1
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Vitecek B, Likos CN, Gârlea IC. Adsorption characteristics of Janus tadpole polymers. J Chem Phys 2024; 160:224902. [PMID: 38856071 DOI: 10.1063/5.0213433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
The shape of Janus particles is directly connected to their adsorption behavior. Janus tadpole polymers offer a unique topological architecture that includes competition between entropic, enthalpic, and topological terms in the adsorption free energy; accordingly, non-trivial adsorption behavior patterns are expected. We study the surface adsorption of Janus tadpole polymers by means of Monte Carlo simulations, finding that, depending on which part of the tadpole polymers is preferentially adsorbing on the surface, very different types of behavior for both the adsorbed polymeric phase and of the brush arise. The adsorbed phase and the brush mutually influence each other, leading to a variety of phenomena such as nematic ordering of the adsorbed stiff tadpole tails and intriguing changes in the territoriality of adsorbed ring polymers on the surface. We analyze in detail our findings, revealing the mechanisms behind the organization and ordering, and opening up new possibilities to tune and control the structure of such systems.
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Affiliation(s)
- Benedikt Vitecek
- 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
| | - Ioana C Gârlea
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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2
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Hernández Velázquez JD, Alas SJ, Pérez E, Goicochea AG. Universal scaling of the osmotic pressure for dense, quasi-two-dimensionally confined polymer melts reveals transitions between fractal dimensions. J Chem Phys 2024; 160:084907. [PMID: 38415832 DOI: 10.1063/5.0185634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
A scaling law for the osmotic pressure of quasi-two-dimensional polymer melts as a function of concentration is obtained, which shows fractal characteristics. Structural properties such as the chains' contour length and their inner-monomer pair distribution function display fractal scaling properties as well. These predictions are confirmed with mesoscale numerical simulations. The chains are swollen and highly entangled, yet Flory's exponent is always ν = 1/2. The melt can be considered a fluid of "blobs" whose size becomes renormalized in terms of the contour's length while the fractal dimension df increases monotonically between 5/4 and 2, as the monomer concentration is increased. The semidilute scaling of the pressure is recovered when df = 1. Our results agree with recent experiments and with numerical reports on quasi-2d melts. This work provides a new paradigm to study and interpret thermodynamic and structural data in low-dimensional polymer melts, namely as fractal macromolecular objects.
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Affiliation(s)
- J D Hernández Velázquez
- Tecnológico Nacional de México, Tecnológico de Estudios Superiores de Ecatepec, División de Ingeniería Química y Bioquímica, 55210 Estado de México, Mexico
| | - S J Alas
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Unidad Cuajimalpa, 05300 Ciudad de México, Mexico
| | - E Pérez
- Instituto de Física, Universidad Autónoma de San Luis Potosí, 78000 San Luis Potosí, Mexico
| | - A Gama Goicochea
- Tecnológico Nacional de México, Tecnológico de Estudios Superiores de Ecatepec, División de Ingeniería Química y Bioquímica, 55210 Estado de México, Mexico
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3
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Andrew LJ, Kly S, Moloney EG, Moffitt MG. Effects of Microfluidic Shear on the Plasmid DNA Structure: Implications for Polymeric Gene Delivery Vectors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11545-11555. [PMID: 37552625 DOI: 10.1021/acs.langmuir.3c00934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Microfluidic manufacturing of advanced gene delivery vectors necessitates consideration of the effects of microfluidic shear forces on the structural integrity of plasmid DNA (pDNA). In this paper, we expose pDNA to variable shear forces in a two-phase, gas-liquid microfluidic reactor and apply gel electrophoresis to analyze the products of on-chip shear-induced degradation. The effects of shear rate, solvent environment, pDNA size, and copolymer complexation on shear-induced degradation are investigated. We find that small naked pDNA (pUC18, 2.7 kb) exhibits shear rate-dependent shear degradation in the microfluidic channels in a mixed organic solvent (dioxane/water/acetic acid; 90/10/<0.1 w/w/w), with the extents of both supercoil isoform relaxation and complete fragmentation increasing as the maximum shear rates increase from 4 × 105 to 2 × 106 s-1. However, over the same range of shear rates, the same pDNA sample shows no evidence of microfluidic shear-induced degradation in a pure aqueous environment. Quiescent control experiments in the same mixed organic solvent prove that a combination of solvent and shear forces is involved in the observed shear-induced degradation. Furthermore, we show that shear degradation effects in mixed organic solvents can be significantly attenuated by complexation of pDNA with the block copolymer polycaprolactone-block-poly(2-vinylpyridine) prior to exposure to microfluidic shear. Finally, we demonstrate that medium (pDSK519, 8.1 kb) and large (pRK290, 20 kb) naked pDNA are more sensitive to shear-induced microfluidic degradation in the mixed organic solvent environment than small pDNA, with both plasmids showing complete fragmentation even at the lowest shear rate, although we found no evidence of shear-induced damage in water for the largest investigated naked pDNA even at the highest flow rate. The resulting understanding of the interplay of the solvent and shear effects during microfluidic processing should inform microfluidic manufacturing routes to new gene therapy formulations.
