1
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Neill P, Crist N, McGorty R, Robertson-Anderson R. Enzymatic cleaving of entangled DNA rings drives scale-dependent rheological trajectories. SOFT MATTER 2024; 20:2750-2766. [PMID: 38440846 DOI: 10.1039/d3sm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA, which naturally occurs in linear, ring, and supercoiled topologies, frequently undergoes enzyme-driven topological conversion and fragmentation in vivo, enabling it to perform a variety of functions within the cell. In vitro, highly concentrated DNA polymers form entanglements that yield viscoelastic properties dependent on the topologies and lengths of the DNA. Enzyme-driven alterations of DNA size and shape therefore offer a means of designing active materials with programmable viscoelastic properties. Here, we incorporate multi-site restriction endonucleases into dense DNA solutions to linearize and fragment circular DNA molecules. We pair optical tweezers microrheology with differential dynamic microscopy and single-molecule tracking to measure the linear and nonlinear viscoelastic response and transport properties of entangled DNA solutions over a wide range of spatiotemporal scales throughout the course of enzymatic digestion. We show that, at short timescales, relative to the relaxation timescales of the polymers, digestion of these 'topologically-active' fluids initially causes an increase in elasticity and relaxation times followed by a gradual decrease. Conversely, for long timescales, linear viscoelastic moduli exhibit signatures of increasing elasticity. DNA diffusion, likewise, becomes increasingly slowed, in direct opposition to the short-time behavior. We hypothesize that this scale-dependent rheology arises from the population of small DNA fragments, which increases as digestion proceeds, driving self-association of larger fragments via depletion interactions, giving rise to slow relaxation modes of clusters of entangled chains, interspersed among shorter unentangled fragments. While these slow modes likely dominate at long times, they are presumably frozen out in the short-time limit, which instead probes the faster relaxation modes of the unentangled population.
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Affiliation(s)
- Philip Neill
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Natalie Crist
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Ryan McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Rae Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
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2
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Goto S, Kim K, Matubayasi N. Unraveling the Glass-like Dynamic Heterogeneity in Ring Polymer Melts: From Semiflexible to Stiff Chain. ACS POLYMERS AU 2023; 3:437-446. [PMID: 38107414 PMCID: PMC10722566 DOI: 10.1021/acspolymersau.3c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 12/19/2023]
Abstract
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and monomer density on the static and dynamic behaviors of ring polymer melts using molecular dynamics simulations. Our first focus is on the non-Gaussian parameter of center-of-mass displacement as a measure of dynamic heterogeneity, which is commonly observed in glass-forming liquids. We find that the non-Gaussianity in the displacement distribution increases with the monomer density and stiffness of the polymer chains, suggesting that excluded volume interactions between centers of mass have a strong effect on the dynamics of ring polymers. We then analyze the relationship between the radius of gyration and monomer density for semiflexible and stiff ring polymers. Our results indicate that the relationship between the two varies with chain stiffness, which can be attributed to the competition between repulsive forces inside the ring and from adjacent rings. Finally, we study the dynamics of bond-breakage virtually connected between the centers of mass of rings to analyze the exchanges of intermolecular networks of bonds. Our results demonstrate that the dynamic heterogeneity of bond-breakage is coupled with the non-Gaussianity in ring polymer melts, highlighting the importance of the bond-breaking method in determining the intermolecular dynamics of ring polymer melts. Overall, our study sheds light on the factors that govern the dynamic behaviors of ring polymers.
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Affiliation(s)
- Shota Goto
- Division of Chemical Engineering, Department
of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department
of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department
of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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3
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Marfai J, McGorty RJ, Robertson-Anderson RM. Cooperative Rheological State-Switching of Enzymatically-Driven Composites of Circular DNA And Dextran. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305824. [PMID: 37500570 DOI: 10.1002/adma.202305824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, composites of circular DNA and dextran are pushed out-of-equilibrium via enzymatic digestion of DNA rings to linear fragments. These time-resolved rheology measurements reveal discrete state-switching, with composites undergoing abrupt transitions between dissipative and elastic-like states. The gating time and lifetime of the elastic-like states, and the magnitude and sharpness of the transitions, are surprisingly decorrelated from digestion rates and non-monotonically depend on the DNA fraction. These results are modeled using sigmoidal two-state functions to show that bulk state-switching can arise from continuous molecular-level activity due to the necessity for cooperative percolation of entanglements to support macroscopic stresses. This platform, coupling the tunability of topological composites with the power of enzymatic reactions, may be leveraged for diverse material applications from wound-healing to self-repairing infrastructure.
