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Register a new userProbing DNA-amyloid interaction and gel formation by active magnetic wire microrheology
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Added by
Jean-Francois Berret
Publication date
2021
fields
Physics
and research's language is
English
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Recent studies have shown that bacterial nucleoid-associated proteins (NAPs) can bind to DNA and result in altered structural organization and bridging interactions. Under spontaneous self-assembly, NAPs may form anisotropic amyloid fibers, whose effects are still more significant on DNA dynamics. To test this hypothesis, microrheology experiments on dispersions of DNA associated with the amyloid terminal domain (CTR) of the bacterial protein Hfq were performed using the technique of magnetic rotational spectroscopy (MRS). In this chapter, we survey this microrheology technique which is based on the remote actuation of magnetic wires embedded in a sample. MRS is interesting as it is easy to implement, and does not require complex procedures regarding data treatment. Pertaining to the interaction between DNA and amyloid fibers, it is found that DNA and Hfq-CTR protein dispersion behave like a gel, an outcome that suggests the formation of a network of amyloid fibers cross-linked with the DNA strands. In contrast, the pristine DNA and Hfq-CTR dispersions behave as purely viscous liquids. To broaden the scope of the MRS technique, we include theoretical predictions for the rotation of magnetic wires regarding the generic behaviors of basic rheological models from continuum mechanics, and we list the complex fluids studied by this technique over the past 10 years.
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Mucus is a viscoelastic gel secreted by the pulmonary epithelium in the tracheobronchial region of the lungs. The coordinated beating of cilia moves mucus upwards towards pharynx, removing inhaled pathogens and particles from the airways. The efficacy of this clearance mechanism depends primarily on the rheological properties of mucus. Here we use magnetic wire based microrheology to study the viscoelastic properties of human mucus collected from human bronchus tubes. The response of wires between 5 and 80 microns in length to a rotating magnetic field is monitored by optical time-lapse microscopy and analyzed using constitutive equations of rheology, including those of Maxwell and Kelvin-Voigt. The static shear viscosity and elastic modulus can be inferred from low frequency (from 0.003 to 30 rad s-1) measurements, leading to the evaluation of the mucin network relaxation time. This relaxation time is found to be widely distributed, from one to several hundred seconds. Mucus is identified as a viscoelastic liquid with an elastic modulus of 2.5 +/- 0.5 Pa and a static viscosity of 100 +/- 40 Pa s. Our work shows that beyond the established spatial variations in rheological properties due to microcavities, mucus exhibits secondary inhomogeneities associated with the relaxation time of the mucin network that may be important for its flow properties.
A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing-wave spectroscopy (DWS) to investigate the viscoelastic behavior of a hydrogel made of Y-shaped DNA nano-stars over a wide range of frequencies and temperatures. Results show a clear liquid-to-equilibrium-gel transition as the temperature cycles up and down across the melting-temperature region for which the Y-DNA bind to each other. These first measurements reveal the crossover of the elastic G({omega}) and loss modulus G({omega}) when the DNA-hydrogel formed at low temperatures is heated to a fluid phase of DNA nano-stars well above the melt temperature Tm. We show that the crossover relates to the life-time of the DNA-bond and also that percolation coincides with the systems Tm. The approach demonstrated here can be easily extended to more complicated DNA hydrogel systems and provides guidance for the future design of such transient, semi-flexible networks that can be adapted to the application of molecular sensing and controlled release.
In the technique of microrheology, macroscopic rheological parameters as well as information about local structure are deduced from the behavior of microscopic probe particles under thermal or active forcing. Microrheology requires knowledge of the relation between macroscopic parameters and the force felt by a particle in response to displacements. We investigate this response function for a spherical particle using the two-fluid model, in which the gel is represented by a polymer network coupled to a surrounding solvent via a drag force. We obtain an analytic solution for the response function in the limit of small volume fraction of the polymer network, and neglecting inertial effects. We use no-slip boundary conditions for the solvent at the surface of the sphere. The boundary condition for the network at the surface of the sphere is a kinetic friction law, for which the tangential stress of the network is proportional to relative velocity of the network and the sphere. This boundary condition encompasses both no-slip and frictionless boundary conditions as limits. Far from the sphere there is no relative motion between the solvent and network due to the coupling between them. However, the different boundary conditions on the solvent and network tend to produce different far-field motions. We show that the far field motion and the force on the sphere are controlled by the solvent boundary conditions at high frequency and by the network boundary conditions at low frequency. At low frequencies compression of the network can also affect the force on the sphere. We find the crossover frequencies at which the effects of sliding of the sphere past the polymer network and compression of the gel become important.
Soft solids like colloidal glasses exhibit a yield stress, above which the system starts to flow. The microscopic analogon in microrheology is the delocalization of a tracer particle subject to an external force exceeding a threshold value, in a glassy host. We characterize this delocalization transition based on a bifurcation analysis of the corresponding mode-coupling theory equations. A schematic model is presented first, that allows analytical progress, and the full physical model is studied numerically next. This analysis yields a continuous type A transition with a critical power law decay of the probe correlation functions with exponent $-1/2$. In order to compare with simulations with a limited duration, a finite time analysis is performed, which yields reasonable results for not-too-small wave vectors. The theoretically predicted findings are verified by Langevin dynamics simulations. For small wave vectors we find anomalous behavior for the probe position correlation function, which can be traced back to a wave vector divergence of the critical amplitude. In addition we propose and test three methods to extract the critical force from experimental data, which provide the same value of the critical force when applied to the finite-time theory or simulations.
We analyze the dynamics of a tracer particle embedded in a bath of hard spheres confined in a channel of varying section. By means of Brownian dynamics simulations we apply a constant force on the tracer particle and discuss the dependence of its mobility on the relative magnitude of the external force with respect to the entropic force induced by the confinement. A simple theoretical one-dimensional model is also derived, where the contribution from particle-particle and particle-wall interactions is taken from simulations with no external force. Our results show that the mobility of the tracer is strongly affected by the confinement. The tracer velocity in the force direction has a maximum close to the neck of the channel, in agreement with the theory for small forces. Upon increasing the external force, the tracer is effectively confined to the central part of the channel and the velocity modulation decreases, what cannot be reproduced by the theory. This deviation marks the regime of validity of linear response. Surprisingly, when the channel section is not constant the effective friction coefficient is reduced as compared to the case of a plane channel. The transversal velocity, which cannot be studied with our model, follows the qualitatively the derivative of the channel section, in agreement previous theoretical calculations for the tracer diffusivity in equilibrium.
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