Most people who have run polyacrylamide gels have at one point or another gotten confused with the gel’s orientation. This is especially true following protein transfer from the gel to a membrane for the purpose of western blotting or other downstream processing. This can be extremely frustrating and may even jeopardize your entire experiment if you are unable to tell the right side of the gel from the left or your control samples from your treatment group.
Several methods have been created to help bench scientists avoid this problem. These include the use of multicolored protein ladders and marking a predefined corner of your membrane once the protein has been transfered (I cut the bottom left corner of the membrane).
Today, Arefeh Seyedarabiclose from the Department of Structural and Molecular Biology, University College London published a new and very basic method for labeling polyacrylamide gels on the Nature Protocol Exchange website. Essentially, Arefeh suggests labeling the bottom inside corner of the long glass plate (facing the gel) with permanent marker). During electrophoresis the label will transfer from the plate to the gel, thereby permanently labeling your gel. Simple and brilliant!
To see the full method and associated figures click on A method for labeling polyacrylamide gels.
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Arefeh Seyedarabi, A method for labeling polyacrylamide gels, Protocol Exchange (2011) doi:10.1038/protex.2011.222, Published online 24 March 2011