Both TAE (Tris-Acetate EDTA) and TBE (Tris-Borate EDTA) are common electrophoresis buffers for DNA agarose gel electrophoresis. However, they are quite different in nature, have some useful features and also some disadvantages. You can maximize your results by choosing an electrophoresis buffer that is most compatible for your application. The following table lists their properties, and advantages and disadvantages, and also provides explanation for their peculiar behaviour.
| Properties | TAE | TBE | Remarks |
| Buffering capacity | Low | Low | TAE become exhausted during extended or repeated electrophoresis |
| Migration of (double-stranded) DNA | Fast | Slow | TAE has better conductivity |
| Resolution | High resolution for short DNA fragments | High resolution for large DNA fragments | TBE supports agarose cross-linking better than TAE |
| Enzymatic modification of gel-purified DNA | Good | Poor | Borate from TBE buffer is an inhibitor of many commonly used enzymes in molecular biology |
| Recovery of DNA from agarose gel | Good | Poor | Borate from TBE buffer interacts with DNA |
| Integrity of DNA | Low | High | Borate from TBE buffer inhibits many enzyme activities including DNA modifying enzymes |
| Cost | Cheaper | Costly | |
| Active buffer | Tris -Acetate | Tris – Borate | |
| Working concentration for DNA electrophoresis | 1X | 0.5X |
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