Xylene cyanol

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Xylene cyanol
Xylene cyanol.png
CAS number 2650-17-1 N
ChemSpider 21106494 YesY
Jmol-3D images Image 1
Molecular formula C25H27N2NaO6S2
Molar mass 538.61 g/mol
Except where noted otherwise, data are given for materials in their standard state (at 25 °C (77 °F), 100 kPa)
 N (verify) (what is: YesY/N?)
Infobox references

Xylene cyanol can be used as a color marker, or tracking dye, to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Bromophenol blue and orange G can also be used for this purpose.

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

Migration speed[edit]

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.


Due to its large number of double bonds separated by single bonds, the molecule is said to be highly conjugated.


  1. ^ Lela Buckingham & Maribeth L. Flaws. Molecular Diagnostics.- Fundamentals, Methods, & Clinical Applications. F.A. Davis Company, 2007, p. 91

External links[edit]