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How to Compare DNA Gel Electrophoresis Methods

Gel electrophoresis is a standard technique separating DNA, RNA or protein through a gel using an electric current. It uses the electrical charge of the molecules to separate them in a gel using an electric current.

  1. Agarose

    • Agarose gel is the most common method for visualizing DNA. Different percentages of agarose can be used depending on the size of the DNA to be visualized. A low percentage of agarose, such as 0.7 percent, has the resolution to visualize large DNA fragments. A higher percentage, such as 2 percent, is often used to visualize small fragments of DNA. To visualize DNA, ethidium bromide is often used as it intercalates with DNA and fluoresces in UV light.

    Polyacrylamide

    • Polyacrylamide gels are used to separate DNA fragments as small as 10 base pairs up to 1 kb. These gels have a small separating range but with a high resolution. However, they are also more complicated to prepare. It is also possible to load large amounts of DNA without affecting the resolution. As with agarose, ethidium bromide is often used to visualize the DNA fragments, but polyacrylamide can quench the fluorescence, making it difficult to visualize small amounts of DNA.

    Pulse-Field

    • This form of electrophoresis is used to separate large DNA molecules and is often used for genotyping. Large DNA fragments migrate at a similar rate. It can be difficult, therefore, to resolve different bands. Pulse-field electrophoresis alternates the electric field. This allows greater separation and resolution of the DNA.

    Capillary

    • Capillary electrophoresis is a quick and sensitive method for separating DNA. Small amounts of DNA can be resolved. The DNA can be visualized with fluorescent labeling or using UV light.

    Denaturing

    • The separation of DNA can be complicated by its structure. It is possible using urea and formamide to destroy the structure by lowering the melting point of DNA. This can be used in both agarose and polyacrylamide gels.

    Considerations

    • The electrophoresis method selected will depend on the size of the DNA fragments to be separated. How the DNA will be used after separation will also determine the final method.

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