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Affiliation(s)
- Juexin Marfai
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, 92110, USA
| | - Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, 92110, USA
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4
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Staňo R, Likos CN, Smrek J. To thread or not to thread? Effective potentials and threading interactions between asymmetric ring polymers. SOFT MATTER 2022; 19:17-30. [PMID: 36477247 PMCID: PMC9768673 DOI: 10.1039/d2sm01177h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
We use computer simulations to study a system of two unlinked ring polymers, whose length and bending stiffness are systematically varied. We derive the effective potentials between the rings, calculate the areas of minimal surfaces of the same, and characterize the threading between them. When the two rings are of the same kind, threading of a one ring through the surface of the other is immanent for small ring-ring separations. Flexible rings pierce the surface of the other ring several times but only shallowly, as compared to the stiff rings which pierce less frequently but deeply. Typically, the ring that is being threaded swells and flattens up into an oblate-like conformation, while the ring that is threading the other takes a shape of an elongated prolate. The roles of the threader and the threaded ring are being dynamically exchanged. If, on the other hand, the rings are of different kinds, the symmetry is broken and the rings tend to take up roles of the threader and the threaded ring with unequal probabilities. We propose a method how to predict these probabilities based on the parameters of the individual rings. Ultimately, our work captures the interactions between ring polymers in a coarse-grained fashion, opening the way to large-scale modelling of materials such as kinetoplasts, catenanes or topological brushes.
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Affiliation(s)
- Roman Staňo
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
- Vienna Doctoral School in Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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5
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Ubertini MA, Smrek J, Rosa A. Entanglement Length Scale Separates Threading from Branching of Unknotted and Non-concatenated Ring Polymers in Melts. Macromolecules 2022; 55:10723-10736. [DOI: 10.1021/acs.macromol.2c01264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Mattia Alberto Ubertini
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136Trieste, Italy
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090Vienna, Austria
| | - Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136Trieste, Italy
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6
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Grest GS, Ge T, Plimpton SJ, Rubinstein M, O’Connor TC. Entropic Mixing of Ring/Linear Polymer Blends. ACS POLYMERS AU 2022; 3:209-216. [PMID: 37065717 PMCID: PMC10103188 DOI: 10.1021/acspolymersau.2c00050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022]
Abstract
The topological constraints of nonconcatenated ring polymers force them to form compact loopy globular conformations with much lower entropy than unconstrained ideal rings. The closed-loop structure of ring polymers also enables them to be threaded by linear polymers in ring/linear blends, resulting in less compact ring conformations with higher entropy. This conformational entropy increase promotes mixing rings with linear polymers. Here, using molecular dynamics simulations for bead-spring chains, ring/linear blends are shown to be significantly more miscible than linear/linear blends and that there is an entropic mixing, negative χ, for ring/linear blends compared to linear/linear and ring/ring blends. In analogy with small angle neutron scattering, the static structure function S(q) is measured, and the resulting data are fit to the random phase approximation model to determine χ. In the limit that the two components are the same, χ = 0 for the linear/linear and ring/ring blends as expected, while χ < 0 for the ring/linear blends. With increasing chain stiffness, χ for the ring/linear blends becomes more negative, varying reciprocally with the number of monomers between entanglements. Ring/linear blends are also shown to be more miscible than either ring/ring or linear/linear blends and stay in single phase for a wider range of increasing repulsion between the two components.
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Affiliation(s)
- Gary S. Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Steven J. Plimpton
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Michael Rubinstein
- Thomas Lord Department of Mechanical Engineering and Materials Science, Biomedical Engineering, Chemistry, and Physics Departments, Duke University, Durham, North Carolina 27708, United States
| | - Thomas C. O’Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburg, Pennsylvania 15213, United States
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7
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Topological digestion drives time-varying rheology of entangled DNA fluids. Nat Commun 2022; 13:4389. [PMID: 35902575 PMCID: PMC9334285 DOI: 10.1038/s41467-022-31828-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this feat, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalise using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents. Understanding and controlling the rheology of polymeric complex fluids is of fundamental importance in both industry and biology. Here, Michieletto et al. show how to achieve time-dependent rheology of DNA solutions via enzymatically-driven architectural alterations by restriction endonucleases.
