Xylene Cyanol FF

Xylene cyanol is used in gel electrophoresis as a "tracking" dye to control electrophoresis. For this purpose it is added to the DNA sample as sample buffer (6-fold). In total, the molecule is negatively charged and, due to this net negative charge, migrates in the same direction as DNA, so that the dye can be used to monitor the electrophoresis progress. The speed of migration varies with the gel composition. In an agarose gel, at one percent agarose concentration, it runs like DNA at 4000 to 5000 bp, and at two percent concentration like 800 bp.[1]

Xylene cyanol, due to its four additional methyl groups and thus increased hydrophobicity, moves more slowly than the also used in electrophoresis "tracking dye" Bromophenol blue and thus with larger DNA fragments.[2]

References:
1. Lela Buckingham: Molecular Diagnostics. F.A. Davis, 2011, ISBN 978-0-803-62975-2. S. 98.
2. Budin Michov: Elektrophorese Theorie und Praxis. Walter de Gruyter, 1996, ISBN 978-3-11-081942-7, S. 339