1
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Paiva WA, Alakwe SD, Marfai J, Jennison-Henderson MV, Achong RA, Duche T, Weeks AA, Robertson-Anderson RM, Oldenhuis NJ. From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2405490. [PMID: 38935929 DOI: 10.1002/adma.202405490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/10/2024] [Indexed: 06/29/2024]
Abstract
DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.
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Affiliation(s)
- Wynter A Paiva
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Somkene D Alakwe
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Juexin Marfai
- Department of Physics and Biophysics, College of Arts and Sciences, University of San Diego, Shiley Center for Science and Technology, 5998 Alcala Park, San Diego, CA, 92110, USA
| | - Madigan V Jennison-Henderson
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Rachel A Achong
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Tinotenda Duche
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - April A Weeks
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Rae M Robertson-Anderson
- Department of Physics and Biophysics, College of Arts and Sciences, University of San Diego, Shiley Center for Science and Technology, 5998 Alcala Park, San Diego, CA, 92110, USA
| | - Nathan J Oldenhuis
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
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2
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Schneck C, Smrek J, Likos CN, Zöttl A. Supercoiled ring polymers under shear flow. NANOSCALE 2024. [PMID: 38639709 DOI: 10.1039/d3nr04258h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatically deform and inflate under shear [Liebetreu et al., Commun. Mater. 2020, 1, 4], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts. In the presence of hydrodynamic interactions, the coupling of the polymer to solvent flow is capable of bringing about a topological transformation of writhe to twist at strong shear upon conservation of the overall linking number.
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Affiliation(s)
- Christoph Schneck
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Andreas Zöttl
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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3
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Micheletti C, Chubak I, Orlandini E, Smrek J. Topology-Based Detection and Tracking of Deadlocks Reveal Aging of Active Ring Melts. ACS Macro Lett 2024:124-129. [PMID: 38198592 PMCID: PMC10883035 DOI: 10.1021/acsmacrolett.3c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Connecting the viscoelastic behavior of stressed ring melts to the various forms of entanglement that can emerge in such systems is still an open challenge. Here, we consider active ring melts, where stress is generated internally, and introduce a topology-based method to detect and track consequential forms of ring entanglements, namely, deadlocks. We demonstrate that, as stress accumulates, more and more rings are co-opted in a growing web of deadlocks that entrap many other rings by threading, bringing the system to a standstill. The method ought to help the study of topological aging in more general polymer contexts.
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Affiliation(s)
- Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136 Trieste, Italy
| | - Iurii Chubak
- Sorbonne Université CNRS, Physico-Chimie des électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
| | - Enzo Orlandini
- Università degli studi di Padova, Dipartimento di Fisica "G. Galilei", Via Marzolo 8, I-35100 Padova, Italy
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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4
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Sleiman JL, Conforto F, Fosado YAG, Michieletto D. Geometric learning of knot topology. SOFT MATTER 2023; 20:71-78. [PMID: 37877330 PMCID: PMC10732224 DOI: 10.1039/d3sm01199b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023]
Abstract
Knots are deeply entangled with every branch of science. One of the biggest open challenges in knot theory is to formalise a knot invariant that can unambiguously and efficiently distinguish any two knotted curves. Additionally, the conjecture that the geometrical embedding of a curve encodes information on its underlying topology is, albeit physically intuitive, far from proven. Here we attempt to tackle both these outstanding challenges by proposing a neural network (NN) approach that takes as input a geometric representation of a knotted curve and tries to make predictions of the curve's topology. Intriguingly, we discover that NNs trained with a so-called geometrical "local writhe" representation of a knot can distinguish curves that share one or many topological invariants and knot polynomials, such as mutant and composite knots, and can thus classify knotted curves more precisely than some knot polynomials. Additionally, we also show that our approach can be scaled up to classify all prime knots up to 10-crossings with more than 95% accuracy. Finally, we show that our NNs can also be trained to solve knot localisation problems on open and closed curves. Our main discovery is that the pattern of "local writhe" is a potentially unique geometric signature of the underlying topology of a curve. We hope that our results will suggest new methods for quantifying generic entanglements in soft matter and even inform new topological invariants.
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Affiliation(s)
- Joseph Lahoud Sleiman
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Filippo Conforto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | | | - 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 Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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5
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Verweij RW, Melio J, Chakraborty I, Kraft DJ. Brownian motion of flexibly linked colloidal rings. Phys Rev E 2023; 107:034602. [PMID: 37072967 DOI: 10.1103/physreve.107.034602] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/04/2023] [Indexed: 04/20/2023]
Abstract
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on the conformation and diffusion of molecular ring polymers simultaneously are challenging due to their inherently small size. Here, we study an experimental model system for cyclic polymers, that consists of rings of flexibly linked micron-sized colloids with n=4-8 segments. We characterize the conformations of these flexible colloidal rings and find that they are freely jointed up to steric restrictions. We measure their diffusive behavior and compare it to hydrodynamic simulations. Interestingly, flexible colloidal rings have a larger translational and rotational diffusion coefficient compared to colloidal chains. In contrast to chains, their internal deformation mode shows slower fluctuations for n≲8 and saturates for higher values of n. We show that constraints stemming from the ring structure cause this decrease in flexibility for small n and infer the expected scaling of the flexibility as function of ring size. Our findings could have implications for the behavior of both synthetic and biological ring polymers, as well as for the dynamic modes of floppy colloidal materials.
