Edge-effects dominate copying thermodynamics for finite-length molecular oligomers

TL;DR

This paper investigates the thermodynamics of finite-length oligomer copying, revealing that initiation and termination dominate the thermodynamic costs, and that copy accuracy is not directly linked to thermodynamic expense, with implications for biological and synthetic systems.

Contribution

It introduces a framework separating informational and chemical thermodynamics in oligomer copying, highlighting the dominant role of edge effects over accuracy in thermodynamic costs.

Findings

Copy accuracy is thermodynamically neutral or favored depending on the environment.

Edge effects dominate the thermodynamics of finite-length oligomer copying.

Kinetic barriers for accuracy constraints are more relevant in finite-length oligomers.

Abstract

Living systems produce copies of information-carrying molecules such as DNA by assembling monomer units into finite-length oligomer (short polymer) copies. We explore the role of initiation and termination of the copy process in the thermodynamics of copying. By splitting the free-energy change of copy formation into informational and chemical terms, we show that copy accuracy plays no direct role in the overall thermodynamics. Instead, it is thermodynamically costly to produce outputs that are more similar to the oligomers in the environment than sequences obtained by randomly sampling monomers. Copy accuracy can be thermodynamically neutral, or even favoured, depending on the surroundings. Oligomer copying mechanisms can thus function as information engines that interconvert chemical and information-based free energy. Hard thermodynamic constraints on accuracy derived for infinite-length polymers instead manifest as kinetic barriers experienced while the copy is template-attached. These barriers are easily surmounted by shorter oligomers.