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Choosing an Electrophoresis Buffer

Which One Should You Use?

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Choosing an Electrophoresis Buffer

DNA on an agarose gel.©Phillips, 2001

There are different types of buffers you can use for agarose gel electrophoresis of purified DNA or PCR products, so how you decide which one to use? The type of buffer to use for running DNA through a gel depends primarily on the size of the DNA fragments you are separating and what you intend to do with the nucleic acids once separated. The two most popular types of buffers for running agarose gels are Tris acetate with EDTA (TAE) and Tris borate with EDTA (TBE). Both buffers are useful because they have a basic pH. The alkaline environment results in a net negative charge on the DNA phosphate groups, which allows migration of the DNA through the gel toward the positive anode.

TAE buffer is a good choice for large DNA fragments (larger than 20 kb), or when the DNA is to be recovered. It has a low ionic strength and buffering capacity.

TBE buffer gives better resolution for separation of small (

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