Self-assembly of mesogenic bent-core DNA nanoduplexes

Short cylinder-like DNA duplexes, comprising 6 to 20 base pairs, self-assemble into semi-flexible chains, due to coaxial stacking interactions between their blunt ends. The mutual alignment of these chains gives rise to macroscopically orientationally ordered liquid crystals phases. Interestingly, experiments show that the isotropic-nematic phase boundary is sequence-dependent. We perform all atom simulation of several sequences to gain insights in the structural properties of the duplex and correlate the resulting geometric properties with the observed location of the isotropic-nematic phase boundary. We identify in the duplex bending the key parameter for explaining the sequence dependence, suggesting that DNA duplexes can be assimilated to bent-core mesogens. We also develop a coarse-grained model for the different DNA duplexes to evaluate in details how bending affect persistence length and excluded volume of the aggregates. These informations are fed into a recently developed formalism to predict the isotropic-nematic phase boundary for bent-core mesogens. The theoretical results agree with the experimental observation.