix simplifies PCR setup, while the QIAquick PCR Purification Kit can be used to clean up amplified DNA.
Acridine orange is another fluorescent dye that can be used to stain and visualize nucleic acids.
By combining the insights from EB usage with these related techniques and tools, researchers can optimize their nucleic acid analysis workflows, ensuring reproducible and accurate results in their studies.
The AI-powered capabilities of PubCompare.ai can be particularly helpful in this process, empowering scientists to quickly identify and implement the most effective EB protocols from the existing body of research.