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.
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| Names | |
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| 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)
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| ChemSpider | |
| ECHA InfoCard | 100.018.334 |
| EC Number |
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PubChem CID
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CompTox Dashboard (EPA)
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| Properties | |
| C25H27N2NaO6S2 | |
| Molar mass | 538.61 g·mol−1 |
| Hazards | |
| GHS labelling: | |
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| 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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Once mixed with the sample, the concentration of xylene cyanol is typically about 0.005% to 0.03%.
Migration speed
editIn 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
edit- ^ Lela Buckingham and Maribeth L. Flaws (2007). Molecular Diagnostics: Fundamentals, Methods, & Clinical Applications. F.A. Davis Company. p. 91. ISBN 9780803616592.