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Affiliation(s)
- Ruben W Verweij
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - Julio Melio
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - Indrani Chakraborty
- Department of Physics, Birla Institute of Technology and Science, Pilani-K K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Daniela J Kraft
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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6
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Rheaume SN, Klotz AR. Nanopore translocation of topologically linked DNA catenanes. Phys Rev E 2023; 107:024504. [PMID: 36932513 DOI: 10.1103/physreve.107.024504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
The electrical signal associated with a biopolymer translocating through a nanoscale pore depends on the size, topology, and configuration of each molecule. Building upon recent interest in using solid-state nanopores for studying the topology of knotted and supercoiled DNA, we present experimental observations of topologically linked catenanes translocating through a solid-state nanopore. Using restriction enzymes, linked circular molecules were isolated from the mitochondrial DNA of Crithidia fasciculata, a structure known as a kinetoplast that comprises thousands of topologically interlocked minicircles. Digested kinetoplasts produce a spectrum of catenane topologies, which are identified from their nanopore translocation signals by spikes in the blockade current associated with the topological linkages. We attribute the different patterns of the measured electrical signals to 2-catenanes, linear and triangular 3-catenanes, and several types of 4- and 5-catenanes as well as more complex structures. Measurements of the translocation time of signals consistent with 2- and 3-catenanes suggest that topological friction between the linkages and the pore slows the translocation time of these structures, as predicted in recent simulations.
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Affiliation(s)
- Sierra N Rheaume
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, Long Beach, California 90815, USA
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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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Roy PK, Chaudhuri P, Vemparala S. Effect of ring stiffness and ambient pressure on the dynamical slowdown in ring polymers. SOFT MATTER 2022; 18:2959-2967. [PMID: 35348146 DOI: 10.1039/d1sm01754c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Using extensive molecular dynamics simulations, we investigate the slowdown of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowdown, albeit only in a certain stiffness range. Our results suggest a possible framework for exploring the phase space spanned by ring stiffness and pressure to obtain spontaneously emerging topologically constrained polymer glasses.
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Affiliation(s)
- Projesh Kumar Roy
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Pinaki Chaudhuri
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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9
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Soh BW, Doyle PS. Equilibrium Conformation of Catenated DNA Networks in Slitlike Confinement. ACS Macro Lett 2021; 10:880-885. [PMID: 35549205 DOI: 10.1021/acsmacrolett.1c00299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A kinetoplast is a planar network of catenated DNA rings with topology that resembles that of chain mail armor. In this work, we use single-molecule experiments to probe the conformation of kinetoplasts confined to slits. We find that the in-plane size of kinetoplasts increases with degree of confinement, akin to the slitlike confinement of linear DNA. The change in kinetoplast size with channel height is consistent with the scaling prediction from a Flory-type approach for a 2D polymer. With an increase in extent of confinement, the kinetoplasts appear to unfold and take on more uniform circular shapes, in contrast to the broad range of conformations observed for kinetoplasts in bulk.
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Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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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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11
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Rauscher PM, Rowan SJ, de Pablo JJ. Hydrodynamic interactions in topologically linked ring polymers. Phys Rev E 2020; 102:032502. [PMID: 33076028 DOI: 10.1103/physreve.102.032502] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/21/2020] [Indexed: 11/07/2022]
Abstract
Despite decades of interdisciplinary research on topologically linked ring polymers, their dynamics remain largely unstudied. These systems represent a major scientific challenge as they are often subject to both topological and hydrodynamic interactions (HI), which render dynamical solutions either mathematically intractable or computationally prohibitive. Here we circumvent these limitations by preaveraging the HI of linked rings. We show that the symmetry of ring polymers leads to a hydrodynamic decoupling of ring dynamics. This decoupling is valid even for nonideal polymers and nonequilibrium conditions. Physically, our findings suggest that the effects of topology and HI are nearly independent and do not act cooperatively to influence polymer dynamics. We use this result to develop highly efficient Brownian dynamics algorithms that offer enormous performance improvements over conventional methods and apply these algorithms to simulate catenated ring polymers at equilibrium, confirming the independence of topological effects and HI. The methods developed here can be used to study and simulate large systems of linked rings with HI, including kinetoplast DNA, Olympic gels, and poly[n]catenanes.
