Molar mass 538.61 g/mol ChemSpider 21106494 | Formula C25H27N2NaO6S2 | |
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Xylene cyanol can be used as a 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.
Contents
Once mixed with the sample, 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.
Conjugation
Due to its large number of double bonds separated by single bonds, the molecule is said to be highly conjugated.
