The key difference between xylene cyanol and bromophenol blue is that in 1% agarose gel, xylene cyanol migrates slower, whereas bromophenol blue migrates faster.
Xylene cyanol and bromophenol blue are important as color markers that can be used in monitoring the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis.
CONTENTS
1. Overview and Key Difference
2. What is Xylene Cyanol
3. What is Bromophenol Blue
4. Xylene Cyanol vs Bromophenol Blue in Tabular Form
5. Summary – Xylene Cyanol vs Bromophenol Blue
What is Xylene Cyanol?
Xylene cyanol is an electrophoretic color marker or a tracking dye. It is useful in monitoring the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. When this substance is mixed with the sample, the concentration of this substance becomes typically about 0.005% to 0.03%. Some synonyms that we can use for xylene cyanol include Acid Blue 147, xylene cyanole, xylene cyanol FF, xylene cyanole FF, etc.
The chemical formula of this compound is C25H27N2NaO6S2. The molar mass of xylene cyanol is 538.61 g/mol. This substance can migrate at a rate of about 4 – 5 kilobase pair DNA fragments in 1% agarose gels. However, this depends on the buffer that we use. Typically, xylene cyanol on 6% polyacrylamide gel can migrate at a speed of about 140 base pair DNA fragments. On the other hand, it can migrate in 20% denaturing polyacrylamide gel electrophoresis at a rate of 25 bases oligonucleotide.
The hydrogen bond donor count of xylene cyanol is 2m, and the hydrogen bond acceptor count is 8. The rotatable bond count of this compound can be given as 7. The complexity of xylene cyanol can be described as 1120 degrees. It has a defined bond stereocenter count of 1.
What is Bromophenol Blue?
Bromophenol blue is a useful pH indicator that is useful as an electrophoretic color marker and a dye. It has the chemical name 3’,3”,5’,5”-tetrabromophenolsulfonphthalein, BPB. The chemical formula of this compound is C19H10Br4O5S. The molar mass of this compound is 669.96 g/mol. It is odorless, and its density can be given as 2.2 g/mL. Its melting point is 273 degrees Celsius, and its boiling point is 279 degrees Celsius. We can prepare it by slowly adding excess bromine to a hot solution of phenolsulfonphthalein in glacial acetic acid.
Bromophenol blue is useful as an acid-base indicator in the range between pH 3.0 to 4.6. It is able to change from yellow at pH 3.0 to pH 4.6. Moreover, it is a reversible reaction. Structurally, bromophenol blue is similar to phenolphthalein.
Besides, we can use it as a color marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. This substance can carry a negative charge at moderate pH, where it can migrate in the same direction as DNA or protein in a gel. The migration rate can vary according to gel density and buffer composition. However, in a typical 1% agarose gel in 1 time TAE buffer or TBE buffer, this substance migrates at the same rate as a DNA fragment of about 300 base pairs.
What is the Difference Between Xylene Cyanol and Bromophenol Blue?
Xylene cyanol and bromophenol blue are important color markers. The key difference between xylene cyanol and bromophenol blue is that in 1% agarose gel, xylene cyanol migrates slower, whereas bromophenol blue migrates faster.
Below is a summary of the difference between xylene cyanol and bromophenol blue in tabular form for side-by-side comparison.
Summary – Xylene Cyanol vs Bromophenol Blue
Xylene cyanol and bromophenol blue are important as color markers used in monitoring the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. The key difference between xylene cyanol and bromophenol blue is that in 1% agarose gel, xylene cyanol migrates slower whereas bromophenol blue migrates faster.
Reference:
1. “Xylene Cyanole Ff.” National Center for Biotechnology Information. PubChem Compound Database, U.S. National Library of Medicine.
Image Courtesy:
1. “Xylencyanol” By Kopiersperre – Own work (Public Domain) via Commons Wikimedia
2. “Bromophenol Blue” By Panoramix303 – Own work (Public Domain) via Commons Wikimedia