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Electrophoretic color markers are chemicals used in gel electrophoresis to visualize the progress of an electrophoretic separation of proteins and nucleic acids. The color markers are made up of a mixture of dyes that migrate through the gel matrix alongside the various components of a mixture containing the sample of interest. They are also referred to as tracking dyes, and are frequently present in loading dyes as well as molecular weight ladders.

Electrophoretic color markers 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. Color markers are often used as molecular wight standards to estimate the size of DNA and protein fragments by comparing their migration distance to that of the colored bands. Electrophoretic color markers are also used to monitor the progress of agarose gel electrophoresis and sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE), since DNA, RNA, and most proteins are colourless.

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.

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Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-

PAGE) is a very common and elegant molecular biology technique

for analyzing and separating complex mixture of proteins and other

biological macromolecules by using a discontinuous polyacryl-

amide gel as a support medium and sodium dodecyl sulfate (SDS)

to denature proteins [1, 2]. To detect a protein band on the elec-

trophoretic gel, either a poststaining or prestaining technique is

applied. In conventional poststaining technique, after electropho-

retic separation, the gel is usually stained by immersing it in a dye

such as Amido Black, Coomassie Brilliant Blue, or silver stain.

Silver stains are more sensitive as compared to the other two, how-

ever, these techniques have its own limitations: (1) long destaining

time is required for obtaining clear background; (2) faint bands are

difficult to analyze due to background from some of the retained

dyes, thus affecting the quality of resolution [3]. Alternatively, pro-

teins can be fluorescently labeled with dansyl chloride,

2-methoxy-2,4,-diphenyl-3(2H) furanone, or fluorescamine and

can be visualized by ultraviolet illumination [4–6]. These simple

staining techniques help to avoid the problem of altered electro-

phoretic mobility on the gels

Color Markers for Electrophoresis. (1997). Science, 277(5328), 979–979. http://www.jstor.org/stable/2892922

Chang, Hsu, H.-Y., & Lee, H.-J. (2005). Dye-free protein molecular weight markers. Electrophoresis, 26(16), 3062–3068. https://doi.org/10.1002/elps.200500041

 

Compton, Lapp, S. A., & Pedemonte, R. (2002). Generation of multicolored, prestained molecular weight markers for gel electrophoresis. Electrophoresis, 23(19), 3262–3265. https://doi.org/10.1002/1522-2683(200210)23:193.0.CO;2-8

José Bubis, Proposal of a laboratory course dedicated to the generation of protein molecular weight standards for sodium dodecyl sulfate‐polyacrylamide gel electrophoresis, Biochemistry and Molecular Biology Education, 10.1002/bmb.21476, 49, 3, (353-360), (2020)

.In order to visualize nucleic acid molecules in agarose gels, ethidium bromide or SYBR Green are commonly used dyes. Illumination of the agarose gels with 300-nm UV light is subsequently used for visualizing the stained nucleic acids. Throughout this chapter, the common methods for staining and visualization of DNA are described in details.