  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.