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8
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Hughes MD, Cussons S, Mahmoudi N, Brockwell DJ, Dougan L. Tuning Protein Hydrogel Mechanics through Modulation of Nanoscale Unfolding and Entanglement in Postgelation Relaxation. ACS NANO 2022; 16:10667-10678. [PMID: 35731007 PMCID: PMC9331141 DOI: 10.1021/acsnano.2c02369] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Globular folded proteins are versatile nanoscale building blocks to create biomaterials with mechanical robustness and inherent biological functionality due to their specific and well-defined folded structures. Modulating the nanoscale unfolding of protein building blocks during network formation (in situ protein unfolding) provides potent opportunities to control the protein network structure and mechanics. Here, we control protein unfolding during the formation of hydrogels constructed from chemically cross-linked maltose binding protein using ligand binding and the addition of cosolutes to modulate protein kinetic and thermodynamic stability. Bulk shear rheology characterizes the storage moduli of the bound and unbound protein hydrogels and reveals a correlation between network rigidity, characterized as an increase in the storage modulus, and protein thermodynamic stability. Furthermore, analysis of the network relaxation behavior identifies a crossover from an unfolding dominated regime to an entanglement dominated regime. Control of in situ protein unfolding and entanglement provides an important route to finely tune the architecture, mechanics, and dynamic relaxation of protein hydrogels. Such predictive control will be advantageous for future smart biomaterials for applications which require responsive and dynamic modulation of mechanical properties and biological function.
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Affiliation(s)
- Matt D.
G. Hughes
- School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sophie Cussons
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
- School of
Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Najet Mahmoudi
- ISIS
Neutron
and Muon Spallation Source, STFC Rutherford
Appleton Laboratory, Oxfordshire OX11 0QX, U.K.
| | - David J. Brockwell
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
- School of
Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Lorna Dougan
- School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, U.K.
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
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9
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Sleiman JL, Burton RH, Caraglio M, Gutierrez Fosado YA, Michieletto D. Geometric Predictors of Knotted and Linked Arcs. ACS POLYMERS AU 2022; 2:341-350. [PMID: 36254317 PMCID: PMC9562465 DOI: 10.1021/acspolymersau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Inspired by how certain proteins “sense”
knots and
entanglements in DNA molecules, here, we ask if local geometric features
that may be used as a readout of the underlying topology of generic
polymers exist. We perform molecular simulations of knotted and linked
semiflexible polymers and study four geometric measures to predict
topological entanglements: local curvature, local density, local 1D
writhe, and nonlocal 3D writhe. We discover that local curvature is
a poor predictor of entanglements. In contrast, segments with maximum
local density or writhe correlate as much as 90% of the time with
the shortest knotted and linked arcs. We find that this accuracy is
preserved across different knot types and also under significant spherical
confinement, which is known to delocalize essential crossings in knotted
polymers. We further discover that nonlocal 3D writhe is the best
geometric readout of the knot location. Finally, we discuss how these
geometric features may be used to computationally analyze entanglements
in generic polymer melts and gels.
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Affiliation(s)
- Joseph L. Sleiman
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Robin H. Burton
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Yair Augusto Gutierrez Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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10
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Shen Z, Carrillo JMY, Sumpter BG, Wang Y. Decoding polymer self-dynamics using a two-step approach. Phys Rev E 2022; 106:014502. [PMID: 35974619 DOI: 10.1103/physreve.106.014502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correlation functions of polymers. We show that the interpretation of non-Gaussian behavior of polymers is generally complicated by intrachain averaging of distinct self-dynamics of different segments. By the very nature of the mathematics involved, the averaging process not only conceals critical dynamical information, but also contributes to the observed non-Gaussian dynamics. To fully expose this issue and provide a thorough benchmark of polymer self-dynamics, we perform analyses of coarse-grained molecular dynamics simulations of linear and ring polymer melts as well as several theoretical models using a "two-step" approach, where interchain and intrachain averagings of segmental self-dynamics are separated. While past investigations primarily focused on the average behavior, our results indicate that a more nuanced approach to polymer self-dynamics is clearly required.
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Affiliation(s)
- Zhiqiang Shen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yangyang Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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11
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Wang J, O'Connor TC, Grest GS, Ge T. Superstretchable Elastomer from Cross-linked Ring Polymers. PHYSICAL REVIEW LETTERS 2022; 128:237801. [PMID: 35749195 DOI: 10.1103/physrevlett.128.237801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
The stretchability of polymeric materials is critical to many applications such as flexible electronics and soft robotics, yet the stretchability of conventional cross-linked linear polymers is limited by the entanglements between polymer chains. We show using molecular dynamics simulations that cross-linked ring polymers are significantly more stretchable than cross-linked linear polymers. Compared to linear polymers, the entanglements between ring polymers do not act as effective cross-links. As a result, the stretchability of cross-linked ring polymers is determined by the maximum extension of polymer strands between cross-links, rather than between trapped entanglements as in cross-linked linear polymers. The more compact conformation of ring polymers before deformation also contributes to the increase in stretchability.
