Magnesium Chloride is the important entity in any PCR reaction. Mg++ forms a complex with dNTP's, which is a substrate of the polymerase enzymes. An adequate concentration of MgCl2 is required for optimal results, which is 1.5mM (when the concentration of each dNTP is 200mM). Mg++ also has an affect on enzyme activity, tend to raise the Tm of double stranded DNA.
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