Xylene cyanol

Xylene cyanol
Other names Acid Blue 147 xylene cyanole xylene cyanol FF xylene cyanole FF C.I. 42135
Identifiers
CAS number	2650-17-1
ChemSpider	21106494 Y
Jmol-3D images	Image 1
SMILES [Na+].CCNc1ccc(cc1C)/C(=C2/C=C\C(=[NH+]\CC) C(=C2)C)c3ccc(OS([O-])=O)cc3OS([O-])=O
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-; Y Key: NLIVDORGVGAOOJ-KRQUPCAFSA-M Y 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-;
Properties
Molecular formula	C25H27N2NaO6S2
Molar mass	538.61 g/mol
Y (verify) (what is: Y/N?) Except where noted otherwise, data are given for materials in their standard state (at 25 °C, 100 kPa)
Infobox references

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

Migration speed

In 1% agarose gels, Xylene cyanol typically migrates at about the same rate as a 4000 base pair DNA fragment. Xylene cyanol or tracking dye on a 6% polyacrylamide gel migrates at the speed of a 140 base pair DNA fragment. On 20% denaturating (7 M UREA) polyacrylamide PAGE gel electrophoresis Xylene cyanol migrates at about rate of 25 base oligonucleotide. Typically 0.005-0.03% of final concentration of Xylene cyanol is used.

External links

• Xylene cyanol at OpenWetWare