FAQ: Why is the separation of the lower bands incomplete?

The low molecular weight ladders contain small fragments and require long run times to resolve the bands effectively. To visualize the smaller bands, a higher percentage gel is helpful (up to 3% agarose, which is most effectively performed using a specially formulated low melt agarose). Smaller bands also tend to diffuse more than larger bands as the electrophoresis is being carried out, so running faster (at higher voltage) can be useful, as long as not too much heat is generated. In most systems, gels of 2% or higher can be run at a voltage of 200 for several hours without excessive heat damage.