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Xylene cyanol

Xylene cyanol is a blue dye commonly used in molecular biology and biochemistry applications.
It is frequently employed as a tracking dye in gel electrophoresis to monitor the progress of DNA or RNA separation.
Xylene cyanol exhibits low toxicity and good visibility, making it a valuable tool for researchers studying nucleic acid structures and interactions.
The PubCompare.ai platform can help locate the best protocols for working with xylene cyanol from the scientific literature, preprints, and patent data, ensuring reproducibility and accuracy in your research.
Streamline your experiments and ensuare reliable results with the power of AI-driven protocol optimization.

Most cited protocols related to «Xylene cyanol»

1
Bacterial Community Profiling via 16S rRNA Gene Amplicon Sequencing
Clinical samples were amplified using eubacterial primers flanking the V3 region of the 16S rRNA gene: HDA-1 (5-ACTCCTACGGGAGGCAGCAGT-3) at position 339–357 (with a GC clamp located at the 5 end), and HDA-2 (5-GTATTACCGCGGCTGCTGGCA-3) at position 518–539, with an annealing temperature of C. PCR reactions were carried out in 50 reactions for 30 cycles using the profile: C, a gradient of annealing temperatures C at 45sec each, elongation C all for 45sec.
Preparation of the 8% polyacrylamide denaturing gradient and gel electrophoresis was done according to the manufacturers instructions for the D-Code Universal Detection System (Bio-Rad) with a 30–50% gradient of urea and formamide. The gel was run in Tris-acetate buffer and pre-heated to C. The gel was run at 130V for 2 hours or until the xylene cyanol dye front reached the lower end of the gel. DNA was visualized by UV irradiation following stain with ethidium bromide. Bands were excised and re-amplified, using the same primers and profile but without the GC clamp. This second PCR product was purified and sequenced with the HDA forward primer via dideoxy chain termination. Analysis of results was carried out using the GenBank nucleotide database and BLAST algorithm [39] (link).
Gloor G.B., Hummelen R., Macklaim J.M., Dickson R.J., Fernandes A.D., MacPhee R, & Reid G. (2010). Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products. PLoS ONE, 5(10), e15406.
Publication 2010
Acetate Bacteria Electrophoresis Ethidium Bromide formamide Nucleotides Oligonucleotide Primers polyacrylamide Ribosomal RNA Genes Stains Tromethamine Ultraviolet Rays Urea xylene cyanol
2
Polyacrylamide Gel Electrophoresis of DNA Fragments

