Effect of concentration of MgCl2 on random-amplified DNA polymorphism

The influence of MgCl2 concentration on products in PCR to generate random-amplified polymorphic DNA (RAPD) was evaluated between two highly polymorphic cotton lines. Varying the concentration of MgCl2 (1.5 to 6.0 mM) in the PCR mixtures resulted in both quantitative differences in RAPD PCR-derived DNA bands and qualitative changes in the DNA band patterns. The optimum concentration of MgCl2 was within the range of 1.5 to 4.5 mM in the PCR mixtures for 154 of 200 random primers tested. The optimum concentration of MgCl2 for each primer was independent of the GC/AT ratio of the primer and the number of DNA band(s) amplified.