In my first trial with electrophoresis, I used TAE buffer as recommended in Maniatis, 2001 which consisted of 40mM Tris-Acetate, pH 7.0 and 0.5M EDTA pH8.0. This trial I failed to obtain any bands including the DNA ladder (Fermentas).
The next few trials, I tried using TE buffer as recommended by Kado and Liu based on the literature by Mickel, Arena and Bauer (Physical properties and gel electrophoresis behaviour of R12-derived plasmid DNAs, Nucleic Acids Research
) which consisted of 0.04M Tris-Acetate, and 2mM EDTA, pH 8.1. The latest trial, I had faint bands for my samples of plasmids and stronger bands for the control (pUC19), however, the ladder did not show at all although I have loaded the ladder in wells at both ends of the gel. Why is it so? What could have been wrong?
Another question is, under UV-illumination, half of the gel (the negative end with sample wells) seems to be brighter than the other half. There is a clear difference between both ends somewhere in the middle of the gel. Why is it so?