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.
| Criteria | TAE (Tris-Acetate-EDTA) | TBE (Tris-Borate-EDTA) | Remarks |
| Full Name | Tris-Acetate-EDTA | Tris-Borate-EDTA | Both are Tris-based buffers commonly used for nucleic acid electrophoresis |
| Composition | Tris base, acetic acid, and EDTA | Tris base, boric acid, and EDTA | Differ in acid component: acetate in TAE and borate in TBE |
| Buffering Capacity | Lower buffering capacity | Higher buffering capacity | TBE better maintains pH over long or high-voltage runs |
| Ionic Strength | Lower ionic strength | Higher ionic strength | TBE runs slower but maintains sharper bands due to stronger buffering |
| Resolution of Small Fragments | Lower resolution for small (<100 bp) DNA fragments | Higher resolution for small DNA fragments | TBE is preferred for high-resolution or small fragment applications |
| Resolution of Large Fragments | Higher resolution for large (>2 kbp) DNA fragments | Lower resolution for large (>2 kbp) DNA fragments | TBE supports agarose cross-linking better than TAE (Stellwagen et al., 2000) |
| Migration Speed of DNA | Faster migration | Slower migration | TAE allows faster runs, beneficial for routine large-fragment separation |
| Downstream Applications | Better for DNA recovery from gel (e.g., cloning) | Not ideal for DNA recovery (inhibitory salts may interfere with enzymes) | TAE is more compatible with enzymatic reactions like PCR or ligation |
| Heat Generation During Run | Less heat generation | More heat generation | TBE may require cooling for longer runs to prevent band smearing |
| Reusability | Less reusable due to lower buffering capacity | More reusable; can be used multiple times | TBE can be reused with less loss in performance than TAE |
| Best Use Case | Routine agarose gel electrophoresis, cloning, large DNA fragments | High-resolution separation of small DNA/RNA fragments | Selection depends on desired speed, resolution, and downstream application |
| 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 (Stellwagen et al., 2000) |
| Integrity of DNA | Low | High | Borate from TBE buffer inhibits many enzyme activity 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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