Electrophoresis Dyes: Hi, We have recently purchased our own equipment for doing electrophoresis and would like to know what the best dyes to use are and their preparation please?
Submitted by sat on 11 December 2015
Answer reviewed 22 February 2023
The electrophoresis of food dyes and scientific stains in school science laboratories demonstrates the basic principles and procedures of gel electrophoresis in a simple way. The dyes and stains used are affordable, safe, and the procedure simpler than using DNA. A big advantage is that they behave in a similar way to DNA molecules during electrophoresis, and any bands produced can be visualized directly in the gel, without any further staining.
Different scientific stains produce distinct bands of colour during electrophoresis, whilst food dyes can be separated into their different pigments.
Samples of stains or food dyes are required to be mixed with a 20% v/v glycerol/distilled water solution prior to electrophoresing. The glycerol will make the sample denser than the electrophoresis buffer and allow the sample to sink and remain in the well rather than float into the buffer. This is an important step, so that no dye floats into the buffer and cross contaminates other samples.
Samples can be loaded into the gel using micropipettes, transfer or Pasteur pipettes. Care needs to be taken not to puncture the bottom of the well or overfill the wells. Loading every second well is also a good idea to minimise the chance of contamination between adjacent wells. A 10–20 uL (1drop) sample size is generally used and the samples are electrophoresed at 90–100 volts for 30–35 min.
Food dyes can be purchased at the supermarket. They are negatively charged molecules like DNA molecules and will migrate to the anode (+ve terminal).
Preparation of food dyes for electrophoresis
Electrophoresis of food dyes will result in the following pigment separations.
Scientific stains such as Bromophenol Blue1, Tartrazine2, Rose Bengal3, Xylene Cyanol4, and Orange G5 are commonly used. These can be purchased from various scientific suppliers as ready-to-use reagents or can be made up from individual powdered stains at a concentration of 0.2% w/v in 20% glycerol/distilled water. NB Bromophenol Blue is not soluble in water. Dissolve in a small amount of ethanol before diluting in water. Stains can be used as a mixture, often referred to as a ‘ladder’. They produce distinct bands of colour when electrophoresed.
Most scientific stains are negatively charged and will migrate towards the anode (+ve terminal). Methyl Green is positively charged and will migrate towards the cathode (-ve terminal). The smaller the molecule the further it will migrate.
Gel electrophoresis is the separation of molecules through their migration in an electric field. The molecules are separated based on their size, electrical charge and shape when applied to a gel medium. Electrophoresis is a commonly used technique in laboratories to analyse DNA, RNA and protein samples, plus other compounds in mixed samples. The principle of electrophoresis is that molecules are placed into a gel that is subjected to an electric current. Any negatively charged molecules will move towards the anode (+ve terminal) , whilst positively charged molecules will move towards the cathode (-ve terminal). The smaller the molecule, the further it will migrate. The density of the gel and the type of buffer used will affect how a molecule migrates. Most biological molecules are electrically charged, causing them to move when subjected to an electric field.
Southern Biological (nd) ‘Gel Electrophoresis of dyes’, Retrieved (22 February 2023) from the Southern Biological website: https://www.southernbiological.com/dyes-for-electrophoresis/
Southern Biological (nd) ‘Biotechnology: Getting started with Gel Electrophoresis’, Retrieved (22 February 2023) from the Southern Biological website: https://www.southernbiological.com/getting-started-with-gel-electrophore...
1Chem-Supply. (2019) Bromophenol Blue, Safety Data Sheet. Search https://shop.chemsupply.com.au/ to source the latest Safety Data Sheet via the product information page.
2Chem-Supply. (2018) Tartrazine Yellow, Safety Data Sheet. Search https://shop.chemsupply.com.au/ to source the latest Safety Data Sheet via the product information page.
3Sigma-Aldrich. (2022) Rose Bengal, Safety Data Sheet. Search https://www.sigmaaldrich.com/AU/en/sds/aldrich/330000 to source the latest Safety Data Sheet via the product information page.
4Sigma-Aldrich. (2020) Xylene Cyanol FF, Safety Data Sheet. Search https://www.sigmaaldrich.com/AU/en/sds/sigma/x4126 to source the latest Safety Data Sheet via the product information page.
5Sigma-Aldrich. (2022) Orange G, Safety Data Sheet. Search https://www.sigmaaldrich.com/AU/en/sds/sigma/o3756 to source the latest Safety Data Sheet via the product information page.
Submitted by VIC003 on 10 February 2025
What is the buffer that is used with this food dye method please? Is the buffer used in making the agar gel? Thank you.
Submitted by on 08 December 2015
We found it easier to buy the dyes from Southern Biological.