Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

TL;DR

This study combines simulations and theory to understand how short DNA duplexes self-assemble into chains and form liquid crystal phases, aligning well with experimental data and enabling free energy estimation.

Contribution

It introduces a parameter-free theoretical framework linked with a coarse-grained DNA model to predict self-assembly and phase behavior of short DNA duplexes.

Findings

Accurate theoretical predictions of phase boundaries

Simulation results match experimental observations

Method estimates stacking free energy effectively

Abstract

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [ J. Chem. Phys. 134, 08501 (2011) ]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameter-free theoretical predictions provide an accurate description of the simulation results in the isotropic phase. In addition, the theoretical isotropic-nematic phase boundaries are in line with experimental findings, providing a route to estimate the stacking free energy.