Mechanisms of triplex-caused polymerization arrest

Pyrimidine/purine/purine triplexes are known to inhibit DNA polymerization. Here we have studied the mech-anisms of this inhibition by comparing the efficiency of Vent DNA polymerase on triplex- and duplex-contain-ing templates at different temperatures, Mg2+ con-centrations and time intervals with the thermal stability of the corresponding structures. Our results show that triplexes can only be by-passed at temperatures where thermal denaturation initiates, while duplexes, in contrast, are overcome at temperatures where they are quite stable. These results show that DNA polymerase cannot untangle triplex regions within DNA templates and seems to entirely depend on their thermal fluctu-ations. The high stability of triplexes at physiological temperatures and ambient conditions make them a barrier to polymerization