How to Stain Agarose Gels

Visualization of nucleic acid or protein is essential in performing agarose gel electrophoresis. If you work without staining the gel, you will not be able to see where the sample you are testing has reached, and therefore measurements of molecular size, for example, will be severely restricted. Stain your gel using a common, well-trialled dye such as ethidium bromide (EtBr) which fluoresces under ultraviolet (UV) light when intercalated into DNA or RNA molecules. The dye will assist you in performing your experiment by showing up the molecules in your sample as dark blue marks.

Things You'll Need

• Safety gloves and goggles
• Agarose gel
• Ethidium bromide
• Pipette (Gilson for small quantities)
• Loading buffer

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Instructions

• 1

  Wear safety gloves that are thin but protective and allow your fingers and hands unrestricted motion. Use a small pipette to draw some EtBr (or equivalent stain) out of its container.

• 2

  Add 0.5 micrograms per milliliter of your chosen stain to your sample. Cover the sample and mix manually. Several shakes should be sufficient.

• 3

  Add a negatively charged loading buffer to the mix using a pipette. This enables the stained sample to be seen with the naked eye, in natural light and eliminates the need for expensive, harmful UV that would otherwise degrade the molecules in which you are interested. Xylene cyanol is a commonly used loading buffer, but others are available. Ensure you select a loading buffer that will run at the same speed as the molecule you are measuring. Xylene cyanol runs at the same speed as DNA fragments that are 5000 base pairs (bp) in length.

• 4

  Use a clean pipette to apply your enhanced sample to the wells at the start of your agarose gel. The volume you apply depends on the size of the gel combs (well thickness and length and gel thickness). Stain your sample and not the control so that you can determine the parameters you are interested in (such as molecular weight) correctly and effectively.

• 5

  Alternatively, perform Southern Blotting as a way of visualizing your sample. Transfer the DNA to a nitrocellulose membrane. Expose it to a hybridization probe. This is not staining, as such, but provides a suitable alternative, as described by Access Excellence.