Template-directed biopolymerization: tape-copying Turing machines

TL;DR

This paper reviews the mechanisms and collective behavior of natural tape-copying Turing machines like DNA, RNA, and protein polymerizers, highlighting their common features and inspiring new kinetic models from a physics perspective.

Contribution

It provides a comprehensive analysis of template-directed biopolymerization machines and introduces the concept of modular machines with different polymerization types.

Findings

Natural polymerizers function as tape-copying Turing machines

Common features identified across different biopolymerization machines

Introduction of modular machines with distinct template-directed polymerization

Abstract

DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using another linear polymer as the corresponding template. The machine utilizes input chemical energy to move along the template which also serves as a track for the movements of the machine. In the Alan Turing year 2012, it is worth pointing out that these machines are "tape-copying Turing machines". We review the operational mechanisms of the polymerizer machines and their collective behavior from the perspective of statistical physics, emphasizing their common features in spite of the crucial differences in their biological functions. We also draw attention of the physics community to another class of modular machines that carry out a different type of template-directed polymerization. We hope this review will inspire new kinetic models for these modular machines.