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 components 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

References


How does gel electrophoresis work?

Agarose gel electrophoresis allows you to separate nucleic acids, such as DNA and RNA, based on the negative charge of the 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, the movement of DNA on an agarose matrix depends on the composition and the ionic strength of the buffer.


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 nuclease from degrading the nucleic acids.

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 difference between TAE and TBE buffer is the composition of these buffers. The main composition in TBE is boric acid, whereas TAE buffer contains acetic acid. These weak acids provide the proper ion concentration 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.


How to prepare 10X TBE buffer stock solution

  • Combine 108 g of Tris Base with 55 g of Boric Acid.
  • Add 750 mL of dH2O
  • Start stirring by using a magnetic stirrer to dissolve.
  • Add 0.5M (7.5 g) EDTA Disodium
  • Fill to a final volume of 1 L with dH2O
  • Store at room temperature
  • Before using, dilute the stock solution by 10x to make a 1x working solution with a pH of about 8.3 in dH2O

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

10xTBE Stock Solution Protocol


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 3 kb.
  • TAE works better for cloning, because TBE contains borate. Borate in TBE is an inhibitor for many enzymes, such as ligase.
  • TAE works better for performing DNA extraction from agarose gel.

How to prepare 50X TAE buffer stock solution

To prepare 50x TAE buffer:

  • Combine 242.28 g of Tris Base with 18.61 g EDTA Disodium.
  • Add 750 mL of dH2O and dissolve.
  • Start stirring by using a magnetic stirrer to dissolve.
  • Add 57.1 mL glacial acetic acid and fill to a volume of 1 L with dH2O.
  • Store at room temperature.
  • Before using, dilute the stock solution by 50x with dH2O to make a 1X working solution with a pH of about 8.6 (no pH adjustment is needed).


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

50x TAE Stock Solution Protocol

Related Products

Browse our products below:

Tris Base (Catalog no. T-400)

EDTA Sodium (Catalog no E-210)



Article | Dr. Tyas Kroemer


References

Agarose gel electrophoresis buffer. (2018, September 3). Genetic Education. https://geneticeducation.co.in/agarose-gel-electro...

How to Prepare Your Most Frequently Used Buffers | GoldBio. (n.d.). Www.goldbio.com. Retrieved June 15, 2021, from https://www.goldbio.com/articles/article/how-to-pr...

Koontz, L. (2013). Agarose gel electrophoresis. Methods Enzymol, 529, 35-45.

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). https://doi.org/10.3791/3923.

Matsumura, I. (2015). Why Johnny can’t clone: Common pitfalls and not so common solutions. BioTechniques, 59(3). https://doi.org/10.2144/000114324.

TBE or not TBE that is the question... (2019). Nagoya-Cu.ac.jp. http://www.med.nagoya-cu.ac.jp/NMJ/43-1-1full.html.

TECHNIQUES IN MOLECULAR BIOLOGY -AGAROSE GELS (HORIZONTAL GEL ELECTROPHORESIS). (n.d.). http://home.sandiego.edu/~josephprovost/Agarose%20Gel%20Electrophoresis%20Handout.pdf.