FAQ: Why are some of the bands in the DNA Ladder fainter at the bottom of the gel?

Most stains run in the opposite direction from that of the migrating DNA. As a result, the bottom of the gel might have a lower concentration of stain, which might result in un-uniform staining of the bottom bands. How much of the gel will end up with a lower stain concentration is highly dependent on the migration conditions (gel percentage, voltage, buffer, run time, etc.). This effect can be counteracted by adding some stain to the running buffer. When using the DNA ladder for agarose gel electrophoresis, we recommend using ethidium bromide at 0.5 ug/ml in both the gel and the migration buffer, for proper visualization of the smallest DNA fragments.
We do not recommend casting gels exceeding 5mm in thickness, as the smaller DNA fragments might diffuse more easily and might be harder to stain efficiently in thicker gels. If using wide combs (10 mm), we recommend loading 15 µl (1.5 µg) of TriDye™ Ultra Low Range DNA Ladder per gel lane for efficient visualization of the smallest DNA fragments.
For optimal visualization of all the bands, we recommend exposing the gel to UV without any casting tray whenever possible. Even UV-transparent trays can obscure DNA fragments under UV exposure.