In molecular biology, agarose gel electrophoresis is a common method used for many applications, such as cloning, visualizing your PCR products, or checking whether your DNA is intact. One of the main requirements of gel electrophoresis is a running buffer, such as TBE buffer and TAE buffer.

But what is the difference between TBE and TAE? And when is TBE or TAE the most appropriate to choose?

The main difference between TBE and TAE, chemically, has to do with composition. TBE includes Tris, boric acid and EDTA. TAE includes Tris base, glacial acetic acid, and EDTA. TBE is a good choice when you need high resolution for small DNA fragments. TAE is a good choice when working with larger DNA fragments or for cloning.

In this article, we will provide more in-depth information to help you decide which one to use for your research. We’ll provide more information about the functions of each buffer and the differences between the two buffers.

In this article

How does gel electrophoresis work?

What is the function of TBE buffer and TAE buffer in gel electrophoresis?

What is the difference between TAE and TBE buffer?

TBE Buffer

When to use TBE or TAE for gel electrophoresis?

TAE Buffer

Related Products


How does gel electrophoresis work?

Agarose gel electrophoresis allows you to separate nucleic acids, such as DNA and RNA, based on molecular weight using electricity, and capitalizes on the inherent negatively charged nature of nucleic acids because of their sugar-phosphate backbone.

The negative charge allows the nucleic acids to move through an agarose matrix in an electric field towards the positive charged pole.

Therefore, based on their molecular weight and net charge, the nucleic acids move either slowly or rapidly towards the positive pole. The smaller molecules run faster than the bigger molecules during the gel electrophoresis.

illustration of how gel electrophoresis works. DNA, pictured, has a negatively charged phosphate backbone. When a positive current is run, negatively charged DNA moves through the gel toward the positive pole. Larger fragments will move slower than smaller fragments

When the gel electrophoresis is finished running, the nucleic acid fragments are separated based on their size. Then, the result is visualized, interpreted and analyzed.

To find out more about gel electrophoresis, find our article below:

How to Interpret DNA Gel Electrophoresis Results

In gel electrophoresis, while the movement of the DNA molecules is in part governed by the agarose gel concentration, a lot depends also on the running buffer; its composition and ionic strength.

What is the function of TBE buffer and TAE buffer in gel electrophoresis?

The function of TBE and TAE buffer is to allow nucleic acids to move through the agarose matrix. Therefore, the agarose gel must be completely submerged in the buffer.

In addition, the TBE or TAE buffer maintains the pH and ion concentration during electrophoresis. The pH stays within the appropriate range because the buffer contains weak acid.

Maintaining pH of the solution is important because the changes in pH affect the net charge of the nucleic acids. Therefore, if the pH is within the desired range, the net charge stays the same and the nucleic acids move properly.

Both TBE and TAE buffer contains EDTA. EDTA prevents nucleases from degrading the nucleic acids.

Nucleases might accidentally contaminate your nucleic acid sample. EDTA prevents these enzymes from degrading your sample even in case of such contamination.

To explore more about how a biological buffer works, find our article below:

What is a Biological Buffer and How to Choose the Best Buffer for Your Experiment

What is the difference between TAE and TBE buffer?

The main difference in the composition of these buffers is that while TBE contains boric acid, TAE contains glacial acetic acid.

These weak acids provide the proper ion concentration and maintain appropriate pH while nucleic acids move through the agarose matrix.

The difference between TAE and TBE buffer has to do with the acid used. TAE uses acetic acid, and TBE uses boric acid.

TBE Buffer

What is TBE Buffer?

TBE stands for Tris-borate-EDTA. It consists of Tris base, boric acid and EDTA. This buffer is commonly used in agarose gel electrophoresis. In addition, it’s often used for analyzing DNA products from PCRs by using agarose gel electrophoresis or polyacrylamide gel electrophoresis.

When to use TBE or TAE for gel electrophoresis?

When to use TBE:

TBE buffer is ideal for the following situations:

  • TBE is suitable for obtaining a higher resolution of smaller fragments, smaller than 2 kb. Using TBE for small fragments provides sharper bands.
  • TBE has a higher buffering capacity than TAE, so it works better for a longer run.

TAE Buffer

What is TAE buffer?

TAE stands for Tris-acetate-EDTA. This buffer contains Tris base, glacial acetic acid, and EDTA. It is commonly used as a running buffer in gel electrophoresis to separate nucleic acids.

When to Use TAE:

  • TAE produces a better separation of larger fragments, which is greater than 2 kb.
  • TAE works better for cloning, because TBE contains borate. Borate in TBE is an inhibitor for many enzymes, such as ligase,
    • which may be used in the later steps of cloning.
  • TAE works better for performing DNA extraction from agarose gel.

To print the pdf version of this protocol, click the link below:

50x TAE Stock Solution Protocol

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Browse our products below:

Tris Base (Catalog no. T-400)

EDTA Sodium (Catalog no E-210)

Article | Dr. Tyas Kroemer


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How to Prepare Your Most Frequently Used Buffers | GoldBio. (n.d.). Retrieved June 15, 2021, from

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Lee, P. Y., Costumbrado, J., Hsu, C.-Y., & Kim, Y. H. (2012). Agarose Gel Electrophoresis for the Separation of DNA Fragments. Journal of Visualized Experiments, (62).

Matsumura, I. (2015). Why Johnny can’t clone: Common pitfalls and not so common solutions. BioTechniques, 59(3).

TBE or not TBE that is the question... (2019).