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Tris-Acetate-EDTA (TAE) is preferably used in electrophoresis because of its high recovery of nucleic acids from agarose gels (compared with TBE).

TAE is advantageous for high resolution of long nucleic acid fragments (longer than 1500 bp) on agarose gels. It has a lower buffering capacity than TBE and in general, nucleic acid fragments move slower in TAE gels (apart from linear dsDNA, which tends to run faster). However, gel temperature increases when running a TAE gel for a long time, so the pH might significantly decrease because of the temperature dependency of the Tris pKa.

TAE buffer also offers advantages in subsequent enzymatic applications of the DNA sample. For example, if the downstream application is a cloning experiment, the step following agarose gel electrophoresis is ligation to a cloning vector. A DNA sample from TAE buffer is suitable for this purpose, whereas DNA from TBE buffer is not, since TBE inhibits ligases.

TAE is also used for native (non-denaturing) RNA analysis and in denaturing gels (instead of MOPS buffer) using prior denaturation of the RNA samples in hot formamide.