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When you run a gel electrophoresis, you add your gel and then submerge it in TAE or TBE buffer before you pipette your ladder, DNA, loading dye, etc. Why must the gel be submerged in buffer before you add anything? If anything, doesn't this make it harder to pipette into the well due to the diffraction of the buffer?

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This has a very simple reason: Adding the buffer later poses the risk to wash out your sample from the well as well as mixing samples.

There is another reason: It makes loading easier. The sample is mixed with loading dye which contains glycerol. This mixture is denser than the buffer and makes the sample sink to the bottom of the well. So you only need to get your pipette tip into the well (and not all the way down the bottom to deposit a very small drop of sample) and then you can release the sample from the tip. It will sink down due to gravity to the bottom of the well.

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