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Publication 2008
Bromphenol Blue Buffers DNA Replication Edetic Acid Enzymes formamide Gels polyacrylamide gels Strains xylene cyanol
3
HCR Reactions for RNA and DNA Visualization
RNA HCR reactions for Figure 2a were performed in 40% hybridization buffer without blocking agents (40% formamide, 2× SSC, 9 mM citric acid (pH 6.0), 0.1% Tween 20), and DNA HCR reactions for Figure 2b were performed in 5× SSC with 0.1% Tween 20. For 1.5 h reactions with each hairpin at 200 nM, RNA hairpins were snap-cooled separately at 3 μM in 1× TE with 150 mM NaCl, and DNA hairpins were snap-cooled separately at 3 μM in 5× SSC. The RNA and DNA initiators were diluted to three concentrations (3, 0.3, and 0.03 μM) in ultrapure water. In the RNA HCR gel, each lane was prepared by mixing 6 μL of formamide, 3 μL of 5× hybridization buffer supplements without blocking agents (10× SSC, 45 mM citric acid (pH 6.0), 0.5% Tween 20), 3 μL of ultrapure water, and 1 μL of each hairpin. In the DNA HCR gel, each lane was prepared by mixing 10 μL of 5× SSC, 1.5 μL of 10× SSC with 1% Tween 20, 0.5 μL of ultrapure water, and 1 μL of each hairpin. When an initiator was absent (lane 1), 1 μL of ultrapure water was added to bring the reaction volume to 15 μL. For the lanes with initiator at different dilutions (lanes 2–4), 1 μL of initiator was added. The reactions were incubated at 45 °C (RNA HCR) or room temperature (DNA HCR) for 1.5 h. The samples were supplemented with 3.75 μL of 5× gel loading buffer (50% glycerol with bromophenol blue and xylene cyanol tracking dyes) and loaded into a native 2% agarose gel, prepared with 1× LB buffer (Faster Better Media). The gel was run at 100 V for 100 min at room temperature and imaged using an FLA-5100 fluorescent scanner (Fujifilm Life Science) with a 635 nm laser and a 665 nm long-pass filter. The 1kb DNA ladder (red) was prestained with SYBR Gold (Invitrogen) and imaged using a 488 nm laser and a 575 nm long-pass filter. For overnight reactions with each hairpin at 1 μM, reactions were performed analogously. In this case, the RNA hairpins were snap-cooled separately at 7.5 μM in 1× TE with 150 mM NaCl in order to maintain the 15 μL reaction volume. Gel electrophoresis was performed as for the 1.5 h reactions.
DNA multiplexed reactions for Figure 3 were performed in 5× SSC with 0.1% Tween 20. Each of the eight hairpin species (two for each of the four HCR amplifiers) was snap-cooled at 4 μM in 5× SSC. The DNA initiator for each HCR system was diluted to 0.1 μM in ultrapure water. Each lane was prepared by mixing 2.5 μL of 10× SSC with 1% Tween 20, 1.5 μL of ultrapure water, and 2.5 μL of each of the eight hairpins. When an initiator was absent (lane 1), 1 μL of ultrapure water was added to bring the reaction volume to 25 μL. For lanes 2 to 5, 1 μL of 0.1 μM initiator for one HCR amplifier was added. The reactions were incubated at room temperature for 4 h. The samples were supplemented with 6.25 μL of 5× gel loading buffer and loaded into a native 2% agarose gel. The gel was run at 100 V for 90 min at room temperature and imaged using an FLA-5100 fluorescent scanner. The excitation laser sources and emission filters were as follows: 473 nm laser with 530 ± 10 nm bandpass filter (amplifier B2, Alexa 488), 532 nm laser with 570 ± 10 nm bandpass filter (amplifier B1, Alexa 546), 635 nm laser with 665 nm long-pass filter (amplifier B4, Alexa 647), and 670 nm laser with 705 nm long-pass filter (amplifier B3, Alexa 700).
Choi H.M., Beck V.A, & Pierce N.A. (2014). Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability. ACS Nano, 8(5), 4284-4294.
Publication 2014
4
Methylation-Sensitive AFLP Analysis of Genomic DNA
Total genomic DNA was isolated from about 100 mg of 7-day-old seedling leaf, using the Dneasy MiniPrep kit (Qiagen). Oligonucleotides for metAFLP (Table 5) were obtained from the Centre for Macromolecular Studies of the Polish Academy of Sciences (Łódź). The AFLP procedure followed standard methods [31 (link)] with some minor modifications [32 (link)], using either Acc65I/MseI or KpnI/MseI for the initial digestion of genomic DNA. Acc65I and KpnI are isoschizomers, which differ in their sensitivity to template methylation. The former is insensitive to dam methylation, but its activity is blocked by both dcm and CpG methylation, while the latter is insensitive to all forms of methylation. About 500 