Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions

The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthesis of synthetic chemical complexes. Unlike the superficially similar process of self-assembly, however, the development of synthetic systems that implement templated copying of copolymers under constant environmental conditions has been challenging. The main difficulty has been overcoming product inhibition or the tendency of products to adhere strongly to their templates-an effect that gets exponentially stronger with the template length. We develop coarse-grained models of copolymerization on a finite-length template and analyze them through stochastic simulation. We use these models first to demonstrate that product inhibition prevents reliable template copying and then ask how this problem can be overcome to achieve cyclic production of polymer copies of the right length and sequence in an autonomous and chemically driven context. We find that a simple addition to the model is sufficient to generate far longer polymer products that initially form on, and then separate from, the template. In this approach, some of the free energy of polymerization is diverted into disrupting copy-template bonds behind the leading edge of the growing copy copolymer. By additionally weakening the final copy-template bond at the end of the template, the model predicts that reliable copying with a high yield of full-length, sequence-matched products is possible over large ranges of parameter space, opening the way to the engineering of synthetic copying systems that operate autonomously. (c) 2022 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

Automated summary

The production of sequence-specific copolymers using copolymer templates is crucial for the synthesis of complex biological molecules and synthetic chemical complexes. Overcoming product inhibition has been a major challenge in implementing templated copying of copolymers. In this study, we develop coarse-grained models and use stochastic simulation to analyze copolymerization on a finite-length template. We demonstrate that product inhibition hinders reliable template copying and propose a solution to achieve cyclic production of polymer copies by disrupting copy-template bonds and weakening the final copy-template bond. This research opens up possibilities for engineering synthetic copying systems that operate autonomously.