Modelling the melting of DNA oligomers with non-inert dangling ends.

In this work, we investigate the dependence of the melting temperature of low-valency DNA constructs on the length of non-inert dangling ends, controlling their sequence composition. We compare two computational models to evaluate their effectiveness and limitations in predicting the melting behavior of DNA oligomers (bivalent linkers) and more complex structures (trivalent nanostars), benchmarking the results against experimental spectroscopic data. Our results suggest that the length of non-inert dangling ends has minimal impact on the melting point of the DNA duplex for the duplexes we studied, informing the future design of DNA supramolecular constructs.

Mechanically Tunable DNA Hydrogels as Prospective Biosensing Modules.

Sequence-programmable DNA building blocks offer high degree of freedom in designing arbitrarily complex networks of tunable viscoelastic properties. Yet, the deployment of DNA-based functional materials remains limited due to insufficient control over the emerging structures and their mechanics. In an ongoing effort to place structure-property relations in stimuli-responsive DNA materials on a firm foundation, here a systematic rheological study of self-assembling DNA networks is presented, comprised of short DNA nanomotifs, namely trivalent nanostars and bivalent linkers, where the latter differ in their composition on a single base-pair level.

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.

Probe-free optical chromatin deformation and measurement of differential mechanical properties in the nucleus.

The nucleus is highly organized to facilitate coordinated gene transcription. Measuring the rheological properties of the nucleus and its sub-compartments will be crucial to understand the principles underlying nuclear organization. Here, we show that strongly localized temperature gradients (approaching 1°C/µm) can lead to substantial intra-nuclear chromatin displacements (>1 µm), while nuclear area and lamina shape remain unaffected.

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).

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.

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.

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.