ng of DNA were digested at 37°C for 3 h, stopping the reaction with a 70°C incubation for 15 min. The relevant adaptors were ligated to the restriction digest in a 25 μl volume at 20°C for 12 h and diluted 1:3 in TE buffer. Non-selective PCR was conducted with pre-selective primers in 25 μl reactions, using a standard amplification profile. The products of the pre-selective reaction were diluted 1:20 in TE, and selective 10 μl PCRs were carried out in the presence of 5'-(32P) labeled selective primers. Seven selective primer combinations (CpXpG-TGC/MCCG, CpG-GAC/MCCA, CpG-GCA/MCGC, CpG-GGC/MCAA, CpXpG-AGG/CAG, CpXpG-AGA/MCAA, CpXpG-AGC/MCCA) were applied to the regenerants from all four donors, CpXpG-AGG/MCAC to those from DH4, 8 and 16, and CpG-GAC/MCAA to those from DH4 and 16. Post PCR, samples were denatured with 6 μl of 80% formamide loading buffer in the presence of bromophenol blue and xylene cyanol. After further denaturation (95°C for 10 min followed by quenching at 5°C), 6 μl of the reaction mix were electrophoresed in 7% 50 cm × 0.4 mm denaturing polyacrylamide gels, and finally the gels were exposed to X-ray film overnight at -70°C.
Bednarek P.T., Orłowska R., Koebner R.M, & Zimny J. (2007). Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.). BMC Plant Biology, 7, 10.
Publication 2007
Bromphenol Blue Buffers Digestion Donors formamide Gels Genome Hypersensitivity Methylation Oligonucleotide Primers Oligonucleotides Plant Leaves polyacrylamide gels X-Ray Film xylene cyanol
5
Plant Small RNA Northern Blot Analysis
Total RNA was extracted from 1 g plant tissue, derived from the pools of three plants ground in liquid nitrogen, using a Trizol reagent (Invitrogen) according to the manufacturer's protocol. In most cases, total RNA was fractionated using Midi RNeasy kit (Qiagen) and the RNA cleanup protocol. An aliquot of 20 µg RNA was re-suspended in 10 µl loading buffer (95% formamide, 20 mM EDTA, pH 8.0, 0.05% bromophenol blue and 0.05% xylene cyanol), heated at 95°C for 2 min and loaded on 15% polyacrylamide gel (a 19:1 ratio of acrylamide to bis-acrylamide, 8 M urea). The gel was run using the SE 600 electrophoresis machine (Hoefer) at 300 V for 4 h and then the RNA was transferred to a Hybond N+ membrane by electroblotting in 1× TBE buffer at 10 V overnight. The blot hybridization was performed at 35°C for 14–24 h in an UltraHyb-oligo buffer (Ambion) using, as a probe, one or several short DNA oligos (Table 1) end-labeled with 32P by T4 polynucleotide kinase (Roche) and purified through MicroSpin™ G-25 columns (Amersham) according to the manufacturers' recommendations. The blot was washed two times with 2× SSC, 0.5% SDS for 30 min at 35°C. The signal was detected after 1–3 days exposure to a phosphor screen using a Molecular Imager (BioRad). For repeated hybridization the membrane was stripped with 0.5× SSC, 0.5% SDS for 30 min at 80°C and then with 0.1× SSC, 0.5% SDS for 30 min at 80°C.
The RNA size-markers (‘21’ and ‘24 nt’, Figure 1) were prepared using T7 RNA polymerase (Promega) and a pair of DNA oligonucleotides as a template—the T7 promoter oligo 5′-TAATACGACTCACTATAG-3′ and for ‘21 nt’, 5′-ACGGTTGGCCCCTTGGTTTCCCTATAGTGAGTCGTATTA-3′, or for ‘24 nt’, 5′-ACGGTTGGCCCCTTGGTTGTCTCCCTATAGTGAGTCGTATTA-3′—according to the Promega protocol in the presence of [α-32P]rUTP (Hartman) and then purified through the G-25 columns (Amersham). The markers were verified by using synthetic RNA oligonucleotides (data not shown) as well as by comparing them to the Arabidopsis endogenous sRNAs, the sizes of which are known from the cloning data (miR173, siR255 and siR1003, Figure 4). Note that the 21 and the 24 nt bands of the respective markers become more intensive when the ‘NONA as’ probe, which is partially complementary to the marker RNA, is used for hybridization (Figure 1).
Akbergenov R., Si-Ammour A., Blevins T., Amin I., Kutter C., Vanderschuren H., Zhang P., Gruissem W., Meins F J.r., Hohn T, & Pooggin M.M. (2006). Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Research, 34(2), 462-471.
Publication 2006
2',5'-oligoadenylate Acrylamide Arabidopsis bacteriophage T7 RNA polymerase Bromphenol Blue Buffers Complementary RNA Crossbreeding DNA, A-Form Edetic Acid Electrophoresis formamide Nitrogen Oligonucleotides Phosphorus Plants polyacrylamide gels Polynucleotide 5'-Hydroxyl-Kinase Tissue, Membrane Tissues Tris-borate-EDTA buffer trizol Urea xylene cyanol

