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Essentially it is the separation of DNA, RNA and proteins according to their size. The molecules are loaded at the (-) electrode and when switched on (running the gel) the migrate towards the (+) electrode. The molecules move through a medium (agarose or polyacrylamide etc) which acts as a sieve. This allows the separation of molecules according to size, as the larger molecules will get stuck earlier on in the medium whereas the smaller ones will travel further. Higher percentage (concentration) gels will separate smaller molecules.

 

The general process is as follows:

 

Make up gel

Cast gel and add the comb (this creates the wells where you load your sample)

Wait for it to dry

Remove comb and place gel into apparatus (wells closest to (-) electrode)

Add the appropriate buffer

Load samples, molecular marker

Add stain(some protocols do this after the whole process)

Run the gel (add the current at x Volt for y time)

Visualise (UV camera etc)

http://en.wikipedia.org/wiki/Gel_electrophoresis

Or check out the Sigma-Aldrich website, I think they have a few protocols too

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