My second attempt at plasmid purification for my last five splice variants again yielded very poor results. Today I did a PCR on the results to see if there's any relevant DNA in those tubes at all. This is somewhat confounded by using a different (cheaper) polymerase with which I have no experience - hopefully I picked a reasonable annealing temperature - so a previous high-concentration tube was used as a positive control. We'll find out Friday or Monday, depending on when I have time to run the gel.
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