Efficient fidelity control by stepwise nucleotide selection in polymerase elongation

Polymerases select nucleotides before incorporating them for chemical synthesis during gene replication or transcription. How the selection proceeds stepwise efficiently to achieve sufficiently high fidelity and speed is essential for polymerase function. We examined step-by-step selections that have conformational transition rates tuned one at time in the polymerase elongation cycle, with a controlled differentiation free energy at each checkpoint. The elongation is sustained at non-equilibrium steady state with constant free energy input and heat dissipation. It is found that error reduction capability does not improve for selection checkpoints down the reaction path. Hence, it is essential to select early to achieve an efficient fidelity control. In particular, for two consecutive selections that reject the wrong substrate back and inhibit it forward from a same kinetic state, the same error rates are obtained at the same free energy differentiation. The initial screening is indispensible for maintaining the elongation speed high, as the wrong nucleotides can be removed quickly and replaced by the right nucleotides at the entry. Overall, the elongation error rate can be repeatedly reduced through multiple selection checkpoints. The study provides a theoretical framework to conduct further detailed researches, and assists engineering and redesign of related enzymes.