SignificanceWhile widely known as the molecule of life, DNA is also an amazing building block at the nanoscale, since it allows us to design and program the structure and dynamics of functional nanomaterials. We exploit the programmability of DNA to achieve control over the rheology of self-assembled hydrogels, which have elastic or viscous behavior (similar to that of slime) that is finely regulated by temperature. Using microrheology to investigate the mechanical properties of DNA hydrogels at the microlength scale, we map the viscoelastic response over a broad range of frequencies and temperatures. The deep understanding in the fundamental physics provides a way to design DNA-based materials with precise control over the structure stability and rigidity at molecular level.
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.
The use of optical tweezers to measure forces acting upon microscopic particles has revolutionised fields from material science to cell biology. However, despite optical control capabilities, this technology is highly constrained by the material properties of the probe, and its use may be limited due to concerns about the effect on biological processes. Here we present a novel, optically controlled trapping method based on light-induced hydrodynamic flows. Specifically, we leverage optical control capabilities to convert a translationally invariant topological defect of a flow field into an attractor for colloids in an effectively one-dimensional harmonic, yet freely rotatable system. Circumventing the need to stabilise particle dynamics along an unstable axis, this novel trap closely resembles the isotropic dynamics of optical tweezers. Using magnetic beads, we explicitly show the existence of a linear force-extension relationship that can be used to detect femtoNewton-range forces with sensitivity close to the thermal limit. Our force measurements remove the need for laser-particle contact, while also lifting material constraints, which renders them a particularly interesting tool for the life sciences and engineering.
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.
One important aspect of the complete physical characterization of novel viscoelastic materials is the assessment of their response on short timescales. Optical tweezers, equipped with a fast quadrant photodiode, aid in fulfilling this task by providing high-frequency viscoelastic information about the sample. In passive microrheology, this is normally achieved by extracting rheological information from the thermal motion of an optically trapped bead embedded in a test fluid. Here we present the calibration and use of optical tweezers to study the formation of thermally reversible DNA hydrogels. We complement our results with rheological data from dynamic light scattering, video microscopy and conventional bulk rheology. Merging experimental data from different techniques allows us to study the viscoelastic behavior of these DNA networks over a wide frequency-band and the scaling of the complex viscoelastic modulus at the two frequency extremes. By analyzing the high-frequency behavior of our transient network, we prove the semi-flexible polymer nature of DNA and provide an estimate of its persistence length.
Recently, it has been demonstrated that thermoviscous flows can be used for a range of fine micromanipulations, such as moving the cytoplasm of cells and developing embryos, intracellular rheology, and femtonewton-range force measurements. These flows, also known as focused-light-induced cytoplasmic streaming (FLUCS), are induced by mid-infrared laser scanning of a temperature spot through the sample. However, localized laser scanning can inflict temperature perturbations of several Kelvins on the sample, potentially eliciting unspecific biological responses. In this study, we demonstrate how exploiting symmetry relations during laser scanning effectively disentangles laser heating and flow induction. We introduce flow-neutral scan sequences that use dynamic photothermal stimuli and spatiotemporal symmetry relations of scanning bridging up to three distinct time scales. We leverage further insights from a recently published analytical model of flow fields to present quasi-homogenous temperature distributions that leave flow lines and their local and directed character largely invariant. We present practical, intuitive solutions through predesigned sets of scan lines with near isothermal distributions and demonstrate that they are sufficient to generate and control flows in Caenorhabditis elegans embryos on a magnitude well in excess of endogenous flow velocities. Our results enable the separation of two previously tightly linked classes of physical stimuli, introduce a new, even less invasive standard for performing FLUCS perturbations, and pave the way for new unexplored avenues in the fields of soft matter and biomedicine. Graphical Abstract
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. Using particle image velocimetry (PIV), intra-nuclear displacement fields can be calculated and converted into spatio-temporally resolved maps of various strain components. Using this approach, we show that chromatin displacements are highly reversible, indicating that elastic contributions are dominant in maintaining nuclear organization on the time scale of seconds. In genetically inverted nuclei, centrally compacted heterochromatin displays high resistance to deformation, giving a rigid, solid-like appearance. Correlating spatially resolved strain maps with fluorescent reporters in conventional interphase nuclei reveals that various nuclear compartments possess distinct mechanical identities. Surprisingly, both densely and loosely packed chromatin showed high resistance to deformation, compared to medium dense chromatin. Equally, nucleoli display particularly high rigidity and strong local anchoring to heterochromatin. Our results establish how localized temperature gradients can be used to drive nuclear compartments out of mechanical equilibrium to obtain spatial maps of their material responses.Main FindingsNovel non-invasive active micro-rheology method to probe spatial intranuclear material responses, unhindered by the nuclear lamina, using strongly localized temperature gradientsChromatin shows both elastic and viscous properties at the mesoscale with a retardation time of τ ∼ 1sCompacted heterochromatin in a model of nuclear inversion shows high resistance to deformation, suggesting dominantly solid-like behaviorThe nucleus displays spatially distinct material properties for different compartmentsThe nucleolus shows high resistance to deformation on the time scale of secondsImmobile nucleoli appear solidly anchored to and retain the deformation of surrounding chromatin
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