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Affiliation(s)
- Lucas J Andrew
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
| | - Sundiata Kly
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
| | - Erin G Moloney
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
| | - Matthew G Moffitt
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
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4
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Kuriata A, Sikorski A. Structure of adsorbed linear and cyclic block copolymers: A computer simulation study. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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5
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Chardon F, Japaridze A, Witt H, Velikovsky L, Chakraborty C, Wilhelm T, Dumont M, Yang W, Kikuti C, Gangnard S, Mace AS, Wuite G, Dekker C, Fachinetti D. CENP-B-mediated DNA loops regulate activity and stability of human centromeres. Mol Cell 2022; 82:1751-1767.e8. [PMID: 35320753 DOI: 10.1016/j.molcel.2022.02.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022]
Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
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Affiliation(s)
- Florian Chardon
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hannes Witt
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Camellia Chakraborty
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos Kikuti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Stephane Gangnard
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anne-Sophie Mace
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gijs Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France.
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6
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Kim J, Kim JM, Baig C. Intrinsic structure and dynamics of monolayer ring polymer melts. SOFT MATTER 2021; 17:10703-10715. [PMID: 34783328 DOI: 10.1039/d1sm01192h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present the general structural and dynamical characteristics of flexible ring polymers in narrowly confined two-dimensional (2D) melt systems using atomistic molecular dynamics simulations. The results are further analyzed via direct comparison with the 2D linear analogue as well as the three-dimensional (3D) ring and linear melt systems. It is observed that dimensional restriction in 2D confined systems results in an increase in the intrinsic chain stiffness of the ring polymer. Fundamentally, this arises from an entropic penalty on polymer chains along with a reduction in the available chain configuration states in phase space and spatial choices for individual segmental walks. This feature in combination with the intermolecular interactions between neighboring ring chains leads to an overall extended interpenetrated chain configuration for the 2D ring melt. In contrast to the generally large differences in structural and dynamical properties between ring and linear polymers in 3D melt systems, relatively similar local-to-global chain structures and dynamics are observed for the 2D ring and linear melts. This is attributed to the general structural similarity (i.e., extended double-stranded chain conformations), the less effective role of the chain ends, and the absence of complex topological constraints between chains (i.e., interchain entanglement and mutual ring threading) in the 2D confined systems compared with the corresponding 3D bulk systems.
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Affiliation(s)
- Jinseong Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea.
| | - Jun Mo Kim
- Department of Chemical Engineering, Kyonggi University, 154-42 Gwanggyosan-ro, Yeongtong-gu, Suwon, Kyonggi-do 16227, South Korea
| | - Chunggi Baig
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan 44919, South Korea.
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7
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Kim JM. Influence of chain stiffness on semiflexible polymer melts in two dimensions via molecular dynamics simulation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1970155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jun Mo Kim
- Department of Chemical Engineering, Kyonggi University, Suwon, South Korea
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8
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Zhou J, Venturelli L, Keiser L, Sekatskii SK, Gallaire F, Kasas S, Longo G, Knowles TPJ, Ruggeri FS, Dietler G. Environmental Control of Amyloid Polymorphism by Modulation of Hydrodynamic Stress. ACS NANO 2021; 15:944-953. [PMID: 33348981 DOI: 10.1021/acsnano.0c07570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The phenomenon of amyloid polymorphism is a key feature of protein aggregation. Unravelling this phenomenon is of great significance for understanding the underlying molecular mechanisms associated with neurodegenerative diseases and for the development of amyloid-based functional biomaterials. However, the understanding of the molecular origins and the physicochemical factors modulating amyloid polymorphs remains challenging. Herein, we demonstrate an association between amyloid polymorphism and environmental stress in solution, induced by an air/water interface in motion. Our results reveal that low-stress environments produce heterogeneous amyloid polymorphs, including twisted, helical, and rod-like fibrils, whereas high-stress conditions generate only homogeneous rod-like fibrils. Moreover, high environmental stress converts twisted fibrils into rod-like fibrils both in-pathway and after the completion of mature amyloid formation. These results enrich our understanding of the environmental origin of polymorphism of pathological amyloids and shed light on the potential of environmentally controlled fabrication of homogeneous amyloid biomaterials for biotechnological applications.
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Affiliation(s)
- Jiangtao Zhou
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Leonardo Venturelli
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ludovic Keiser
- Laboratory of Fluid Mechanics and Instabilities, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sergey K Sekatskii
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - François Gallaire
- Laboratory of Fluid Mechanics and Instabilities, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sandor Kasas
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giovanni Longo
- Istituto di Struttura della Materia, CNR, Via del Fosso del Cavaliere 100, 00133, Roma, Italy
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Francesco S Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Laboratory of Physical Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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9
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Kim J, Kim JM, Baig C. Intrinsic chain stiffness in flexible linear polymers under extreme confinement. POLYMER 2021. [DOI: 10.1016/j.polymer.2020.123308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Chen SWW, Banneville AS, Teulon JM, Timmins J, Pellequer JL. Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy. NANOSCALE 2020; 12:22628-22638. [PMID: 33150905 DOI: 10.1039/d0nr05320a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Deinococcus radiodurans protein HU (DrHU) was shown to be critical for nucleoid activities, yet its functional and structural properties remain largely unexplored. We have applied atomic force microscopy (AFM) imaging to study DrHU binding to pUC19-DNA in vitro and analyzed the topographic structures formed at the nanoscale. At the single-molecule level, AFM imaging allows visualization of super-helical turns on naked DNA surfaces and characterization of free DrHU molecules observed as homodimers. When enhancing the molecular surface structures of AFM images by the Laplacian weight filter, the distribution of bound DrHUs was visibly varied as a function of the DrHU/DNA molar ratio. At a low molar ratio, DrHU binding was found to reduce the volume of condensed DNA configuration by about 50%. We also show that DrHU is capable of bridging distinct DNA segments. Moreover, at a low molar ratio, the binding orientation of individual DrHU dimers could be perceived on partially "open" DNA configuration. At a high molar ratio, DrHU stiffened the DNA molecule and enlarged the spread of the open DNA configuration. Furthermore, a lattice-like pattern could be seen on the surface of DrHU-DNA complex, indicating that DrHU multimerization had occurred leading to the formation of a higher order architecture. Together, our results show that the functional plasticity of DrHU in mediating DNA organization is subject to both the conformational dynamics of DNA molecules and protein abundance.
