Balancing Non-Equilibrium Driving with Nucleotide Selectivity at Kinetic Checkpoints in Polymerase Fidelity Control.

Abstract

High fidelity gene transcription and replication require kinetic discrimination of nucleotide substrate species by RNA and DNA polymerases under chemical non-equilibrium conditions. It is known that sufficiently large free energy driving force is needed for each polymerization or elongation cycle to maintain far-from-equilibrium to achieve low error rates. Considering that each cycle consists of multiple kinetic steps with different transition rates, one expects that the kinetic modulations by polymerases are not evenly conducted at each step. We show that accelerations at different kinetic steps impact quite differently to the overall elongation characteristics. In particular, for forward transitions that discriminate cognate and non-cognate nucleotide species to serve as kinetic selection checkpoints, the transition cannot be accelerated too quickly nor retained too slowly to obtain low error rates, as balancing is needed between the nucleotide selectivity and the non-equilibrium driving. Such a balance is not the same as the speed-accuracy tradeoff in which high accuracy is always obtained at sacrifice of speed. For illustration purposes, we used three-state and five-state models of nucleotide addition in the polymerase elongation and show how the non-equilibrium steady state characteristics change upon variations on stepwise forward or backward kinetics. Notably, by using the multi-step elongation schemes and parameters from T7 RNA polymerase transcription elongation, we demonstrate that individual transitions serving as selection checkpoints need to proceed at moderate rates in order to sustain the necessary non-equilibrium drives as well as to allow nucleotide selections for an optimal error control. We also illustrate why rate-limiting conformational transitions of the enzyme likely play a significant role in the error reduction.