Where in gel is DNA?

[Dr. Volker Blaschke]

Dear fellow researchers,

I am trying (more or less successfully) to extract PCR products from
agarose gels. So far, I have been cutting out the slices from the lanes,
thus having a lot of gel mass to start with.

I have noticed that when I had the slices "flat" on the
transilluminator, that the fluorescence is mainly located on the UPPER
part of the gel and not evenly distributed over the whole depth of the
slice, and this is also true when having EtBr-stained the gel for an
hour or so, so that for sure the whole slice is evenly soaked.

So, should I still take the "whole" slice or just excise the small "top"
fraction?

Any input is highly appreciated...


   Volker


Dr. Volker Blaschke
Dept. of Dermatology
Göttingen University, Germany