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Affiliation(s)
- Shu-Wen W Chen
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France.
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11
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Rolińska K, Sikorski A. Adsorption of Linear and Cyclic Multiblock Copolymers from Selective Solvent. A Monte Carlo Study. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Karolina Rolińska
- Faculty of Chemistry Warsaw University of Technology Noakowskiego 3 Warsaw 00‐664 Poland
- Department of Chemistry University of Warsaw Pasteura 1 Warsaw 02‐093 Poland
| | - Andrzej Sikorski
- Department of Chemistry University of Warsaw Pasteura 1 Warsaw 02‐093 Poland
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12
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Alexiou TS, Alatas PV, Tsalikis DG, Mavrantzas VG. Conformational and Dynamic Properties of Short DNA Minicircles in Aqueous Solution from Atomistic Molecular Dynamics Simulations. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00821] [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)
- Terpsichori S. Alexiou
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
| | - Panagiotis V. Alatas
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
| | - Dimitrios G. Tsalikis
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
| | - Vlasis G. Mavrantzas
- Department of Chemical Engineering, University of Patras & FORTH-ICE/HT, Patras, GR 26504, Greece
- Department of Mechanical and Process Engineering, Particle Technology Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
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13
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Miermans CA, Broedersz CP. A lattice kinetic Monte-Carlo method for simulating chromosomal dynamics and other (non-)equilibrium bio-assemblies. SOFT MATTER 2020; 16:544-556. [PMID: 31808764 DOI: 10.1039/c9sm01835b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological assemblies in living cells such as chromosomes constitute large many-body systems that operate in a fluctuating, out-of-equilibrium environment. Since a brute-force simulation of that many degrees of freedom is currently computationally unfeasible, it is necessary to perform coarse-grained stochastic simulations. Here, we develop all tools necessary to write a lattice kinetic Monte-Carlo (LKMC) algorithm capable of performing such simulations. We discuss the validity and limits of this approach by testing the results of the simulation method in simple settings. Importantly, we illustrate how at large external forces Metropolis-Hastings kinetics violate the fluctuation-dissipation and steady-state fluctuation theorems and discuss better alternatives. Although this simulation framework is rather general, we demonstrate our approach using a DNA polymer with interacting SMC condensin loop-extruding enzymes. Specifically, we show that the scaling behavior of the loop-size distributions that we obtain in our LKMC simulations of this SMC-DNA system is consistent with that reported in other studies using Brownian dynamics simulations and analytic approaches. Moreover, we find that the irreversible dynamics of these enzymes under certain conditions result in frozen, sterically jammed polymer configurations, highlighting a potential pitfall of this approach.
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Affiliation(s)
- Christiaan A Miermans
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
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14
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Dabrowski-Tumanski P, Gren B, Sulkowska JI. Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function. Polymers (Basel) 2019; 11:E707. [PMID: 30999683 PMCID: PMC6523798 DOI: 10.3390/polym11040707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
Abstract
The shape and properties of closed loops depend on various topological factors. One of them is loop-threading, which is present in complex lasso proteins. In this work, we analyze the probability of loop-threading by the tail and its influence on the shape of the loop measured by the radius of gyration, distention, asphericity, and prolateness. In particular, we show that the probability of a trivial lasso for phantom polymer is non-zero even for an infinite structure, as well as that the threading flattens the loop by restricting its motion in one dimension. These results are further used to show that there are fewer non-trivial protein lassos than expected and select potentially functional complex lasso proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | - Bartosz Gren
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
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15
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Herrero CP. Self-avoiding walks and connective constants in clustered scale-free networks. Phys Rev E 2019; 99:012314. [PMID: 30780369 DOI: 10.1103/physreve.99.012314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 11/07/2022]
Abstract
Various types of walks on complex networks have been used in recent years to model search and navigation in several kinds of systems, with particular emphasis on random walks. This gives valuable information on network properties, but self-avoiding walks (SAWs) may be more suitable than unrestricted random walks to study long-distance characteristics of complex systems. Here we study SAWs in clustered scale-free networks, characterized by a degree distribution of the form P(k)∼k^{-γ} for large k. Clustering is introduced in these networks by inserting three-node loops (triangles). The long-distance behavior of SAWs gives us information on asymptotic characteristics of such networks. The number of self-avoiding walks, a_{n}, has been obtained by direct enumeration, allowing us to determine the connective constant μ of these networks as the large-n limit of the ratio a_{n}/a_{n-1}. An analytical approach is presented to account for the results derived from walk enumeration, and both methods give results agreeing with each other. In general, the average number of SAWs a_{n} is larger for clustered networks than for unclustered ones with the same degree distribution. The asymptotic limit of the connective constant for large system size N depends on the exponent γ of the degree distribution: For γ>3, μ converges to a finite value as N→∞; for γ=3, the size-dependent μ_{N} diverges as lnN, and for γ<3 we have μ_{N}∼N^{(3-γ)/2}.
