We struggle to get a clean PAGE-TBE electrophoresis to size select DNA libraries. Somehow, we always get DNA stuck in the well for our PCR products (we tried bead-purified, silica-column purification, or directly from the thermocycler). The ladders are always migrating well (i.e., no well retention), so we thought it might have something to do with our DNA (still bound to some nasty chemicals or proteins). We tried different PCR tubes, and different chemicals, ... at that point, I don't know what we should test next. I enclosed an example of the kind of the well retention we get.
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