Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled synthetic rings devoid of linear contaminants. Here, we create blended solutions of entangled ring and linear DNA with varying mass fractions of linear DNA. We use optical tweezers microrheology to measure the linear and nonlinear viscoelastic response of these blends. Our measurements reveal a strong non-monotonic dependence of linear viscoelastic properties on linear DNA fraction, with a pronounced maximum when the mass fraction of rings and linear chains are comparable, suggestive of pervasive threading of rings by linear chains. We observe a similar non-monotonicity in the nonlinear regime; however, a comparatively higher fraction of linear chains (0.5-0.7) is required for a substantial increase in resisitive force and slowing of relaxation dynamics to emerge. This nonlinear response also appears to be rate dependent, which we argue arises from force-induced de-threading of rings at high strain rates. Our results fill a longstanding gap in knowledge regarding the microrheology and nonlinear response of ring-linear polymer blends. Moreover, the uniquely strong mechanical response that ring-linear blends exhibit, along with the ability to finely tune these blends by varying the blend composition, provides new materials design principles.
Composites of flexible and rigid polymers are ubiquitous in biology and industry alike, yet the physical principles determining their mechanical properties are far from understood. Here, we couple force spectroscopy with large-scale Brownian Dynamics simulations to elucidate the unique viscoelastic properties of custom-engineered blends of entangled flexible DNA molecules and semiflexible actin filaments. We show that composites exhibit enhanced stress-stiffening and prolonged mechano-memory compared to systems of actin or DNA alone, and that these nonlinear features display a surprising non-m…
The attenuation of phonon modes of the DNA is due to the exchange of water molecules adsorbed by a molecule of DNA and the bulk solvent. Using Maxwell's mechanism of relaxation and a simple lattice model of the DNA, we show that the attenuation tends to a constant value for phonon frequencies larger than the inverse residence time of water molecules. We come to the conclusion that in the THz range the attenuation could be small enough to allow the propagation of the phonon modes.
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of producing polymers of different topologies, the dynamics of topological polymer blends remains poorly understood. We address this void by using both passive and active microrheology to characterize the linear and nonlinear rheological properties of blends of relaxed circular and supercoiled DNA. We characterize the dynamics as we vary the concentration from belo…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting the rapid transition between different relative strand positions [Biophys. Chem. 2 (1974) 83]. Here, we use a detailed theoretical model to study the basepairing dynamics of periodic and nearly periodic DNA. As suggested by Poerschke, DNA sliding is mediated by basepairing defects (bulge loops), which can diffuse along the DNA. Moreover, a shear force f on opp…
Molecular transport of biomolecules plays a pivotal role in the machinery of life. Yet, this role is poorly understood due the lack of quantitative information. Here, the role and properties of the C-terminal region of Escherichia coli Hfq is reported, involved in controlling the flow of a DNA solution. A combination of experimental methodologies has been used to probe the interaction of Hfq with DNA and to measure the rheological properties of the complex. A physical gel with a temperature reversible elasticity modulus is formed due to formation of non-covalent crosslinks. The mechanical resp…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the inability of the celebrated reptation model to capture their observed dynamics. Macrorheology and differential dynamic microscopy (DDM) are powerful methods to determine entangled polymer dynamics across scales, yet they typically require different samples under different conditions, preventing direct coupling of bulk rheological properties to the underlying…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers have been shown to exhibit enhanced shear thinning and viscosity, as well as prolonged relaxation timescales, compared to pure solutions of rings or linear chains. These emergent properties arise in part from the synergistic threading of rings by linear polymers. Topology has also been shown to play an important role in composites of flexible (e.g., DNA) and s…
Rheology and Programmable Gelation of DNA Origami Polymer Tadpoles
School of Physics and Astronomy, University of Edinburgh（爱丁堡大学物理与天文学学院）；School of Chemical, Materials and Biological Engineering, University of Sheffield（谢菲尔德大学化学、材料与生物工程学院）；MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh（爱丁堡大学生物遗传研究所人类遗传学单元）；International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM 2 ), Hiroshima University（广岛大学可拓手性超物质可持续发展国际研究所）
