Xylene cyanol

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. Bromophenol blue and orange G can also be used for this purpose.

Xylene cyanol
Names
Preferred IUPAC name
Sodium 4-{(Z)-[3-methyl-4-(ethylamino)phenyl][3-methyl-4-(ethylimino)cyclohexa-2,5-dien-1-ylidene]methyl}-3-sulfobenzene-1-sulfonate
Other names
Acid Blue 147
xylene cyanole
xylene cyanol FF
xylene cyanole FF
C.I. 42135
Identifiers
3D model (JSmol)
ChemSpider
ECHA InfoCard 100.018.334
EC Number
  • 220-167-5
  • InChI=1S/C25H28N2O6S2.Na/c1-5-26-22-11-7-18(13-16(22)3)25(19-8-12-23(27-6-2)17(4)14-19)21-10-9-20(32-34(28)29)15-24(21)33-35(30)31;/h7-15,26H,5-6H2,1-4H3,(H,28,29)(H,30,31);/q;+1/p-1/b25-19-,27-23-; checkY
    Key: NLIVDORGVGAOOJ-KRQUPCAFSA-M checkY
  • InChI=1S/C25H28N2O6S2.Na/c1-5-26-22-11-7-18(13-16(22)3)25(19-8-12-23(27-6-2)17(4)14-19)21-10-9-20(32-34(28)29)15-24(21)33-35(30)31;/h7-15,26H,5-6H2,1-4H3,(H,28,29)(H,30,31);/q;+1/p-1/b25-19-,27-23-;
  • Key: NLIVDORGVGAOOJ-KRQUPCAFSA-M
  • [Na+].CCNc1ccc(cc1C)/C(=C2/C=C\C(=[NH+]\CC)C(=C2)C)c3ccc(OS([O-])=O)cc3OS([O-])=O
Properties
C25H27N2NaO6S2
Molar mass 538.61 g·mol−1
Hazards
GHS labelling:
GHS07: Exclamation mark
Warning
H315, H319, H335
P261, P264, P271, P280, P302+P352, P304+P340, P305+P351+P338, P312, P321, P332+P313, P337+P313, P362, P403+P233, P405, P501
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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Infobox references

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,[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.

References
  1. Lela Buckingham and Maribeth L. Flaws (2007). Molecular Diagnostics: Fundamentals, Methods, & Clinical Applications. F.A. Davis Company. p. 91. ISBN 9780803616592.
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