Carbohydrate markers are employed in a technique known as polysaccharide analysis by carbohydrate gel electrophoresis (PACE), which is a measurable separation technique.
It allows for the analysis of enzyme hydrolysis products. It has been used in applications such as characterizing enzymes involved in hemicellulose degradation, determining the structure of hemicellulose polysaccharides, and analysis of enzymatic cleavage of cellulose products.
PACE depends on derivitization, which is the conversion of a chemical compound into a derivative. Here monosaccharides, oligosaccharides, and polysaccharides are the compounds of interest. They are labeled at their reducing ends with a fluorescent label (i.e. a fluorophore). This derivitization with a fluorophore permits both separation on a gel under the desired circumstances and fluorescence imaging of the gel. In this case, a polyacrylamide gel is used.
As with DNA, RNA, and protein electrophoresis, markers are run alongside the samples of interest in carbohydrate gel electrophoresis. The markers consist of oligosaccharides of known molecular weight. Like the samples of interest, the marker is also derivitized with a fluorophore (usually with 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS) or 2-aminoacridone).