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
Other names Acid Blue 147 xylene cyanole xylene cyanol FF xylene cyanole FF C.I. 42135
Identifiers
CAS Number	2650-17-1
3D model (JSmol)	Interactive image
ChemSpider	21106494
ECHA InfoCard	100.018.334
CompTox Dashboard (EPA)	DTXSID20883877
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 [Na+].CCNc1ccc(cc1C)/C(=C2/C=C\C(=[NH+]\CC)C(=C2)C)c3ccc(OS([O-])=O)cc3OS([O-])=O
Properties
Chemical formula	C25H27N2NaO6S2
Molar mass	538.61 g·mol^−1
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.

External links

• Xylene cyanol at OpenWetWare