Electrophoretic color marker

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Close-up of DNA ladders on an agarose gel. GelRed stain was used. Close-up of DNA ladders on an agarose gel. GelRed staining.jpg
Close-up of DNA ladders on an agarose gel. GelRed stain was used.
Loading of a sample into a polyacrylamide gel electrophoresis well. Load a sample into a polyacrylamide gel electrophoresis well.jpg
Loading of a sample into a polyacrylamide gel electrophoresis well.

An electrophoretic color marker is a chemical used to monitor the progress of agarose gel electrophoresis and polyacrylamide gel electrophoresis (PAGE) since DNA, RNA, and most proteins are colourless. [1] The color markers are made up of a mixture of dyes that migrate through the gel matrix alongside the sample of interest. They are typically designed to have different mobilities from the sample components and to generate colored bands that can be used to assess the migration and separation of sample components. [2]

Contents

Color markers are often used as molecular weight standards, loading dyes, tracking dyes, or staining solutions. Molecular weight ladders are used to estimate the size of DNA and protein fragments by comparing their migration distance to that of the colored bands. [2] DNA and protein standards are available commercially in a wide range of sizes, and are often provided with pre-stained or color-coded bands for easy identification. Loading dyes are usually added to the sample buffer before loading the sample onto the gel, and they migrate through the gel along with the sample to help track its progress during electrophoresis. [3] Tracking dyes are added to the electrophoresis buffer rather to provide a visual marker of the buffer front. Staining solutions are applied after electrophoresis to visualize the sample bands, and are available in a range of colors.

Different types of electrophoretic color markers are available commercially, with varying numbers and types of dyes or pigments used in the mixture. Some markers generate a series of colored bands with known mobilities, while others produce a single band of a specific color that can be used as a reference point. They are widely used in research, clinical diagnostics, and forensic science. [4]

Progress markers

Loading buffers often contain anionic dyes that are visible under the visible light spectrum, and are added to the gel before the nucleic acid. Tracking dyes should not be reactive so as not to alter the sample, and move down the gel with the DNA or RNA sample. [5] Commonly used color markers include Bromophenol blue, Cresol Red, Orange G and Xylene cyanol. Xylene and bromophenol blue are the most commonly used dyes.[ citation needed ] Generally speaking, Orange G migrates faster than bromophenol blue, which migrates faster than xylene cyanol, but the apparent "sizes" of these dyes (compared to DNA molecules) varies with the concentration of agarose and the buffer system used. For instance, in a 1% agarose gel made in TAE buffer (Tris-acetate-EDTA), xylene cyanol migrates at the speed of a 3000 base pair (bp) molecule of DNA and bromophenol blue migrates at 400 bp. However, in a 1% gel made in TBE buffer (Tris-borate-EDTA), they migrate at 2000 bp and 250 bp respectively. [3]

DNA and RNA staining

Agarose gel electrophoresis is a technique widely used to estimate the size of nucleic acid fragments and identify them based on their differential mobility in the gel. Nucleic acids are commonly stained and detected using either ethidium bromide or SYBR Green dyes.[ citation needed ] The most common electrophoretic stain in agarose gel is ethidium bromide, however, SYBR green presents greater resolution and yield for single-stranded nucleic acid detection.[ citation needed ] The dyes grant fluorescence to DNA and RNA under 300 nm UV light. This occurs due to their intercalating nature. In double helical nucleic acids, the dyes bind between two strands, and in single-stranded nucleic acids, the dyes bind short, duplex segments formed within a strand.[ citation needed ]

Chemical structure of Ethidium Bromide. Ethidium bromide.svg
Chemical structure of Ethidium Bromide.
Chemical structure of SYBR Green I. SYBR Green I.svg
Chemical structure of SYBR Green I.

The most commonly used dye in agarose gel gel electrophoresis of DNA and RNA, dating as far back as the 1970s, is ethidium bromide (2,7-diamino-10-ethyl-9-phenylphenanthridiniumbromide).[ citation needed ] Ethidium Bromide (EtBr) is an orange-colored fluorescent intercalating dye. The dye inserts itself between the double helical structure of nucleic acids, allowing for visualization of the molecules under UV light. [6] EtBr has absorbance maxima at 300-360 nm and fluorescent emission maxima at 500-590 nm, with the detection limit of 0.5-5.0 ng/band. [6] The dye, however, has reduced sensitivity in the detection of single-stranded nucleic acid samples EtBr should be handled with care, as it is a potent mutagen. [6]

A more sensitive alternative for nucleic acid staining in gel electrophoresis is SYBR™ Green I. [7] The dye is 25 times more sensitive than EtBr in the staining of dsDNA, and is especially useful in staining assays containing single-stranded nucleic acids.[ citation needed ] SYBR Green is, however, more expensive when compared to EtBr.

