Self-assembly of bi-functional patchy particles with anisotropic shape into polymers chains: theory and simulations

TL;DR

This paper models the self-assembly of DNA duplexes into polymer chains using a coarse-grained simulation and theoretical analysis, accurately predicting phase behavior and estimating stacking energies.

Contribution

It introduces a novel coarse-grained model of DNA duplexes with reactive sites and compares simulation results with theoretical predictions and experiments.

Findings

Quantitative agreement between simulations and theory for phase boundaries

Successful modeling of DNA duplex self-assembly as equilibrium polymerization

Estimation of stacking energy consistent with experimental data

Abstract

Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes their aggregation into poly-disperse chains with a significant persistence length. Experiments show that liquid crystals phases form above a critical volume fraction depending on the duplex length. We introduce and investigate via numerical simulations, a coarse-grained model of DNA double-helical duplexes. Each duplex is represented as an hard quasi-cylinder whose bases are decorated with two identical reactive sites. The stacking interaction between terminal sites is modeled via a short-range square-well potential. We compare the numerical results with predictions based on a free energy functional and find satisfactory quantitative matching of the isotropic-nematic phase boundary and of the system structure. Comparison of numerical and theoretical results with experimental findings confirm that the DNA duplexes self-assembly can be properly modeled via equilibrium polymerization of cylindrical particles and enables us to estimate the stacking energy.