Bromophenol blue (BPB) is most commonly used as an agarose gel electrophoresis size marker. In a 1% gel it runs at around 500bp but the higher % of the gel the lower it will run. Despite its larger molecular weight of 670g/mol it runs faster than Xylene cyanol (539g/mol) because of its larger negative charge (hydroxyl groups).
Bromophenol blue is also a pH indicator which is yellow below pH=3 and blue-purple at more basic pH.
- 1000bp at 0.7% agarose
- 500bp at 1%
- 150bp at 2%
- 50bp at 3%