Replicative DNA polymerases are molecular motors that catalyze template-directed DNA replication. In each catalytic cycle, these enzymes incorporate the correct nucleotide into the primer or growing strand releasing pyrophosphate as a product. As a result of this reaction replicative polymerases translocate along their DNA substrates in steps of one nucleotide at a time (0.34 nm). Although accurate translocation is essential for genome integrity little is known about the kinetics, energetics and integration of this process in the nucleotide addition cycle during processive DNA replication. To address these subjects we have used optical tweezers to manipulate individual Phi29 DNA polymerase-DNA complexes and measure the effect of mechanical force aiding and opposing translocation on the polymerase activity at varying nucleotide (dNTPs) concentrations. Application of controlled forces on a single polymerase biases the rates of chemical reactions involving translocation and provided quantitative information about the ‘real time’ kinetics of elongation and the conversion of chemical energy to motion (mechano-chemistry) during protein activity. Fits to the replication velocity dependencies on force and dNTP concentration were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release. Instead, our data is consistent with a Brownian ratchet model in which the polymerase oscillates between the pre- and post-translocation states separated by ∼0.34 nm. The post-translocation state is energetically favored only by 0.7 KBT but it is further stabilized by the binding of the correct dNTP.
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