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Battaglia C, Michieletto D. Loops are geometric catalysts for DNA integration. Nucleic Acids Res 2024:gkae484. [PMID: 38864388 DOI: 10.1093/nar/gkae484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024] Open
Abstract
The insertion of DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of DNA insertions are not random and the physical mechanisms underlying the integration site selection are poorly understood. Here, we perform Molecular Dynamics simulations to study the insertion of DNA elements, such as viral DNA or transposons, into naked DNA or chromatin substrates. More specifically, we explore the role of loops within the polymeric substrate and discover that they act as 'geometric catalysts' for DNA integration by reducing the energy barrier for substrate deformation. Additionally, we discover that the 1D pattern and 3D conformation of loops have a marked effect on the distribution of integration sites. Finally, we show that loops may compete with nucleosomes to attract DNA integrations. These results may be tested in vitro and they may help to understand patterns of DNA insertions with implications in genome evolution and engineering.
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Affiliation(s)
- Cleis Battaglia
- 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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2
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Neill P, Crist N, McGorty R, Robertson-Anderson R. Enzymatic cleaving of entangled DNA rings drives scale-dependent rheological trajectories. SOFT MATTER 2024; 20:2750-2766. [PMID: 38440846 DOI: 10.1039/d3sm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA, which naturally occurs in linear, ring, and supercoiled topologies, frequently undergoes enzyme-driven topological conversion and fragmentation in vivo, enabling it to perform a variety of functions within the cell. In vitro, highly concentrated DNA polymers form entanglements that yield viscoelastic properties dependent on the topologies and lengths of the DNA. Enzyme-driven alterations of DNA size and shape therefore offer a means of designing active materials with programmable viscoelastic properties. Here, we incorporate multi-site restriction endonucleases into dense DNA solutions to linearize and fragment circular DNA molecules. We pair optical tweezers microrheology with differential dynamic microscopy and single-molecule tracking to measure the linear and nonlinear viscoelastic response and transport properties of entangled DNA solutions over a wide range of spatiotemporal scales throughout the course of enzymatic digestion. We show that, at short timescales, relative to the relaxation timescales of the polymers, digestion of these 'topologically-active' fluids initially causes an increase in elasticity and relaxation times followed by a gradual decrease. Conversely, for long timescales, linear viscoelastic moduli exhibit signatures of increasing elasticity. DNA diffusion, likewise, becomes increasingly slowed, in direct opposition to the short-time behavior. We hypothesize that this scale-dependent rheology arises from the population of small DNA fragments, which increases as digestion proceeds, driving self-association of larger fragments via depletion interactions, giving rise to slow relaxation modes of clusters of entangled chains, interspersed among shorter unentangled fragments. While these slow modes likely dominate at long times, they are presumably frozen out in the short-time limit, which instead probes the faster relaxation modes of the unentangled population.
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Affiliation(s)
- Philip Neill
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Natalie Crist
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Ryan McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Rae Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
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3
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Zhang Z, Zhao W, Cheng Z, Zhang G, Liu H. Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model. J Chem Phys 2024; 160:054906. [PMID: 38341711 DOI: 10.1063/5.0190580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
Topological regulation of DNA by topoisomerases in cells is very crucial for life. We propose a coarse-grained model to study the catenation process of double-stranded DNA (dsDNA) rings regulated by topoisomerase II (TOP2) and provide a computational method to characterize the topological structures of the Olympic gels obtained. The function of TOP2 in the catenation of dsDNA rings is implicitly fulfilled by operating the length of a stretchable catch bond in the dsDNA ring. After the catenation reaction of initially noncatenated dsDNA rings in the solution, the Olympic gel is obtained and the interlocked topology of the dsDNA rings can be characterized by a computational method derived from the HOMFLY polynomial, based on which the catenation degree and the complexity of catenation are quantified. Detailed dependence of the catenation degree and the complexity of the catenated topology on key parameters, including the size of the transient broken gap and the duration time of the break on the dsDNA ring during operation by TOP2, the initial molar ratio of TOP2 to the dsDNA rings, and the reaction temperature, has been investigated.
