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A molecular-weight size marker in the form of a 1kb DNA ladder in the rightmost lane, used in gel electrophoresis. Gel conditions are 1% agarose, 3 volt/cm, and ethidium bromide stain.
Close-up of DNA ladders on an agarose gel. GelRed stain was used. 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]
Orange G can be used as an electrophoretic color marker to monitor the process of agarose gel electrophoresis, running approximately at the size of a 50 Base pair (bp) DNA molecule, and polyacrylamide gel electrophoresis. Bromophenol blue and xylene cyanol can also be used for this purpose. (However, the apparent "size" of all these dyes varies ...
There are also limitations in determining the molecular weight by SDS-PAGE, especially when trying to find the MW of an unknown protein. Certain biological variables are difficult or impossible to minimize and can affect electrophoretic migration. Such factors include protein structure, post-translational modifications, and amino acid composition.
Agarose gel has large pore size and good gel strength, making it suitable as an anticonvection medium for the electrophoresis of DNA and large protein molecules. The pore size of a 1% gel has been estimated from 100 nm to 200–500 nm, [4] [5] and its gel strength allows gels as dilute as 0.15% to form a slab for gel electrophoresis. [6]
The gel shows bands corresponding to different nucleic acid molecules populations with different molecular weight. Fragment size is usually reported in "nucleotides", "base pairs" or "kb" (for thousands of base pairs) depending upon whether single- or double-stranded nucleic acid has been separated.
[21] [22] The mobility of the complex in the polyacrylamide gel will depend on both the size of the protein complex (i.e., the molecular weight) and the amount of dye bound to the protein. Coomassie blue staining can also be used as a loading control staining method in western blot analysis. [23] It is applied as an anionic pre-antibody stain.
Ethidium bromide (or homidium bromide, [2] chloride salt homidium chloride) [3] [4] is an intercalating agent commonly used as a fluorescent tag (nucleic acid stain) in molecular biology laboratories for techniques such as agarose gel electrophoresis. It is commonly abbreviated as EtBr, which is also an abbreviation for bromoethane.