A friend did PCR and then loaded it on agarose gel. All samples were prepared in the same way; the PCR was identical, with the same template, only primers differed, the same amount loaded on the gel... but 5 of them did something weird. It reminds me visually of the front of an SDS-PAGE elfo. Any idea, what could be wrong with this?
It may be that the comb was set too deeply in the agarose on the left hand side ( gel tray not horizontal on pouring) and there is sample spill over between the wells ( load smaller sample volume) and the spillover sample is very near to the surface of the gel so is running quicker than the sample deep in the gel especially if the gel is thicker on the LHS and is not well covered by running buffer
Paul Rutland , thank you for the suggestion, but I would not suspect the gel to be unevenly poured. You can see that it is specifically the one sample (ran at various Ta), affecting also the markers, but otherwise the markers are OK. Also, when she did new gel with less DNA, it was OK :-/
Well done Tomáš Hluska That is a good result. Possibly the dna template has a lot of salt and this was interfering with the unifrm running of the samples because the ladder bands close to the odd samples are being forced to run enevenly close to the amplified bands but good that you hve sorted the problem
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