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Affiliation(s)
- Phillip M Rauscher
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Stuart J Rowan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.,Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.,Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.,Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA.,Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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12
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Soh BW, Klotz AR, Doyle PS. Topological Simplification of Complex Knots Untied in Elongational Flows. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander R. Klotz
- Department of Physics and Astronomy, California State University, Long Beach, California 90840, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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13
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Michieletto D, Orlandini E, Turner MS, Micheletti C. Separation of Geometrical and Topological Entanglement in Confined Polymers Driven out of Equilibrium. ACS Macro Lett 2020; 9:1081-1085. [PMID: 35653213 DOI: 10.1021/acsmacrolett.0c00366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nanochannels and under periodic compression. By introducing suitable observables, we can distinguish two main forms of entanglement that we term geometrical and topological. The latter is measured by the number of (essential) crossings of the physical knot detected after a suitable bridging of the chain termini. The former is instead measured as the average number of times a linear chain appears to cross itself when viewed under all projections and is irrespective of the physical knotted state. The key discovery of our work is that these two forms of entanglement are uncoupled and evolve with distinct dynamics. While geometrical entanglement is typically in phase with the compression-elongation cycles and it is primarily sensitive to its force f, the topological measure is mildly sensitive to cyclic modulation but strongly depends on both compression force f and duration k. The findings could assist the interpretation of experiments using fluorescence molecular tracers to track physical knots in polymers. Furthermore, we identify optimal regions in the experimentally controllable parameter space in which to obtain more/less topological and geometrical entanglement; this may help designing polymers with targeted topology.
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Affiliation(s)
- 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 Molecular Medicine, University of Edinburgh, North Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá degli Studi di Padova, I-35131 Padova, Italy
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry, CV4 7AL, U.K.,Department of Chemical Engineering, Kyoto University, Kyoto, Japan
| | - Cristian Micheletti
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), Via Bonomea 265, 34136 Trieste, Italy
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14
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Soh BW, Doyle PS. Deformation Response of Catenated DNA Networks in a Planar Elongational Field. ACS Macro Lett 2020; 9:944-949. [PMID: 35648605 DOI: 10.1021/acsmacrolett.0c00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A kinetoplast is a complex catenated DNA network that bears resemblance to a two-dimensional polymeric system. In this work, we use single-molecule experiments to study the transient and steady-state deformation of kinetoplasts in a planar elongational field. We demonstrate that kinetoplasts deform in a stagewise manner and undergo transient deformation at large strains, due to conformational rearrangements from an intermediate metastable state. Kinetoplasts in an elongational field achieve a steady-state deformation that depends on strain rate, akin to the deformation of linear polymers. We do not observe an abrupt transition between the nondeformed and deformed states of a kinetoplast, in contrast to the coil-stretch transition for a linear polymer.
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Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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15
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Rosa A, Smrek J, Turner MS, Michieletto D. Threading-Induced Dynamical Transition in Tadpole-Shaped Polymers. ACS Macro Lett 2020; 9:743-748. [PMID: 33828901 PMCID: PMC8016395 DOI: 10.1021/acsmacrolett.0c00197] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/30/2020] [Indexed: 01/06/2023]
Abstract
The relationship between polymer topology and bulk rheology remains a key question in soft matter physics. Architecture-specific constraints (or threadings) are thought to control the dynamics of ring polymers in ring-linear blends, which thus affects the viscosity to range between that of the pure rings and a value larger, but still comparable to, that of the pure linear melt. Here we consider qualitatively different systems of linear and ring polymers, fused together in "chimeric" architectures. The simplest example of this family is a "tadpole"-shaped polymer, a single ring fused to the end of a single linear chain. We show that polymers with this architecture display a threading-induced dynamical transition that substantially slows chain relaxation. Our findings shed light on how threadings control dynamics and may inform design principles for chimeric polymers with topologically tunable bulk rheological properties.
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Affiliation(s)
- Angelo Rosa
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), Via Bonomea 265, 34136 Trieste, Italy
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemical Engineering, Kyoto University, Kyoto 606-8501, Japan
| | - 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 Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- Department of Mathematical Sciences, University of Bath, North Rd, Bath BA2 7AY, United Kingdom
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16
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Lee E, Paul W. Additional Entanglement Effect Imposed by Small Sized Ring Aggregates in Supramolecular Polymer Melts: Molecular Dynamics Simulation Study. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02209] [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)
- Eunsang Lee
- Institut für Physik, Martin-Luther Universität Halle-Wittenberg, Halle 06120, Germany
| | - Wolfgang Paul
- Institut für Physik, Martin-Luther Universität Halle-Wittenberg, Halle 06120, Germany
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17
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Tsalikis DG, Mavrantzas VG. Size and Diffusivity of Polymer Rings in Linear Polymer Matrices: The Key Role of Threading Events. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Dimitrios G. Tsalikis
- Department of Chemical Engineering, University of Patras and FORTH-ICE/HT, GR 26504 Patras, Greece
| | - Vlasis G. Mavrantzas
- Department of Chemical Engineering, University of Patras and FORTH-ICE/HT, GR 26504 Patras, Greece
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zürich, CH-8092 Zürich, Switzerland
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Klotz AR, Soh BW, Doyle PS. Equilibrium structure and deformation response of 2D kinetoplast sheets. Proc Natl Acad Sci U S A 2020; 117:121-127. [PMID: 31811027 PMCID: PMC6955370 DOI: 10.1073/pnas.1911088116] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.
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Affiliation(s)
- Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Physics and Astronomy, California State University, Long Beach, CA 90840
| | - Beatrice W Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142;
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