Function of MgCl2 in PCR

During replication dntp's gets broken down to dnmp's to form phosphodiester bond between 3' OH of adjacent nucleotide and 5' Phosphate of the upcoming nucleotide. in this reaction Mg++ binds to the alpha phosphate group of dntp and helps in the removal of beta and gamma Phosphate from dntp.

Another school of thought has it that increasing Mg++ increases Taq (DNA-dependent DNA polymerase) activity but at the expense of specificity, whereas less Mg++ lowers Taq's activity but increases its specificity. So the trick is knowing how much (or how little) to use. Generally, 3 mM Mg++ works well for most Taq-based mastermixes (used for PCR/qPCR) although as much as 5.5 mM Mg++ has been used with success in other mastermix formulations. Perhaps just use pi mM (3.14159265359 mM Mg++) and hope for the best~! You want good activity (productivity) but also good specificity...

From Research Gate..