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the DNA sequence information. However, its physical properties as a reaction medium are poorly understood. Here, we exploit mobility measurements of differently sized inert green fluorescent tracer proteins to characterize the viscoelastic properties of the nuclear interior of a living human cell. We find that it resembles a viscous fluid on small and large scale…
We survey the linear viscoelasticity of a new type of transient network: bridged wormlike micelles, whose structure has been characterized recently [Ramos and Ligoure, (2007)]. This composite material is obtained by adding telechelic copolymers (water-soluble chains with hydrophobic stickers at each extremity) to a solution of entangled wormlike micelles (WM). For comparison, naked WM and WM decorated by amphiphilic copolymers are also investigated. While these latter systems exhibit almost a same single ideal Maxwell behavior, solutions of bridged WM can be described as two Maxwell fluids com…
Structuring wheat gluten proteins into gels with tunable mechanical properties would provide more versatility for the production of plant protein-rich food products. Gluten, a strongly elastic protein material insoluble in water, is hardly processable. We use a novel fractionation procedure allowing the isolation from gluten of a water/ethanol soluble protein blend, enriched in glutenin polymers at an unprecedented high ratio (50%). We investigate here the viscoelasticity of suspensions of the protein blend in a water/ethanol (50/50 v/v) solvent, and show that, over a wide range of concentrati…
A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal model based on the physical idea that constraints imposed on a cyclic polymer by infiltrating linear chains have to be released, before it can diffuse beyond a radius of gyration. Both, the simulation, and recently reported experimental data on entangled DNA solutions support the simple model over a wide range of blend compositions, concentrations, and molecular weights.
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…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive characterisation of material properties over a highly-dimensional parameter space, as well as a quantitative understanding of the physical principles underlying desirable features. Here we couple large-scale Molecular Dynamics simulations with optical tweezers microrheology to characterise the viscoelastic response of DNA-actin composites. We discover that the previously…
Complex fluids, such as polymer solutions and blends, colloids and gels, are of growing interest in fundamental and applied soft-condensed-matter science. A common feature of all such systems is the presence of a mesoscopic structural length scale intermediate between atomic and macroscopic scales. This mesoscopic structure of complex fluids is often fragile and sensitive to external perturbations. Complex fluids are frequently viscoelastic (showing a combination of viscous and elastic behaviour) with their dynamic response depending on the time and length scales. Recently, non-invasive method…
How local stresses propagate through polymeric fluids, and, more generally, how macromolecular dynamics give rise to viscoelasticity are open questions vital to wide-ranging scientific and industrial fields. Here, to unambiguously connect polymer dynamics to force response, and map stress propagation in macromolecular materials, we present a powerful approach-Optical Tweezers integrating Differential Dynamic Microscopy (OpTiDMM)-that simultaneously imposes local strains, measures resistive forces, and analyzes the motion of the surrounding polymers. Our measurements with blends of ring and lin…
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular interactions greatly influence chain dynamics. In this work, we directly observe the dynamics of DNA rings in semidilute ring-linear polymer blends using single molecule techniques. We systematically investigate ring polymer relaxation dynamics from high extension and transient and steady-state stretching dynamics in planar extensional flow for a series of …
Within the cell, biopolymers are often situated in constrained, fluid environments, e.g., cytoskeletal networks, stretched DNAs in chromatin. It is of paramount importance to understand quantitatively how they, utilizing their flexibility, optimally respond to a minute signal, which is, in general, temporally fluctuating far away from equilibrium. To this end, we analytically study viscoelastic response and associated stochastic resonance in a stretched single semi-flexible chain to an oscillatory force or electric field. Including hydrodynamic interactions between chain segments, we evaluate …
