Toward new liquid crystal phases of DNA mesogens

Abstract

Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase transition and that sufficiently bent structures can form a biaxial nematic phase. Here, we use numerical simulations to explore how the phase behavior of linear DNA constructs changes as we tune the mechanical properties of the constituent DNA by changing the nucleotide sequence. The IN-phase transition can be suppressed in so-called DNA “nunchakus”: structures consisting of two rigid dsDNA arms, separated by a sufficiently flexible spacer. In this paper, we use simulations to explore what phase behavior to expect for different linear DNA constructs. To this end, we first performed numerical simulations exploring the structural properties of a number of different DNA oligonucleotides using the oxDNA package. We then used the structural information generated in the oxDNA simulations to construct more coarse-grained models of the rod-like, bent-core, and nunchaku DNA. These coarse-grained models were used to explore the phase behavior of suspensions of the various DNA constructs. The approach explored in this paper makes it possible to “design” the phase behavior of DNA constructs by a suitable choice of the constituent nucleotide sequence.