Xylene cyanol can be used as an

electrophoretic color marker An electrophoretic 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 dyes, and are frequ ...

, or tracking

dye A dye is a colored substance that chemically bonds to the substrate to which it is being applied. This distinguishes dyes from pigments which do not chemically bind to the material they color. Dye is generally applied in an aqueous solution an ...

, to monitor the process of

agarose gel electrophoresis Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the ...

and

polyacrylamide gel electrophoresis Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their ...

Bromophenol blue Bromophenol blue (3′,3″,5′,5″-tetrabromophenolsulfonphthalein, BPB), albutest is used as a pH indicator, an electrophoretic color marker, and a dye. It can be prepared by slowly adding excess bromine to a hot solution of phenolsulfonpht ...

and

orange G Orange G also called C.I. 16230, Acid Orange 10, 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 Orange G ...

can also be used for this purpose. Once mixed with the sample, the concentration of xylene cyanol is typically about 0.005% to 0.03%.

Migration speed

In 1% agarose gels, xylene cyanol migrates at about the same rate as a 4 to 5 kilobase pair DNA fragment,{{cite book , author = Lela Buckingham and Maribeth L. Flaws , title = Molecular Diagnostics: Fundamentals, Methods, & Clinical Applications , url = https://archive.org/details/moleculardiagnos00lela , url-access = limited , publisher = F.A. Davis Company , date = 2007 , page
91
} 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.

References

External links

Xylene cyanol at OpenWetWare
Triarylmethane dyes Benzenesulfonates Organic sodium salts Anilines Acid dyes