Chemical structure of Coomassie Brilliant Blue R-250 Coomassie Brilliant Blue R-250.svg
Chemical structure of Coomassie Brilliant Blue R-250

Protein staining

Coomassie Blue is the most commonly used non-covalent stain in SDS polyacrylamide gel electrophoresis for protein quantification. The staining dye binds to the protein bands and creates a blue color that can be detected visually. Coomassie Brilliant Blue R-250 (red), is typically used for electrophoresis, while Coomassie Brilliant Blue G-250 (green), for Bradford Assay. [8] The limitation of this dye is that it is non-specific, and will bind to almost any protein in solution, and is less sensitive.[ citation needed ] Another common method of visualization of proteins in the gel is silver staining, where soluble silver ions permanently mark proteins and are reduced by formaldehyde to form a brown precipitate.[ citation needed ] Silver staining is a more sensitive staining method when compared to Coomassie Blue, however, results are more vulnerable to contamination.

Applications

Color markers are sometimes added to loading dyes for gel electrophoresis in the separation of DNA fragments. Loading dyes keep DNA samples below the surface of the agarose gel, and the color markers within help keep track of the migration front of the DNA as it moves along the gel. [9]

For PAGE, some commercially available molecular weight markers (also called "ladders" because they look like the rungs of a ladder after separation) contain pre-stained proteins of different colours, so it is possible to determine more accurately where the proteins of interest in the samples might be.

Related Research Articles

<span class="mw-page-title-main">Agarose gel electrophoresis</span> Method for separation and analysis of biomolecules using agarose gel

Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. The proteins may be separated by charge and/or size, and the DNA and RNA fragments by length. Biomolecules are separated by applying an electric field to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix.

<span class="mw-page-title-main">Gel electrophoresis</span> Method for separation and analysis of biomolecules

Gel electrophoresis is a method for separation and analysis of biomacromolecules and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.

<span class="mw-page-title-main">Polyacrylamide gel electrophoresis</span> Analytical technique

Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation, and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after electrophoresis, it provides information on the sample composition of the RNA species.

<span class="mw-page-title-main">Gel electrophoresis of nucleic acids</span>

Gel electrophoresis of nucleic acids is an analytical technique to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules are placed on a gel, where an electric field induces the nucleic acids to migrate toward the positively charged anode. The molecules separate as they travel through the gel based on the each molecule's size and shape. Longer molecules move more slowly because they the gel resists their movement more forcefully than it resists shorter molecules. After some time, the electricity is turned off and the positions of the different molecules are analyzed.

<span class="mw-page-title-main">Ethidium bromide</span> DNA gel stain and veterinary drug

Ethidium bromide is an intercalating agent commonly used as a fluorescent tag in molecular biology laboratories for techniques such as agarose gel electrophoresis. It is commonly abbreviated as EtBr, which is also an abbreviation for bromoethane. To avoid confusion, some laboratories have used the abbreviation EthBr for this salt. When exposed to ultraviolet light, it will fluoresce with an orange colour, intensifying almost 20-fold after binding to DNA. Under the name homidium, it has been commonly used since the 1950s in veterinary medicine to treat trypanosomiasis in cattle. The high incidence of antimicrobial resistance makes this treatment impractical in some areas, where the related isometamidium chloride is used instead. Despite its reputation as a mutagen, tests have shown it to have low mutagenicity without metabolic activation.

<span class="mw-page-title-main">Gel electrophoresis of proteins</span> Technique for separating proteins

Protein electrophoresis is a method for analysing the proteins in a fluid or an extract. The electrophoresis may be performed with a small volume of sample in a number of alternative ways with or without a supporting medium, namely agarose or polyacrylamide. Variants of gel electrophoresis include SDS-PAGE, free-flow electrophoresis, electrofocusing, isotachophoresis, affinity electrophoresis, immunoelectrophoresis, counterelectrophoresis, and capillary electrophoresis. Each variant has many subtypes with individual advantages and limitations. Gel electrophoresis is often performed in combination with electroblotting or immunoblotting to give additional information about a specific protein.

<span class="mw-page-title-main">Coomassie brilliant blue</span> Chemical compound

Coomassie brilliant blue is the name of two similar triphenylmethane dyes that were developed for use in the textile industry but are now commonly used for staining proteins in analytical biochemistry. Coomassie brilliant blue G-250 differs from Coomassie brilliant blue R-250 by the addition of two methyl groups. The name "Coomassie" is a registered trademark of Imperial Chemical Industries.

<span class="mw-page-title-main">Bromophenol blue</span> Chemical compound

Bromophenol blue, albutest is used as a pH indicator, an electrophoretic color marker, and a dye. It can be prepared by slowly adding excess bromine to a hot solution of phenolsulfonphthalein in glacial acetic acid.