Most recents protocols related to «Xylene cyanol»

1
EMSA Assay for Protein-DNA Interactions
EMSA assays were done using 14% polyacrylamide (40% (w/v)29:1 Acrylamide:Bis-Acrylamide) gels in TBE buffer (Tris 0.13 M, Borate 45 mM, EDTA 2.5 mM pH 7.6 and run in TBE buffer at 4° at 160 V for 1 h, using Xylene cyanol as loading dye. Gels were stained with toluidine blue for 5 min, then rinsed with water overnight on a gel rotator.
Kara H., Axer A., Muskett F.W., Bueno-Alejo C.J., Paschalis V., Taladriz-Sender A., Tubasum S., Vega M.S., Zhao Z., Clark A.W., Hudson A.J., Eperon I.C., Burley G.A, & Dominguez C. (2024). 2′-19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions. Frontiers in Molecular Biosciences, 11, 1325041.
Publication 2024
2
Agarose Gel Electrophoresis of PCR Products
Not available on PMC !
Eight ul of PCR product was mixed with 2.0 ul of gel-loading buffer (30% glycerol, 0.25% bromophenol blue and 0.25% Xylene Cyanol) and electrophoresed on 1.5% agarose gel (TBE) at 100 volt for about 2 hours. DNA bands were stained with ethidium bromide and photographed with fast Polaroid film using transluminator UV light. DNA band size was determined by comparing with a 100 base-pair DNA ladder run on gel.
Yuliarti N., Hidayat P., & Buchori D. (2024). MOLECULAR IDENTIFICATION OF EGG PARASITOID, TELENOMUS SPP. (HYMENOPTERA: SCELIONIDAE) FROM SEVERAL LOCATIONS IN JAVA USING RAPD-PCR. BIOTROPIA.
Publication 2024
3
Urea-PAGE Analysis of Spliced RNA
Splicing and ligation reactions were carried out as described above, and the reaction products were analyzed by 15% urea-PAGE using stop solution (10 M urea, 0.1% SDS, 1 mM EDTA, 0.1% xylene cyanol, 0.1% bromophenol blue). The gels were run in 1x TBE-buffer at 150 V (constant voltage) at room temperature for 70 min. The gels were subsequently stained with SYBR Gold nucleic acid stain (Invitrogen, Life Technologies) to visualize the RNA by ultraviolet trans-illumination.
Gerber J.L., Morales Guzmán S.I., Worf L., Hubbe P., Kopp J, & Peschek J. (2024). Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease. Nature Communications, 15, 2378.
Publication 2024
4
NMR Characterization of RNA-Protein Interactions
All the samples contained 2 μL of unmodified RNA2 or 2′F-RNA2 or 2′-OCF3-RNA3 at a final concentration of 40 μM. Then, 10 μL of NMR buffer for the free RNA sample or 10 μL of protein in NMR buffer were added to obtain different final concentrations of Sam68: 10 μM, 50 μM, 100 μM or 200 μM. Finally, 3 μL of Xylene Cyanol non denaturing loading dye was added to each sample.
Kara H., Axer A., Muskett F.W., Bueno-Alejo C.J., Paschalis V., Taladriz-Sender A., Tubasum S., Vega M.S., Zhao Z., Clark A.W., Hudson A.J., Eperon I.C., Burley G.A, & Dominguez C. (2024). 2′-19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions. Frontiers in Molecular Biosciences, 11, 1325041.
Publication 2024
5
Radioactive Protein Visualization
The translation mixture was performed in the presence of 50 μM l-[14C(U)]-Aspartic acid (>200 mCi/mmol, 0.1 mCi/ml, NEC268E, Perkin Elmer). After translation, the solution was mixed with 2x tricine SDS-PAGE loading buffer (0.9 M Tris–HCl (pH = 8.45), 8% SDS, 30% glycerol, and 0.001% xylene cyanol) and subjected to 15% tricine SDS-PAGE gels at 150 V for 40 min. The resulting gel was exposed to an IP cassette (Fujifilm) and imaged by Typhoon FLA 7000 fluorescence image analyzer (GE Healthcare).
Lu W., Terasaka N., Sakaguchi Y., Suzuki T., Suzuki T, & Suga H. (2024). An anticodon-sensing T-boxzyme generates the elongator nonproteinogenic aminoacyl-tRNA in situ of a custom-made translation system for incorporation. Nucleic Acids Research, 52(7), 3938-3949.
Publication 2024

