What is the role of magnesium chloride in pcr?
An essential cofactor for the DNA polymerase in PCR is Magnesium chloride. Its concentration must be optimized for every primer:template system. Many components of the reaction bind magnesium ion, including primers, template, PCR products and dNTPs. The main 1:1 binding agent for magnesium ion is the high concentration of dNTPs in the reaction. Because it is necessary for free magnesium ion to serve as an enzyme cofactor in PCR, the total magnesium ion concentration must exceed the total dNTP concentration. Typically, to start the optimization process, 1.5 mM magnesium chloride is added to PCR in the presence of 0.8 mM total dNTPs. This leaves about 0.7 mM free magnesium for the DNA polymerase. In general, magnesium ion should be varied in a concentration series from 1.5-4.0 mM in 0.5 mM steps.