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Affiliation(s)
- Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Thomas C O'Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Gary S Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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12
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Conformation and structure of ring polymers in semidilute solutions: A molecular dynamics simulation study. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Yesbolatova AK, Arai R, Sakaue T, Kimura A. Formulation of Chromatin Mobility as a Function of Nuclear Size during C. elegans Embryogenesis Using Polymer Physics Theories. PHYSICAL REVIEW LETTERS 2022; 128:178101. [PMID: 35570447 DOI: 10.1103/physrevlett.128.178101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases. Despite its biological implications, the underlying mechanism for this transition was unclear. By combining theory and experiment, we analyze the mean-square displacement (MSD) of the chromatin loci, and demonstrate that MSD-vs-time relationships in various nuclei collapse into a single master curve by normalizing them with the mesh size and the corresponding time scale. This enables us to identify the onset of the entangled dynamics with the size of tube diameter of chromatin polymer in the C. elegans embryo. Our dynamical scaling analysis predicts the transition between unentangled and entangled dynamics of chromatin polymers, the quantitative formula for MSD as a function of nuclear size and timescale, and provides testable hypotheses on chromatin mobility in other cell types and species.
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Affiliation(s)
- Aiya K Yesbolatova
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Ritsuko Arai
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Akatsuki Kimura
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
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14
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Mo J, Wang J, Wang Z, Lu Y, An L. Size and Dynamics of a Tracer Ring Polymer Embedded in a Linear Polymer Chain Melt Matrix. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiangyang Mo
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
| | - Jian Wang
- College of Chemistry and Chemical Engineering, Cangzhou Normal University, Cangzhou 061001, P.R. China
| | - Zhenhua Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Hefei 230026, P.R. China
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15
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Chubak I, Pachong SM, Kremer K, Likos CN, Smrek J. Active Topological Glass Confined within a Spherical Cavity. Macromolecules 2022; 55:956-964. [PMID: 35153336 PMCID: PMC8830202 DOI: 10.1021/acs.macromol.1c02471] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Iurii Chubak
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, Sorbonne Université CNRS, F-75005 Paris, France
| | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christos N. Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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16
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Müller M. Selection of Advances in Theory and Simulation during the First Decade of ACS Macro Letters. ACS Macro Lett 2021; 10:1629-1635. [PMID: 35549151 DOI: 10.1021/acsmacrolett.1c00750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcus Müller
- Institute for Theoretical Physics, Georg-August-University, 37077 Göttingen, Germany
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17
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Goto S, Kim K, Matubayasi N. Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts. J Chem Phys 2021; 155:124901. [PMID: 34598563 DOI: 10.1063/5.0061281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamics of ring polymer melts are studied via molecular dynamics simulations of the Kremer-Grest bead-spring model. Rouse mode analysis is performed in comparison with linear polymers by changing the chain length. Rouse-like behavior is observed in ring polymers by quantifying the chain length dependence of the Rouse relaxation time, whereas a crossover from Rouse to reptation behavior is observed in linear polymers. Furthermore, the non-Gaussian parameters of the monomer bead displacement and chain center-of-mass displacement are analyzed. It is found that the non-Gaussianity of ring polymers is remarkably suppressed with slight growth for the center-of-mass dynamics at long chain length, which is in contrast to the growth in linear polymers for both the monomer bead and center-of-mass dynamics.
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Affiliation(s)
- Shota Goto
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Affiliation(s)
- Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Smrek J, Garamella J, Robertson-Anderson R, Michieletto D. Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids. SCIENCE ADVANCES 2021; 7:eabf9260. [PMID: 33980492 PMCID: PMC8115916 DOI: 10.1126/sciadv.abf9260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/26/2021] [Indexed: 05/04/2023]
Abstract
Ring polymers in dense solutions are among the most intriguing problems in polymer physics. Because of its natural occurrence in circular form, DNA has been extensively used as a proxy to study the fundamental physics of ring polymers in different topological states. Yet, torsionally constrained-such as supercoiled-topologies have been largely neglected so far. The applicability of existing theoretical models to dense supercoiled DNA is thus unknown. Here, we address this gap by coupling large-scale molecular dynamics simulations with differential dynamic microscopy of entangled supercoiled DNA plasmids. We find that, unexpectedly, larger supercoiling increases the size of entangled plasmids and concomitantly induces an enhancement in DNA mobility. These findings are reconciled as due to supercoiling-driven asymmetric and double-folded plasmid conformations that reduce interplasmid entanglements and threadings. Our results suggest a way to topologically tune DNA mobility via supercoiling, thus enabling topological control over the (micro)rheology of DNA-based complex fluids.
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Affiliation(s)
- Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Jonathan Garamella
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | | | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh, Edinburgh EH4 2XU, UK
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