A Color marker is used to monitor the progress of agarose gel electrophoresis and polyacrylamide gel electrophoresis (PAGE) since DNA, RNA, and most proteins are colourless. They are also referred to as tracking dye

Dye

A dye is a colored substance that has an affinity to the substrate to which it is being applied. The dye is generally applied in an aqueous solution, and requires a mordant to improve the fastness of the dye on the fiber....

s.

Commonly used color markers include Bromophenol blue

Bromophenol blue

Bromophenol blue is used as an acid-base indicator, a color marker and a dye.-Acid-base indicator:As an acid-base indicator its useful range lies between pH 3.0 and 4.6...

, Cresol Red

Cresol Red

Cresol Red is a triarylmethane dye frequently used for monitoring the pH in aquaria.-pH indicator:-Molecular biology:...

, Orange G

Orange G

Orange G 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.-Staining:...

 and Xylene cyanol

Xylene cyanol

Xylene cyanol can be used as a colour marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Bromophenol blue and orange G can also be used for this purpose.-Migration speed:...

. 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

Buffer solution

A buffer solution is an aqueous solution consisting of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid. It has the property that the pH of the solution changes very little when a small amount of strong acid or base is added to it. Buffer solutions are used as a...

 system used. For instance, in a 1% agarose gel made in TAE buffer (Tris

Tris

Tris is an abbreviation of the organic compound known as trisaminomethane, with the formula 3CNH2. Tris is extensively used in biochemistry and molecular biology. In biochemistry, tris is widely used as a component of buffer solutions, such as in TAE and TBE buffer, especially for solutions of...

-acetate

Acetate

An acetate is a derivative of acetic acid. This term includes salts and esters, as well as the anion found in solution. Most of the approximately 5 billion kilograms of acetic acid produced annually in industry are used in the production of acetates, which usually take the form of polymers. In...

-EDTA

EDTA

Ethylenediaminetetraacetic acid, widely abbreviated as EDTA , is a polyamino carboxylic acid and a colourless, water-soluble solid. Its conjugate base is named ethylenediaminetetraacetate. It is widely used to dissolve limescale. Its usefulness arises because of its role as a hexadentate ligand...

), xylene cyanol migrates at the speed of a 3000 base pair molecule of DNA and bromophenol blue migrates at 400 bp. However, in a 1% gel made in TBE buffer (Tris-borate

Borate

Borates are chemical compounds which contain oxoanions of boron in oxidation state +3. The simplest borate ion, BO33−, has a trigonal planar structure. Other borates are made up of trigonal BO3 or tetrahedral BO4 structural units, sharing oxygen atoms...

-EDTA), they migrate at 2000 bp and 250 bp respectively.

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.