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Affiliation(s)
- Carlos P Herrero
- Instituto de Ciencia de Materiales, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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16
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17
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Ropelewski S, Uehara E, Lehmann C, Deguchi T, Dietler G. Two-point correlation function of ring polymers: Experiments and numerical simulations for the case of circular DNA in 2 dimensions. REACT FUNCT POLYM 2018. [DOI: 10.1016/j.reactfunctpolym.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Chien W, Chen YL. Confinement, curvature, and attractive interaction effects on polymer surface adsorption. J Chem Phys 2017; 147:064901. [DOI: 10.1063/1.4996738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Wei Chien
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department of Physics, National Taiwan University, Taipei, Taiwan
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department of Physics, National Taiwan University, Taipei, Taiwan
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
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19
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Benková Z, Rišpanová L, Cifra P. Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts. Polymers (Basel) 2017; 9:E313. [PMID: 30970991 PMCID: PMC6418663 DOI: 10.3390/polym9080313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter dc and a slit approximating the passage aperture with the width wp. The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio dc/wp regardless of the way the geometry of the post array is varied. However, depending on how the array geometry is modified, the chain span along the posts displays a monotonic (constant post separation) or a non-monotonic behavior (constant passage width) when plotted as a function of the post diameter. In the case of monotonic trend, the width of interstitial spaces increases with the increasing chain occupation number, while, in the case of non-monotonic trend, the width of interstitial spaces decreases with the increasing chain occupation number. In comparison with linear topology, for circular topology, the stiffness affects more significantly the relative chain extension along the posts and less significantly the occupation number. The geometrical parameters of the post arrays are stored in the single-chain structure factors. The characteristic humps are recognized in the structure factor which ensue from the local increase in the density of segments in the circular chains presented in an interstitial volume or from the correlation of parallel chain fragments separated by a row of posts. Although the orientation correlations provide qualitative information about the chain topology and the character of confinement within a single interstitial volume, information about the array periodicity is missing.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal.
| | - Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
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20
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Kasas S, Dietler G. DNA-protein interactions explored by atomic force microscopy. Semin Cell Dev Biol 2017; 73:231-239. [PMID: 28716606 DOI: 10.1016/j.semcdb.2017.07.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022]
Abstract
DNA-protein interactions play an important role in all living organisms on Earth. The advent of atomic force microscopy permitted for the first time to follow and to characterize interaction forces between these two molecular species. After a short description of the AFM and its imaging modes we review, in a chronological order some of the studies that we think importantly contributed to the field.
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Affiliation(s)
- S Kasas
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Plateforme de Morphologie, Faculté de Médecine, Université de Lausanne, Bugnion 9, 1005 Lausanne, Switzerland.
| | - G Dietler
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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21
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Japaridze A, Orlandini E, Smith KB, Gmür L, Valle F, Micheletti C, Dietler G. Spatial confinement induces hairpins in nicked circular DNA. Nucleic Acids Res 2017; 45:4905-4914. [PMID: 28201616 PMCID: PMC5605231 DOI: 10.1093/nar/gkx098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 01/05/2023] Open
Abstract
In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.
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Affiliation(s)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universita di Padova, Via Marzolo 8, 35131 Padova, Italy
| | | | - Lucas Gmür
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via P.Gobetti 101, Bologna 40129, Italy
| | - Cristian Micheletti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
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22
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Japaridze A, Muskhelishvili G, Benedetti F, Gavriilidou AFM, Zenobi R, De Los Rios P, Longo G, Dietler G. Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization. NANO LETTERS 2017; 17:1938-1948. [PMID: 28191853 DOI: 10.1021/acs.nanolett.6b05294] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understand the link between genetic regulation, DNA structure, and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modeling, and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which we call hyperplectonemes. We demonstrate that their formation depends on DNA size, supercoiling, and bacterial physiology. We compare structural, nanomechanic, and dynamic properties of hyperplectonemes bound by three highly abundant nucleoid-associated proteins (FIS, H-NS, and HU). In all these cases, the negative supercoiling of DNA determines molecular dynamics, modulating their 3D shape. Overall, our findings provide a mechanistic insight into the critical role of DNA topology in genetic regulation.
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Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Georgi Muskhelishvili
- Jacobs University , D-28759 Bremen, Germany
- Agricultural University of Georgia , 0159 Tbilisi, Georgia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne , 1015 Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland
| | - Agni F M Gavriilidou
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Paolo De Los Rios
- Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland
- Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Giovanni Longo
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche , Rome, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
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23
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Benková Z, Námer P, Cifra P. Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel. SOFT MATTER 2016; 12:8425-8439. [PMID: 27722460 DOI: 10.1039/c6sm01507g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs. The chain segments do not have any freedom to move in the direction of the narrowest stripe size, being approximately the same size as the segment size. The chains of both ring and linear topologies are extended more in a stripe than in a slab; this effect is strengthened for a ring. For a ring in a stripe, the extension-confinement strength dependence leads to effective Flory exponents even larger than 3/4, which is characteristic for a self-avoiding two-dimensional chain. While the chain extension-confinement strength dependence for both topologies conforms to the de Gennes regime in a stripe, a linear chain undergoes gradual transition to the pseudoideal regime as the slab height increases in the slab-like confinement. For a confined circle, the onset of the pseudoideal regime is shifted to larger slab heights. The structure factor confirms the absence of the pseudoideal and extended de Gennes regime in a stripe and the transition from the extended to the pseudoideal regime of a circular and linear chain upon increasing the slab heights.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia. and LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Pavol Námer
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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24
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Gaididei YB, Archilla JFR, Sánchez-Morcillo VJ, Gorria C. Energy localization and shape transformations in semiflexible polymer rings. Phys Rev E 2016; 93:062227. [PMID: 27415273 DOI: 10.1103/physreve.93.062227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Indexed: 11/07/2022]
Abstract
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the internal excitations and the bending degrees of freedom of the chain modifies the local bending rigidity of the chain. In the absence of driving the array takes a circular shape. When the energy pumped into the system exceeds some critical value the chain undergoes a nonequilibrium phase transition: The circular shape of the aggregate becomes unstable and the chain takes the shape of an ellipse or, in general, of a polygon. The excitation energy distribution becomes spatially nonuniform: It localizes in such places where the chain is more flat. The weak interaction of the chain with a flat surface restricts the dynamics to a flat manifold.
