Quantitative Characterization of RCA-Based DNA Hydrogels - Towards Rational Materials Design.

DNA hydrogels hold significant promise for biomedical applications and can be synthesized through enzymatic Rolling Circle Amplification (RCA). Due to the exploratory nature of this emerging field, standardized RCA protocols specifying the impact of reaction parameters are currently lacking. This study varied template sequences and reagent concentrations, evaluating RCA synthesis efficiency and hydrogel mechanical properties through quantitative PCR (qPCR) and indentation measurements, respectively. Primer concentration and stabilizing additives showed minimal impact on RCA efficiency, while changes in polymerase and nucleotide concentrations had a stronger effect. Concentration of the circular template exerted the greatest influence on RCA productivity. An exponential correlation between hydrogel viscosity and DNA amplicon concentration was observed, with nucleobase sequence significantly affecting both amplification efficiency and material properties, particularly through secondary structures. This study suggests that combining high-throughput experimental methods with structural folding prediction offers a viable approach for systematically establishing structure-property relationships, aiding the rational design of DNA hydrogel material systems.

Feedback-based positioning and diffusion suppression of particles via optical control of thermoviscous flows.

The ability to control the position of micron-size particles with high precision using tools such as optical tweezers has led to major advances in fields such as biology, physics and material science. In this paper, we present a novel optical strategy to confine particles in solution with high spatial control using feedback-controlled thermoviscous flows. We show that this technique allows micron-size particles to be positioned and confined with subdiffraction precision (24 nm), effectively suppressing their diffusion. Due to its physical characteristics, our approach might be particular attractive where laser exposure is of concern or materials are inherently incompatible with optical tweezing since it does not rely on contrast in the refractive index.

On the role of flexibility in linker-mediated DNA hydrogels.

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 flexibility 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 a 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 a much-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. Moreover, we present a systematic study of the strong viscosity increase of aqueous solutions in the presence of these DNA building blocks.

Sprouting Droplets Driven by Physical Effects Alone.

Combining a partially miscible three-liquid system with interfacially trapped silica colloids, we show that small droplets can exhibit dramatic growth phenomena driven by physical effects alone. The mass dense droplets sprout tubes which grow vertically upward in a gravitational field and respond to the presence of other droplets in their path. Two of the liquids in our system are water and toluene. By varying the third liquid, we are able to relate the growth behavior to the details of the underlying three-fluid phase diagram and the changes to the interfacial tension. Additionally, we introduce a pendant drop in the path of our growing drop. We use this to confirm that growth is driven by the partitioning of solvents, that exchange of solvents between droplets is chemically selective, and that the exchange behavior can itself generate further growth phenomena.

Bulk rheology of sticky DNA-functionalized emulsions.

We measure by experiment and particle-based simulation the rheology of concentrated, non-Brownian droplet emulsions functionalized with surface-bound single-stranded (ss), "sticky," DNA. In the absence of ssDNA, the emulsion viscosity increases with the dispersed phase volume fraction ϕ, before passing through a liquid-solid transition at a critical ϕ_{c} related to random close packing. Introducing ssDNA leads to a liquid-solid transition at ϕ<ϕ_{c}, the onset being set by the droplet valency N and the ssDNA concentration (or simulated binding strength ε). Using insight from simulation, we identify three key behaviors: (i) jammed suspensions (ϕ>ϕ_{c}≈0.64) show weak effects of functionalization, with elastic rheology instead governed by droplet stiffness; (ii) suspensions with ϕ<ϕ_{c} and N=1, 2 always exhibit viscous rheology, regardless of functionalization; and (iii) for ϕ<ϕ_{c} and N>3, functionalization leads to a controllable viscous-elastic transition. We present state diagrams showing the range of rheological tuning attainable by these means.