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In gel electrophoresis, what causes effects like these (see collumn 11 in the first one, an collumn 6 in the second).

this this?

(These images were samples that I took from an online activity we did for class)



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These are sequencing gels (in the cases here even radioactive ones) - they are run a lot longer than ordinary agarose gels and they are made from polyacrylamide. Im my experience, the most likely cause for skewing of lanes (not only bands) are samples, which still contain too much salts from the PCR reactions. This can also happen to only a few bands as seen here. Overall these are still pretty nice and clean gels, I have seen much worse.

Other reasons which cause uneven gels are cases where the acrylamide is not mixed good enough (causing the gel to have different concentration and thus causing different running conditions), uneven warming (although this was usually preventing by the gel heating system) and leaky gels where the electric field was not completely even.

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Could please elaborate on why too much salt from PCR can lead to this ? Thanks! –  biogirl Feb 27 at 8:07
The different salt concentrations cause different conditions for the currents which flow through the gel. When the conditions are not uniform, then the field is not uniform, which causes the transported nucleic acids to not move uniform. We could call it a "disturbance in the force" :-) –  Chris Feb 27 at 8:19

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