Why is TBE buffer preferred over TAE for smaller DNA fragments?
Tris-Borate-EDTA possesses greater buffering capacity than Tris-Acetate-EDTA due to borate's multivalent buffering action and lower conductivity. During electrophoresis of small DNA fragments, which require longer runs or higher voltages, TAE exhausts quickly, leading to pH rise, buffer depletion, and band broadening. TBE maintains stable pH and ionic environment, reducing heating and providing sharper resolution for fragments below 1 kb. Although TAE allows easier DNA recovery and is preferred for large fragments, TBE's superior capacity favors small fragment separation in high-resolution applications.
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.