  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.
