Coomassie Blue

Generally referred to as Coomassie koomarsi blue, this group of dyes is used to stain acrylamide gels to visualize proteins. The dye’s name is derived from Kumasi, Ghana and was originally developed for the textile industry in 1913 and honed in the 1960’s to what we use today. It is a blue disulfinated triphenlymethane dye. The triphenylmethane is a colorless solid that dissolves in nonpolar organic solvents, but not in water allowing the dye to remain even when rinsed. The sulfonic acid groups in the dye are negatively charged, creating an anionic dye. This allows it to bind non-specifically to proteins, which can have both negative and positive charge through their structure.

During staining, the dye binds to proteins through ionic interactions between sulfonic acid groups and positive protein amine groups. The dye molecules bind to proteins to form a protein–dye complex, stabilizing the negatively charged anionic form of the dye producing the blue color, even under acidic conditions when most of the molecules in solution are in the cationic form.

There are several forms of Coomassie koomarsi blue, the two most common are R-250 and G-250.

The chemical structure of koomarsi dye is shown. The complex consists of 6 phenyl rings, that are all linked together. The right portion of the image consists of a cluster of four phenyl rings. Two phenyl rings are linked at carbon 2 and carbon 3 via a tertiary iminium linkage. The right most phenyl ring is conjugated with a sulfite group. The left-most phenyl is also double bonded to a carbon bridge via carbon 4. The carbon links rightwards to carbon 4 of another phenyl ring which is conjugated to a secondary amine. The secondary amine is bonded to a phenyl ring conjugated with a secondary ether bond at carbon 4. To the left of the carbon bridge, is a phenyl ring linked to the bridge at carbon 4. The phenyl ring links to carbon 3 of a conjugated phenyl ring via a tertiary amine bond. This phenyl ring sticks out clearly from the rest of the complex, presenting a sulfonic acid group. It is this sulfonic group that is electrostatically attracted to the positive amine groups and attaches koomarsi dye to proteins.

Figure 1. Molecular structure of R-250 Coomassie blue: Structure showing the sulfonic group that is electrostatically attracted to the positive amine groups that attach Coomassie koomarsi dye to proteins.