The Matrix
A high background which obscures the bands, or in combination with fainter than usual bands, indicates dye binding to the gel matrix, or contamination of the matrix with a dye-binding material (most often a protein).…
SDS in the staining solution: Most users save and re-use their staining solutions. This is fine for a couple of cycles, but over time enough SDS elutes from the gels to accumulate to significant levels…
If your gel doesn’t look like this one, click on the problem below to find the solution: Faint bands on a low background Learn More Faint bands on a high background Learn More Uneven Staining…
Bands in gels stained with ethidium bromide fluoresce under ultraviolet light. The most commonly used stain for detecting DNA/RNA is ethidium bromide. Ethidium bromide is a DNA interchelator, inserting itself into the spaces between the…
The buffer system in electrophoresis controls the pH of the gel, preventing damage to sample molecules and, in certain cases, controlling the ionization state of the molecules. A second, though no less significant function, derives…
A natural colloid extracted from seaweed, agarose is a linear polysaccharide made up of the repeating unit agarobiose, which consists of alternating units of 1,3-linked b-D-galactopyranose and 1,4-linked 3,6-anhydro-a-L-galactopyranose. Gels prepared from agarose have a…
Polyacrylamide gels are formed by the polymerization of acrylamide in an aqueous solution in the presence of small amounts of a bifunctional crosslinker. The crosslinker is usually methylenebisacrylamide (bis, or MBA). Polyacrylamide gels are formed…
In-gel electrophoresis the matrix forces sample components to separate by size, as they move through its porous structure. The matrix provides greater resistance to the movement of larger molecules. It also performs additional functions including…
Electrophoresis System Dynamics The apparatus in gel electrophoresis constitutes an electrical/thermodynamic system. The apparatus receives energy from the power source and releases energy as heat. The figure below shows a stylized representation of a typical…
The term “electrophoresis” refers simply to the movement of particles by an electric force. The first electrophoresis experiments were carried out on molecules in a conductive buffer solution, where the only force acting on the…