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Before this is done, the sample will be mixed with some of the solution containing SDS (sodium dodecyl sulfate). This compound dissociates in solution yielding the negative large ions that will be useful for the purpose of the electrophoresis. Since the Alkaline Phosphatase still has some positively charged groups on it, even though it has a net negative charge in the loading buffer, the SDS negative ions will surround these positively charged groups and make the protein a large negative mass of a molecule. This will be the factor that will guide it through the gel under voltage that will be applied to the gel...
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