<span class="mw-page-title-main">Xylene cyanol</span> Chemical compound

Xylene cyanol can be used as an electrophoretic color marker, or tracking dye, to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Bromophenol blue and orange G can also be used for this purpose.

<span class="mw-page-title-main">Orange G</span> Chemical compound and histologic stain

Orange G also called C.I. 16230, Acid Orange 10, or orange gelb is a synthetic azo dye used in histology in many staining formulations. It usually comes as a disodium salt. It has the appearance of orange crystals or powder.

<span class="mw-page-title-main">Electrophoretic mobility shift assay</span>

An electrophoretic mobility shift assay (EMSA) or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein–DNA or protein–RNA interactions. This procedure can determine if a protein or mixture of proteins is capable of binding to a given DNA or RNA sequence, and can sometimes indicate if more than one protein molecule is involved in the binding complex. Gel shift assays are often performed in vitro concurrently with DNase footprinting, primer extension, and promoter-probe experiments when studying transcription initiation, DNA gang replication, DNA repair or RNA processing and maturation, as well as pre-mRNA splicing. Although precursors can be found in earlier literature, most current assays are based on methods described by Garner and Revzin and Fried and Crothers.

<span class="mw-page-title-main">Cresol Red</span> Chemical compound

Cresol red is a triarylmethane dye frequently used for monitoring the pH in aquaria.

<span class="mw-page-title-main">Molecular-weight size marker</span> Set of standards

A molecular-weight size marker, also referred to as a protein ladder, DNA ladder, or RNA ladder, is a set of standards that are used to identify the approximate size of a molecule run on a gel during electrophoresis, using the principle that molecular weight is inversely proportional to migration rate through a gel matrix. Therefore, when used in gel electrophoresis, markers effectively provide a logarithmic scale by which to estimate the size of the other fragments.

<span class="mw-page-title-main">SYBR Green I</span> Dye used for molecular genetics

SYBR Green I (SG) is an asymmetrical cyanine dye used as a nucleic acid stain in molecular biology. The SYBR family of dyes is produced by Molecular Probes Inc., now owned by Thermo Fisher Scientific. SYBR Green I binds to DNA. The resulting DNA-dye-complex best absorbs 497 nanometer blue light and emits green light. The stain preferentially binds to double-stranded DNA, but will stain single-stranded (ss) DNA with lower performance. SYBR Green can also stain RNA with a lower performance than ssDNA.

<span class="mw-page-title-main">Electroblotting</span>

Electroblotting is a method in molecular biology/biochemistry/immunogenetics to transfer proteins or nucleic acids onto a membrane by using PVDF or nitrocellulose, after gel electrophoresis. The protein or nucleic acid can then be further analyzed using probes such as specific antibodies, ligands like lectins, or stains. This method can be used with all polyacrylamide and agarose gels. An alternative technique for transferring proteins from a gel is capillary blotting.

<span class="mw-page-title-main">GelRed</span> DNA gel stain for molecular genetics

GelRed is an intercalating nucleic acid stain used in molecular genetics for agarose gel DNA electrophoresis. GelRed structurally consists of two ethidium subunits that are bridged by a linear oxygenated spacer.

<span class="mw-page-title-main">GelGreen</span> DNA gel stain for molecular genetics

GelGreen is an intercalating nucleic acid stain used in molecular genetics for agarose gel DNA electrophoresis. GelGreen consists of two acridine orange subunits that are bridged by a linear oxygenated spacer.

<span class="mw-page-title-main">SYBR Safe</span> DNA gel stain for molecular genetics

SYBR Safe is a cyanine dye used as a nucleic acid stain in molecular biology. SYBR Safe is one of a number of SYBR dyes made by the Life Technologies Corporation. SYBR Safe binds to DNA. The resulting DNA-dye-complex absorbs blue light and emits green light.

<span class="mw-page-title-main">SDS-PAGE</span> Biochemical technique

SDS-PAGE is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 kDa. The combined use of sodium dodecyl sulfate and polyacrylamide gel eliminates the influence of structure and charge, and proteins are separated by differences in their size. At least up to 2012, the publication describing it was the most frequently cited paper by a single author, and the second most cited overall.

<span class="mw-page-title-main">SYBR Gold</span> Chemical compound

SYBR Gold is an asymmetrical cyanine dye. It can be used as a stain for double-stranded DNA, single-stranded DNA, and RNA. SYBR Gold is the most sensitive fluorescent stain of the SYBR family of dyes for the detection of nucleic acids. The SYBR family of dyes is produced by Molecular Probes Inc., now owned by Thermo Fisher Scientific

References

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