WHY IS THE POLYMERASE CHAIN-REACTION RESISTANT TO IN-VITRO EVOLUTION

A variety of methods have been developed to amplify DNA and RNA. These methods vary in their susceptibility to evolve new molecular species differing from the starting template. PCR is exceptionally resistant t o in vitro evolution, whereas methods such as Q beta replicase and 3SR are much Less robust. This paper develops some simple mathematical mo dels which suggest that PCR is resistant to in vitro evolution because the reaction controls replication in discrete cycles: fast replicatio n is of little advantage during PCR because the reaction limits fast r eplicators as well as slow ones to a single copy per cycle. In contras t, continuous (isothermal) reactions, as in the Q beta replicase react ion, favor fast replicators. The advantage of fast replication is comp ounded in continuous reactions, because a fast replicator can complete many generations of replication during the time it takes a slow repli cator to complete one generation, These models suggest that continuous amplication protocols will never achieve the robustness against in vi tro evolution observed with PCR.