Comparison of TAE and TBE Electrophoresis Buffers

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.

CriteriaTAE (Tris-Acetate-EDTA)TBE (Tris-Borate-EDTA)Remarks
Full NameTris-Acetate-EDTATris-Borate-EDTABoth are Tris-based buffers commonly used for nucleic acid electrophoresis
CompositionTris base, acetic acid, and EDTATris base, boric acid, and EDTADiffer in acid component: acetate in TAE and borate in TBE
Buffering CapacityLower buffering capacityHigher buffering capacityTBE better maintains pH over long or high-voltage runs
Ionic StrengthLower ionic strengthHigher ionic strengthTBE runs slower but maintains sharper bands due to stronger buffering
Resolution of Small FragmentsLower resolution for small (<100 bp) DNA fragmentsHigher resolution for small DNA fragmentsTBE is preferred for high-resolution or small fragment applications
Resolution of Large FragmentsHigher resolution for large (>2 kbp) DNA fragmentsLower resolution for large  (>2 kbp) DNA fragmentsTBE supports agarose cross-linking better than TAE (Stellwagen et al., 2000)
Migration Speed of DNAFaster migrationSlower migrationTAE allows faster runs, beneficial for routine large-fragment separation
Downstream ApplicationsBetter 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 RunLess heat generationMore heat generationTBE may require cooling for longer runs to prevent band smearing
ReusabilityLess reusable due to lower buffering capacityMore reusable; can be used multiple timesTBE can be reused with less loss in performance than TAE
Best Use CaseRoutine agarose gel electrophoresis, cloning, large DNA fragmentsHigh-resolution separation of small DNA/RNA fragmentsSelection depends on desired speed, resolution, and downstream application
Enzymatic modification of gel purified DNAGoodPoorBorate from TBE buffer is an inhibitor of many commonly used enzymes in molecular biology
Recovery of DNA from agarose gelGoodPoorBorate from TBE buffer interacts with DNA (Stellwagen et al., 2000)
Integrity of DNALowHighBorate from TBE buffer inhibits many enzyme activity including DNA modifying enzymes
CostCheaperCostly 
Active bufferTris -AcetateTris – Borate 
Working concentration for DNA electrophoresis1X0.5X 
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