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Affiliation(s)
- Yu B Gaididei
- Bogolyubov Institute for Theoretical Physics, Metrologichna Street 14 B, 03143 Kiev, Ukraine
| | - J F R Archilla
- Grupo de Física No Lineal, Universidad de Sevilla, ETSI Informática, A. Reina Mercedes s/n, E-41012 Sevilla, Spain
| | - V J Sánchez-Morcillo
- Instituto de Investigación para la Gestión Integrada de las Zonas Costeras, Universidad Politécnica de Valencia, Paranimf 1, E-46730 Grao de Gandia, Spain
| | - C Gorria
- Department of Applied Mathematics and Statistics, University of the Basque Country, E-48080 Bilbao, Spain
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25
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Abstract
We present an exact solution for the distribution of sample averaged monomer to monomer distance of ring polymers. For non-interacting and local-interaction models these distributions correspond to the distribution of the area under the reflected Bessel bridge and the Bessel excursion respectively, and are shown to be identical in dimension d ≥ 2, albeit with pronounced finite size effects at the critical dimension, d = 2. A symmetry of the problem reveals that dimension d and 4 - d are equivalent, thus the celebrated Airy distribution describing the areal distribution of the d = 1 Brownian excursion describes also a polymer in three dimensions. For a self-avoiding polymer in dimension d we find numerically that the fluctuations of the scaled averaged distance are nearly identical in dimension d = 2, 3 and are well described to a first approximation by the non-interacting excursion model in dimension 5.
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26
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Li B, Sun ZY, An LJ, Wang ZG. Influence of Topology on the Free Energy and Metric Properties of an Ideal Ring Polymer Confined in a Slit. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b02026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bing Li
- State Key Laboratory of Polymer Physics and Chemistry,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhao-Yan Sun
- State Key Laboratory of Polymer Physics and Chemistry,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Xinjiang
Laboratory of Phase Transitions and Microstructures in Condensed Matters,
College of Physical Science and Technology, Yili Normal University, Yining, 835000, China
| | - Li-Jia An
- State Key Laboratory of Polymer Physics and Chemistry,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhen-Gang Wang
- State Key Laboratory of Polymer Physics and Chemistry,
Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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27
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Iwaki T, Ishido T, Hirano K, Lazutin AA, Vasilevskaya VV, Kenmotsu T, Yoshikawa K. Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms. J Chem Phys 2015; 142:145101. [PMID: 25877594 DOI: 10.1063/1.4916309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We performed monomolecular observations on linear and circular giant DNAs (208 kbp) in an aqueous solution by the use of fluorescence microscopy. The results showed that the degree of conformational fluctuation in circular DNA was ca. 40% less than that in linear DNA, although the long-axis length of circular DNA was only 10% smaller than that of linear DNA. Additionally, the relaxation time of a circular chain was shorter than that of a linear chain by at least one order of magnitude. The essential features of this marked difference between linear and circular DNAs were reproduced by numerical simulations on a ribbon-like macromolecule as a coarse-grained model of a long semiflexible, double-helical DNA molecule. In addition, we calculated the radius of gyration of an interacting chain in a circular form on the basis of the mean field model, which provides a better understanding of the present experimental trend than a traditional theoretical equation.
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Affiliation(s)
- Takafumi Iwaki
- Faculty of Medicine, Oita University, Hasama-cho Idaigaoka 1-1, Yufu, Oita 879-5593, Japan
| | - Tomomi Ishido
- AIST Shikoku, Hayashi-cho 2217-14, Takamatsu, Kagawa 761-0395, Japan
| | - Ken Hirano
- AIST Shikoku, Hayashi-cho 2217-14, Takamatsu, Kagawa 761-0395, Japan
| | - Alexei A Lazutin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Vavilova Street 28, V-334, GSP-1, Moscow 119991, Russia
| | - Valentina V Vasilevskaya
- A.N. Nesmeyanov Institute of Organoelement Compounds, Vavilova Street 28, V-334, GSP-1, Moscow 119991, Russia
| | - Takahiro Kenmotsu
- Faculty of Life and Medical Science, Doshisha Universiy, Tatara Miyakodani 1-3, Kyotanabe, Kyoto 610-0321, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Science, Doshisha Universiy, Tatara Miyakodani 1-3, Kyotanabe, Kyoto 610-0321, Japan
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28
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Japaridze A, Benke A, Renevey S, Benadiba C, Dietler G. Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy. Macromolecules 2015. [DOI: 10.1021/ma502537g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Alexander Benke
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Sylvain Renevey
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Carine Benadiba
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
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29
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Usov I, Mezzenga R. FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Filaments, Biomacromolecules, and Fibrous Objects. Macromolecules 2015. [DOI: 10.1021/ma502264c] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Ivan Usov
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO E23, 8092 Zurich, Switzerland
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO E23, 8092 Zurich, Switzerland
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30
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van der Vaart A. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2014; 1850:1091-1098. [PMID: 25161164 DOI: 10.1016/j.bbagen.2014.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. SCOPE OF REVIEW This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. MAJOR CONCLUSIONS Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. GENERAL SIGNIFICANCE Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, FL 33620, USA.
