Xylene cyanol can be used as an electrophoretic color marker, or tracking dye, to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis.

Once mixed with the sample, the concentration of xylene cyanol is typically about 0.005% to 0.03%.

In 1% agarose gels, xylene cyanol migrates at about the same rate as a 4 to 5 kilobase pair DNA fragment,[1] although this depends on the buffer used.

Xylene cyanol on a 6% polyacrylamide gel migrates at the speed of a 140 base pair DNA fragment.

On 20% denaturating (7 M urea) polyacrylamide gel electrophoresis (PAGE), xylene cyanol migrates at about the rate of 25 bases oligonucleotide.