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

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., 2011, 134, 08501]. 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 and theoretical values for the isotropic-nematic phase boundaries which are in line with experimental findings. In addition, the developed theoretical framework makes it possible to provide a route to estimate the stacking free energy.