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31
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Polanowski P, Jeszka JK, Sikorski A. Dynamic Properties of Linear and Cyclic Chains in Two Dimensions. Computer Simulation Studies. Macromolecules 2014. [DOI: 10.1021/ma500460b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Andrzej Sikorski
- Department
of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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32
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Dolgushev M, Guérin T, Blumen A, Bénichou O, Voituriez R. Gaussian semiflexible rings under angular and dihedral restrictions. J Chem Phys 2014; 141:014901. [PMID: 25005305 DOI: 10.1063/1.4885445] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys. 138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others.
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Affiliation(s)
- Maxim Dolgushev
- Theoretical Polymer Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - Thomas Guérin
- Laboratoire de Physique Théorique de la Matière Condensée, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France
| | - Alexander Blumen
- Theoretical Polymer Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - Olivier Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France
| | - Raphaël Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France
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33
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Chen YL, Lin YH, Chang JF, Lin PK. Dynamics and Conformation of Semiflexible Polymers in Strong Quasi-1D and -2D Confinement. Macromolecules 2014. [DOI: 10.1021/ma401923t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yeng-Long Chen
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
- Department
of Physics, National Taiwan University, Taipei, Taiwan
- Department
of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
| | - Yu-Hui Lin
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
| | | | - Po-keng Lin
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
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34
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Bohr J, Olsen KW. Total positive curvature of circular DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052714. [PMID: 24329303 DOI: 10.1103/physreve.88.052714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 08/15/2013] [Indexed: 06/03/2023]
Abstract
The properties of double-stranded DNA and other chiral molecules depend on the local geometry, i.e., on curvature and torsion, yet the paths of closed chain molecules are globally restricted by topology. When both of these characteristics are to be incorporated in the description of circular chain molecules, e.g., plasmids, it is shown to have implications for the total positive curvature integral. For small circular micro-DNAs it follows as a consequence of Fenchel's inequality that there must exist a minimum length for the circular plasmids to be double stranded. It also follows that all circular micro-DNAs longer than the minimum length must be concave, a result that is consistent with typical atomic force microscopy images of plasmids. Predictions for the total positive curvature of circular micro-DNAs are given as a function of length, and comparisons with circular DNAs from the literature are presented.
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Affiliation(s)
- Jakob Bohr
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kasper W Olsen
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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35
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Vanderlinden W, De Feyter S. Chain relaxation dynamics of DNA adsorbing at a solid-liquid interface. NANOSCALE 2013; 5:2264-2268. [PMID: 23407892 DOI: 10.1039/c3nr34231j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have used scanning force microscopy (SFM) to elucidate the dynamic behavior of open (torsionally unconstrained) circular and long linear DNA molecules during the relaxation process following adsorption onto mica. We find that bending stress and excluded volume effects drive the conformational equilibration via segmental out-of-plane dynamics.
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Affiliation(s)
- Willem Vanderlinden
- Laboratory of Photochemistry and Spectroscopy, Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
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36
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Jiang J, Xu X, Cao D. Density functional theory for inhomogeneous ring polymeric fluids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:041805. [PMID: 23214608 DOI: 10.1103/physreve.86.041805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Indexed: 06/01/2023]
Abstract
The modeling of ring polymers remains a challenge in classical density functional theory (DFT) due to the difficulty in solving the direct bond connectivity of the ring architecture without free ends. By considering the feature that all of the segments in a ring are equivalent, we give an algorithm to solve the integral of direct bond connectivity for ideal ring polymers, and therefore propose a DFT for inhomogeneous ring polymers, where the excess free energy functional is extended from an equation of state (EOS). This EOS exhibits better agreement than other EOSs for the compressibility factors, compared to Monte Carlo data. Importantly, the DFT satisfactorily reproduces the data of the configurational-bias Monte Carlo (CBMC) simulations for ring polymers. The local density profiles from the DFT show that the bead density of inhomogeneous ring fluids is independent of ring size, which is also confirmed by the CBMC simulations. Interestingly, the behavior of solvation force for ring polymers is quite similar to that of the polymers with infinite chain length.
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Affiliation(s)
- Jian Jiang
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
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37
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Schöpflin R, Brutzer H, Müller O, Seidel R, Wedemann G. Probing the elasticity of DNA on short length scales by modeling supercoiling under tension. Biophys J 2012; 103:323-30. [PMID: 22853910 PMCID: PMC3400772 DOI: 10.1016/j.bpj.2012.05.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/24/2012] [Accepted: 05/24/2012] [Indexed: 01/22/2023] Open
Abstract
The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been obtained because probing the elasticity of DNA on short length scales remains challenging. Here we investigate the limits of the WLC model using coarse-grained Monte Carlo simulations to model the supercoiling of linear DNA molecules under tension. At a critical supercoiling density, the DNA extension decreases abruptly due to the sudden formation of a plectonemic structure. This buckling transition is caused by the large energy required to form the tightly bent end-loop of the plectoneme and should therefore provide a sensitive benchmark for model evaluation. Although simulations based on the WLC energetics could quantitatively reproduce the buckling measured in magnetic tweezers experiments, the buckling almost disappears for the tested linear subelastic chain model. Thus, our data support the validity of a harmonic bending potential even for small bending radii down to 3.5 nm.
