Three-dimensional DNA networks, composed of tri-or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexiblity provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters.

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.

Nano-sized particles functionalised with short single-stranded (ss)DNAs can act as detectors of complementary DNA strands. Here we consider tri-block-copolymer-based, self-assembling DNA-coated nanoparticles. The copolymers are chemically linked to the DNA strands via azide (N3) groups. The micelles aggregate when they are linked with complementary ssDNA. The advantage of such block-copolymer-based systems is that they are easy to make. Here we show that DNA functionalisation results in inter-micellar attraction, but that N3-groups that have not reacted with the DNA detector strands also change the phase behaviour of the tri-block polymer solution. We studied the triblock copolymer, Pluronic® F108, which forms spherical micelles in aqueous solutions upon heating. We find that the triblock chains ending with either an N3 or N3-DNA complex show a dramatic change in phase behaviour. In particular, the N3-functionalisation causes the chain ends to cluster below the critical micelle temperature (CMT) of pure F108, forming flower-micelles with the N3-groups at the core, while the PPO groups are exposed to the solvent. Above the CMT, we see an inversion with the PPO chains forming the micellar core, while the N3-groups are now aggregating on the periphery, inducing an attraction between the micelles. Our results demonstrate that, due to the two competing self-assembling mechanisms, the system can form transient hydrogels.