Top products related to «Xylene cyanol»

1
Imagequant software by GE Healthcare
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ImageQuant software is a data analysis tool designed for quantitative analysis of digital images. It enables users to capture, process, and analyze images from various laboratory equipment, such as gel imagers and blot imaging systems. The software provides tools for image acquisition, image processing, and data analysis, allowing researchers to quantify and compare signals within their samples.
2
Sybr gold by Thermo Fisher Scientific
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SYBR Gold is a nucleic acid stain used for the detection and quantification of DNA and RNA in gel electrophoresis and other applications. It is a sensitive, fluorescent dye that binds to nucleic acids, allowing the visualization and analysis of DNA and RNA samples.
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Typhoon phosphorimager by GE Healthcare
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The Typhoon phosphorimager is a laboratory instrument used for the detection and quantification of radioactively labeled samples. It utilizes a laser-based scanning technology to capture high-resolution images of phosphor-labeled proteins, nucleic acids, and other biomolecules.
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The Typhoon FLA 9500 is a versatile fluorescence imager designed for a wide range of life science applications. It is capable of capturing high-quality images of fluorescently labeled samples, including gels, blots, and microarrays. The system features a compact design, user-friendly software, and advanced imaging capabilities to support various research and analytical needs.
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Phosphorimager by GE Healthcare
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The PhosphorImager is a laboratory imaging device that captures and analyzes the distribution of radioactive signals on a phosphor imaging plate. It provides high-resolution, quantitative data on the spatial distribution of radioactive samples.
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T4 polynucleotide kinase by New England Biolabs
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T4 polynucleotide kinase is an enzyme that catalyzes the transfer of the gamma-phosphate from ATP to the 5' hydroxyl terminus of DNA, RNA, or oligonucleotides. This enzyme is commonly used in molecular biology for labeling nucleic acids with radioactive or fluorescent tags.
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Quantity one software by Bio-Rad
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Quantity One software is a powerful and versatile tool for analyzing and quantifying data from gel electrophoresis and imaging experiments. It provides a suite of analytical tools for researchers to accurately measure and compare the size, intensity, and other properties of bands or spots in their samples.
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γ 32p atp by PerkinElmer
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[γ-32P]ATP is a radiolabeled compound containing the radioactive isotope phosphorus-32 (32P) attached to the gamma phosphate group of adenosine triphosphate (ATP). This product is commonly used as a tracer in various biochemical and molecular biology applications, such as nucleic acid labeling and analysis.

More about "Xylene cyanol"

Xylene cyanol, a widely used blue dye in molecular biology and biochemistry, plays a crucial role in DNA and RNA separation and analysis.
This versatile dye is commonly employed as a tracking agent in gel electrophoresis, allowing researchers to monitor the progress of nucleic acid separation with ease and precision.
Owing to its low toxicity and excellent visibility, xylene cyanol has become an indispensable tool for scientists studying the structures and interactions of nucleic acids.
From applications in agarose and polyacrylamide gel electrophoresis to staining methods like SYBR Gold, this dye has found its way into numerous experimental protocols.
The PubCompare.ai platform offers a powerful solution for optimizing research protocols involving xylene cyanol.
By leveraging AI-driven comparisons of scientific literature, preprints, and patent data, researchers can locate the best protocols, ensuring reproducibility and accuracy in their experiments.
This platform can also be used in conjunction with other commonly used tools, such as ImageQuant software, Typhoon phosphorimager, Quantity One software, and T4 polynucleotide kinase, to streamline the research process and obtain reliable results.
Whether you're working with DNA, RNA, or other nucleic acid structures, xylene cyanol and the PubCompare.ai platform can help you navigate the complexities of your research with confidence.
Explore the versatility of this dye and unlock the power of AI-driven protocol optimization to take your experiments to new heights.