Protocols for copying and proofreading in template-assisted polymerization

TL;DR

This paper analyzes various stochastic protocols for template-assisted polymer copying, including error correction and proofreading mechanisms, to understand their efficiency and limitations in improving copying accuracy.

Contribution

It systematically compares four different copying protocols, extending known models to explore how energetic and kinetic discrimination affect accuracy improvements.

Findings

Limited combinations of energetic and kinetic discrimination improve accuracy

Error correction protocols can enhance fidelity under specific conditions

Proofreading from intermediate steps offers different accuracy regimes

Abstract

We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation pathway. In the first protocol, monomer incorporation occurs in a single stochastic transition. We then move to a more elaborate protocol in which an intermediate step can be used for error correction. Finally, we discuss the operating regimes of two kinetic proofreading protocols: one in which proofreading acts from the final copying step, and one in which it acts from an intermediate step. We review known results for these models and, in some cases, extend them to analyze all possible combinations of energetic and kinetic discrimination. We show that, in each of these protocols, only a limited number of these combinations leads to an improvement of the overall copying accuracy.