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Xylene cyanol

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Xylene cyanol
Names
Preferred IUPAC name Sodium 4-{(Z)-methyl}-3-sulfobenzene-1-sulfonate
Other names Acid Blue 147
xylene cyanole
xylene cyanol FF
xylene cyanole FF
C.I. 42135
Identifiers
CAS Number
3D model (JSmol)
ChemSpider
ECHA InfoCard 100.018.334 Edit this at Wikidata
EC Number
  • 220-167-5
PubChem CID
CompTox Dashboard (EPA)
InChI
  • 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
  • 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
SMILES
  • .CCNc1ccc(cc1C)/C(=C2/C=C\C(=\CC)C(=C2)C)c3ccc(OS()=O)cc3OS()=O
Properties
Chemical formula C25H27N2NaO6S2
Molar mass 538.61 g·mol
Hazards
GHS labelling:
Pictograms GHS07: Exclamation mark
Signal word Warning
Hazard statements H315, H319, H335
Precautionary statements 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 , 100 kPa). ☒N verify (what is  ?) Infobox references
Chemical compound

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.

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, 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.

External links

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