Building up DNA, bit by bit: a simple description of chain assembly

TL;DR

This paper models DNA chain assembly using simple theoretical approaches, showing that limited molecular detail theories can effectively predict the equilibrium features of DNA copolymerization.

Contribution

It demonstrates that a straightforward theoretical model can accurately describe DNA copolymer chain length distributions, bridging detailed simulations and simplified theories.

Findings

The chain length statistics match the simple reversible reaction model.

Reaction constants can be predicted by Santalucia's or Wertheim's theories.

Limited molecular detail theories can predict broad equilibrium features.

Abstract

We simulate the assembly of DNA copolymers from two types of short duplexes (short double strands with a single-stranded overhang at each end), as described by the oxDNA model. We find that the statistics of chain lengths can be well reproduced by a simple theory that treats the association of particles into ideal (i.e., non-interacting) clusters as a reversible chemical reaction. The reaction constants can be predicted either from Santalucia's theory or from Wertheim's thermodynamic perturbation theory of association for spherical patchy particles. Our results suggest that theories incorporating very limited molecular detail may be useful for predicting the broad equilibrium features of copolymerisation.