Mg & extraneous bands

unknown at unknown at
Wed Jan 12 11:31:17 EST 1994

I think I can help, having just finished a class entitled Nucleic Acids.
dsNAs bind cations better than ssNAs do (counterion condensation and coulombic
"screening"), and with divalent cations, the effect is even more pronounced.
Thus, we have an equilibrium that looks something like this:
            dsDNA:Mg <====> ssDNA + Mg + anion
Thus, excess Mg will drive the reaction towards formation of dsDNA, essentially
lowering the Tm observed for a primer/template pair. Thus, what you are seeing
are bona fide artifacts caused by your primer mispairing at a different site on
your template, producing who knows what products. BTW, I have found the "a

Amplify" program for the Macinotosh to be very useful for identifying potential
mispriming sites

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