Category Archives: Electrophoresis

Table: Migration of bromophenol blue and xylene cyanol on agarose gel in TBE and TAE electrophoresis buffer

Position of bromophenol blue and xylene cyanol in agarose gel in relation to the position of double standard DNA fragment in TAE (1x) and TBE (0.5 x) electrophoresis buffer.
For example in 0.5% agarose gel, Bromophenol blue migrates at approximately 750 bp long double standard DNA fragment in TBE buffer and at approximately 1150 bp long double standard DNA fragment in TAE buffer.
Agarose gel, % Bromophenol blue in TBE buffer (0.5x) Xylene cyanol FF) in TBE buffer (0.5x) Bromophenol blue in TAE buffer (1x) Xylene cyanol FF in TAE buffer (1x)
0.5 750 13000 1150 16700
0.6 540 8820 850 11600
0.7 410 6400 660 8500
0.8 320 4830 530 6500
0.9 260 3770 440 5140
1.0 220 3030 370 4160
1.2 160 2070 275 2890
1.5 110 1300 190 1840
2.0 65 710 120 1040

Comparison of TAE and TBE electrophoresis buffer

Properties TBE TAE Remarks
Buffering capacity High Low TAE become exhausted during extended or repeated electrophoresis
Migration of (double stranded) DNA Slow Fast TAE has better conductivity
Resolution High resolution long DNA fragments High resolution for Short DNA fragments TBE supports agarose cross-linking better than TAE
Enzymatic modification of gel purified DNA Poor Good Borate from TBE buffer is an inhibitor of many commonly used enzymes in molecular biology
Recovery of DNA from agarose gel Poor Good Borate from TBE buffer interacts with DNA
Integrity of DNA High Low Borate from TBE buffer inhibits many enzyme activity including DNA modifying enzymes
Cost Costly Cheaper Highly conc. TAE (50X) require less volume to be transported.
Active buffer Tris –┬áBorate Tris -Acetate
Working conc for DNA electrophoresis 1X 0.5X


Agarose gel

  • Agarose gel can be used for the separation of nucleic acids (DNA and RNA) and high molecular weight proteins or protein complexes.
  • The process of using agarose gel to separate or fractionate biomolecules under the influence of electric field is called agarose gel electrophoresis.
  • For moderate and large sized DNA, agarose gel is the most commonly used medium in most molecular biology laboratories.
  • As the name suggest, the agarose gel is prepared from agarose.
  • Chemically, agarose is a polysaccharide, made up of alternating residues of 1,3-linked ╬▓-D-galactopyranose and 1,4-linked 3,6-anhydro-╬▒- L-galactopyranose.