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Affiliation(s)
- Zhongyan Zhang
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Wenbo Zhao
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
| | - Zhiyuan Cheng
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
| | - Guojie Zhang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Hong Liu
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
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4
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Staňo R, Smrek J, Likos CN. Cluster Formation in Solutions of Polyelectrolyte Rings. ACS NANO 2023; 17:21369-21382. [PMID: 37729077 PMCID: PMC10655244 DOI: 10.1021/acsnano.3c06083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023]
Abstract
We use molecular dynamics simulations to explore concentrated solutions of semiflexible polyelectrolyte ring polymers, akin to the DNA mini-circles, with counterions of different valences. We find that the assembly of rings into nanoscopic cylindrical stacks is a generic feature of the systems, but the morphology and dynamics of such a cluster can be steered by the counterion conditions. In general, a small addition of trivalent ions can stabilize the emergence of clusters due to the counterion condensation, which mitigates the repulsion between the like-charged rings. Stoichiometric addition of trivalent ions can even lead to phase separation of the polyelectrolyte ring phase due to the ion-bridging effects promoting otherwise entropically driven clustering. On the other hand, monovalent counterions cause the formation of stacks to be re-entrant with density. The clusters are stable within a certain window of concentration, while above the window the polyelectrolytes undergo an osmotic collapse, disfavoring ordering. The cluster phase exhibits characteristic cluster glass dynamics with arrest of collective degrees of freedom but not the self-ones. On the other hand, the collapsed phase shows arrest on both the collective and single level, suggesting an incipient glass-to-glass transition, from a cluster glass of ring clusters to a simple glass of rings.
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Affiliation(s)
- Roman Staňo
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Vienna
Doctoral School in Physics, University of
Vienna, Boltzmanngasse
5, 1090 Vienna, Austria
| | - 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
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5
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Deblais A, Prathyusha KR, Sinaasappel R, Tuazon H, Tiwari I, Patil VP, Bhamla MS. Worm blobs as entangled living polymers: from topological active matter to flexible soft robot collectives. SOFT MATTER 2023; 19:7057-7069. [PMID: 37706563 PMCID: PMC10523214 DOI: 10.1039/d3sm00542a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Recently, the study of long, slender living worms has gained attention due to their unique ability to form highly entangled physical structures, exhibiting emergent behaviors. These organisms can assemble into an active three-dimensional soft entity referred to as the "blob", which exhibits both solid-like and liquid-like properties. This blob can respond to external stimuli such as light, to move or change shape. In this perspective article, we acknowledge the extensive and rich history of polymer physics, while illustrating how these living worms provide a fascinating experimental platform for investigating the physics of active, polymer-like entities. The combination of activity, long aspect ratio, and entanglement in these worms gives rise to a diverse range of emergent behaviors. By understanding the intricate dynamics of the worm blob, we could potentially stimulate further research into the behavior of entangled active polymers, and guide the advancement of synthetic topological active matter and bioinspired tangling soft robot collectives.
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Affiliation(s)
- Antoine Deblais
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - K R Prathyusha
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Rosa Sinaasappel
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Harry Tuazon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ishant Tiwari
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Vishal P Patil
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Ubertini MA, Rosa A. Topological Analysis and Recovery of Entanglements in Polymer Melts. Macromolecules 2023; 56:3354-3362. [PMID: 37181245 PMCID: PMC10173697 DOI: 10.1021/acs.macromol.3c00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/24/2023] [Indexed: 05/16/2023]
Abstract
The viscous flow of polymer chains in dense melts is dominated by topological constraints whenever the single-chain contour length, N, becomes larger than the characteristic scale Ne, defining comprehensively the macroscopic rheological properties of the highly entangled polymer systems. Even though they are naturally connected to the presence of hard constraints like knots and links within the polymer chains, the difficulty of integrating the rigorous language of mathematical topology with the physics of polymer melts has limited somehow a genuine topological approach to the problem of classifying these constraints and to how they are related to the rheological entanglements. In this work, we tackle this problem by studying the occurrence of knots and links in lattice melts of randomly knotted and randomly concatenated ring polymers with various bending stiffness values. Specifically, by introducing an algorithm that shrinks the chains to their minimal shapes that do not violate topological constraints and by analyzing those in terms of suitable topological invariants, we provide a detailed characterization of the topological properties at the intrachain level (knots) and of links between pairs and triplets of distinct chains. Then, by employing the Z1 algorithm on the minimal conformations to extract the entanglement length Ne, we show that the ratio N/Ne, the number of entanglements per chain, can be remarkably well reconstructed in terms of only two-chain links.
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