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Affiliation(s)
- Robert Schöpflin
- CC Bioinformatics, University of Applied Sciences Stralsund, Stralsund, Germany
| | - Hergen Brutzer
- Biotechnology Center Dresden, University of Technology Dresden, Dresden, Germany
| | - Oliver Müller
- CC Bioinformatics, University of Applied Sciences Stralsund, Stralsund, Germany
| | - Ralf Seidel
- Biotechnology Center Dresden, University of Technology Dresden, Dresden, Germany
| | - Gero Wedemann
- CC Bioinformatics, University of Applied Sciences Stralsund, Stralsund, Germany
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38
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Spiriti J, Kamberaj H, de Graff AMR, Thorpe MF, van der Vaart A. DNA Bending through Large Angles Is Aided by Ionic Screening. J Chem Theory Comput 2012; 8:2145-56. [PMID: 26593845 DOI: 10.1021/ct300177r] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model. Persistence lengths calculated directly from the simulated structures and indirectly through the use of sequence-independent coarse-grained models based on simulation data were similar to literature values. On short length scales, the free energy cost of bending DNA was found to be consistent with the worm-like chain model for small and intermediate bending angles. At large angles, the bending free energy as a function of the roll angle became linear, suggesting a relative increase in flexibility at larger roll angles. Counterions congregated on the concave side of the highly bent DNA and screened the repulsion of the phosphate groups, facilitating the bending.
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Affiliation(s)
- Justin Spiriti
- Department of Chemistry, University of South Florida, 4202 E Fowler Ave. CHE 205, Tampa, Florida 33620, United States
| | - Hiqmet Kamberaj
- Faculty of Technical Sciences, International Balkan University, Skopje, Republic of Macedonia
| | - Adam M R de Graff
- Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States.,Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - M F Thorpe
- Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States.,Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 E Fowler Ave. CHE 205, Tampa, Florida 33620, United States
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39
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Lee NK, Schmatko T, Muller P, Maaloum M, Johner A. Shape of adsorbed supercoiled plasmids: an equilibrium description. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:051804. [PMID: 23004779 DOI: 10.1103/physreve.85.051804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Indexed: 06/01/2023]
Abstract
Inspired by recent atomic force microscope (AFM) images of plasmids deposited on oppositely charged supported lipid bilayers from salt free solution, we propose a model for strongly adsorbed supercoiled cyclic stiff polyelectrolytes. We discuss how the excess linking number Lk of the deposited cycle is shared between writhe Wr and twist Tw at equilibrium and obtain the typical number of self-crossings in the deposited cycle as a function of surface charge density. The number of crossings at equilibrium is simply determined by the crossing penalty which is a local quantity and by the excess linking number. The number of crossings is well defined despite versatile plasmid shapes. For moderate numbers of crossings the loops are rather small and localized along the primary cycle, as expected from entropic loops. In the regime of many crossings, the cycle takes the shape of a regular flat ply ruled by local stiffness. The model allows for a semiquantitative comparison with the AFM images of deposited plasmids which are strongly charged.
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Affiliation(s)
- Nam-Kyung Lee
- Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, South Korea
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40
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Oh YH, Cho HW, Kim JM, Park CH, Sung BJ. Structure and Dynamics of Dilute Two-Dimensional Ring Polymer Solutions. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.3.975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Lin PK, Hsieh CC, Chen YL, Chou CF. Effects of Topology and Ionic Strength on Double-Stranded DNA Confined in Nanoslits. Macromolecules 2012. [DOI: 10.1021/ma202695e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Po-keng Lin
- Institute
of Physics and Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei, Taiwan
| | - Chih-Chen Hsieh
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Yeng-Long Chen
- Institute
of Physics and Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei, Taiwan
- Department of Physics, National Taiwan University, Taipei, Taiwan
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
| | - Chia-Fu Chou
- Institute
of Physics and Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei, Taiwan
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42
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Micheletti C, Orlandini E. Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties. Macromolecules 2012. [DOI: 10.1021/ma202503k] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Cristian Micheletti
- SISSA—Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
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43
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Affiliation(s)
- Jozef Adamcik
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zürich, LFO23, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Raffaele Mezzenga
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zürich, LFO23, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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44
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Lara C, Usov I, Adamcik J, Mezzenga R. Sub-persistence-length complex scaling behavior in lysozyme amyloid fibrils. PHYSICAL REVIEW LETTERS 2011; 107:238101. [PMID: 22182128 DOI: 10.1103/physrevlett.107.238101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 05/31/2023]
Abstract
We combine atomic force microscopy single-molecule analysis with polymer physics concepts to study molecular conformations of lysozyme amyloid fibrils. We resolve a wavy structure of the fibrils in which the scaling behavior varies at multiple length scales. Bond and pair correlation functions, end-to-end distribution, and wormlike chain model identify three characteristic length scales. At short length scales (≈150 nm), there is a first bending transition of the fibrils corresponding to a bending length L(b). At larger length scales (>2L(b)), fibrils become pseudoperiodic and start to undulate. Finally, at length scales larger than the persistence length (~ μm), the fibrils become flexible and follow a 2D self-avoiding random walk. We interpret these results in terms of the twisting of the fibrils and the impact this has on the area moment of inertia and the propensity of the fibril to bend.
