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Contaminants in Buffers
Contaminants in buffer reagents (Tris, borate, acetate, glycine, etc.), gel additives (SDS, urea, etc.), and laboratory water can have a profound effect on polymerization. The most common contaminants of these reagents are metals, non-buffer ions, and breakdown products. The most frequent effect of these contaminants is to inhibit polymerization. When polymerization is partially inhibited, the resulting gel will have greater porosity than intended, and molecules will have greater mobilities. Furthermore, control over polymerization reproducibility is compromised.

Initiator Type and Concentration
Initiators are the effectors of polymerization. Of course, the rate of polymerization depends on the concentration of initiators, but more importantly, the properties of the resulting gel also depend on the concentration of initiators. Increasing the concentration of initiators (e.g., ammonium persulfate and TEMED) results in a decrease in the average polymer chain length, an increase in gel turbidity, and a decrease in gel elasticity. In extreme cases, excess initiator can produce a gel solution that does not appear to polymerize at all. This is due to the formation of polymer chains so short that visible gelation does not take place and the polymer stays in solution. The only indication that a reaction has taken place is an increase in viscosity.

Excess ammonium persulfate and TEMED have other effects, including oxidation of sample proteins (especially sulfhydryl-containing compounds) a
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