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Affiliation(s)
- Cécile Lara
- ETH Zurich, Food & Soft Materials Science, Institute of Food, Nutrition & Health, Schmelzbergstrasse 9, LFO E23, 8092 Zurich, Switzerland
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45
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Rosa A, Orlandini E, Tubiana L, Micheletti C. Structure and Dynamics of Ring Polymers: Entanglement Effects Because of Solution Density and Ring Topology. Macromolecules 2011. [DOI: 10.1021/ma201827f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Angelo Rosa
- SISSA, Scuola Internazionale Superiore di Studi Avanzati and IIT, Italian Institute of Technology (SISSA unit), Via Bonomea 265, 34136 Trieste, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica and Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Luca Tubiana
- SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Cristian Micheletti
- SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
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46
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Jungmann R, Scheible M, Kuzyk A, Pardatscher G, Castro CE, Simmel FC. DNA origami-based nanoribbons: assembly, length distribution, and twist. NANOTECHNOLOGY 2011; 22:275301. [PMID: 21597145 DOI: 10.1088/0957-4484/22/27/275301] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A variety of polymerization methods for the assembly of elongated nanoribbons from rectangular DNA origami structures are investigated. The most efficient method utilizes single-stranded DNA oligonucleotides to bridge an intermolecular scaffold seam between origami monomers. This approach allows the fabrication of origami ribbons with lengths of several micrometers, which can be used for long-range ordered arrangement of proteins. It is quantitatively shown that the length distribution of origami ribbons obtained with this technique follows the theoretical prediction for a simple linear polymerization reaction. The design of flat single layer origami structures with constant crossover spacing inevitably results in local underwinding of the DNA helix, which leads to a global twist of the origami structures that also translates to the nanoribbons.
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Affiliation(s)
- Ralf Jungmann
- Lehrstuhl für Bioelektronik, Physik-Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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47
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Witz G, Rechendorff K, Adamcik J, Dietler G. Conformation of ring polymers in 2D constrained environments. PHYSICAL REVIEW LETTERS 2011; 106:248301. [PMID: 21770605 DOI: 10.1103/physrevlett.106.248301] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Indexed: 05/31/2023]
Abstract
The combination of ring closure and spatial constraints has a fundamental effect on the statistics of semiflexible polymers such as DNA. However, studies of the interplay between circularity and constraints are scarce and single-molecule experimental data concerning polymer conformations are missing. By means of atomic force microscopy we probe the conformation of circular DNA molecules in two dimensions and in the concentrated regime (above the overlap concentration c*). Molecules in this regime experience a collapse, and their statistical properties agree very well with those of simulated vesicles under pressure. Some circular molecules also create confining regions in which other molecules are trapped. Thus we show further that spatially confined molecules fold into specific conformations close to those found for linear chains, and strongly dependent on the size of the confining box.
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Affiliation(s)
- G Witz
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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48
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Benková Z, Cifra P. Stiffening Transition in Semiflexible Cyclic Macromolecules. MACROMOL THEOR SIMUL 2010. [DOI: 10.1002/mats.201000047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Medalion S, Kessler DA, Rabin Y. Effect of spontaneous twist on DNA minicircles. Biophys J 2010; 99:2987-94. [PMID: 21044596 PMCID: PMC2966040 DOI: 10.1016/j.bpj.2010.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/01/2010] [Accepted: 08/05/2010] [Indexed: 10/18/2022] Open
Abstract
Monte Carlo simulations are used to study the effect of spontaneous (intrinsic) twist on the conformation of topologically equilibrated minicircles of dsDNA. The twist, writhe, and radius of gyration distributions and their moments are calculated for different spontaneous twist angles and DNA lengths. The average writhe and twist deviate in an oscillatory fashion (with the period of the double helix) from their spontaneous values, as one spans the range between two neighboring integer values of intrinsic twist. Such deviations vanish in the limit of long DNA plasmids.
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Affiliation(s)
- Shlomi Medalion
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel.
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50
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Cotta-Ramusino L, Maddocks JH. Looping probabilities of elastic chains: a path integral approach. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:051924. [PMID: 21230517 DOI: 10.1103/physreve.82.051924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 08/02/2010] [Indexed: 05/30/2023]
Abstract
We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit continuum mechanics models for the computation of DNA looping probabilities, but here we focus on explaining the novel analytical aspects in the derivation of our approximation formula. Accordingly, and for simplicity, the current presentation is limited to the illustrative case of planar configurations. A path integral formalism is adopted, and, in the standard way, the first approximation to the looping pdf is obtained from a minimal energy configuration satisfying prescribed end conditions. Then we compute an additional factor in the pdf which encompasses the contributions of quadratic fluctuations about the minimum energy configuration along with a simultaneous evaluation of the partition function. The original aspects of our analysis are twofold. First, the quadratic Lagrangian describing the fluctuations has cross-terms that are linear in first derivatives. This, seemingly small, deviation from the structure of standard path integral examples complicates the necessary analysis significantly. Nevertheless, after a nonlinear change of variable of Riccati type, we show that the correction factor to the pdf can still be evaluated in terms of the solution to an initial value problem for the linear system of Jacobi ordinary differential equations associated with the second variation. The second novel aspect of our analysis is that we show that the Hamiltonian form of these linear Jacobi equations still provides the appropriate correction term in the inextensible, unshearable limit that is commonly adopted in polymer physics models of, e.g. DNA. Prior analyses of the inextensible case have had to introduce nonlinear and nonlocal integral constraints to express conditions on the relative displacement of the end points. Our approximation formula for the looping pdf is of quite general applicability as, in contrast to most prior approaches, no assumption is made of either uniformity of the elastic chain, nor of a straight intrinsic shape. If the chain is uniform the Jacobi system evaluated at certain minimum energy configurations has constant coefficients. In such cases our approximate pdf can be evaluated in an entirely explicit, closed form. We illustrate our analysis with a planar example of this type and compute an approximate probability of cyclization, i.e., of forming a closed loop, from a uniform elastic chain whose intrinsic shape is an open circular arc.
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Affiliation(s)
- Ludovica Cotta-Ramusino
- Laboratory for Computation and Visualization in Mathematics and Mechanics, EPFL FSB IMB, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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