1
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Villanueva Valencia JR, Li D, Casjens SR, Evilevitch A. 'SAXS-osmometer' method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state. Nucleic Acids Res 2023; 51:11415-11427. [PMID: 37889048 PMCID: PMC10681747 DOI: 10.1093/nar/gkad852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 10/28/2023] Open
Abstract
We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA-DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.
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Affiliation(s)
| | - Dong Li
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Alex Evilevitch
- Department of Experimental Medical Science and NanoLund, Lund University, Box 124, Lund, Sweden
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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2
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Hsiao PY, Chen WY. A general theory of polymer ejection tested in a quasi two-dimensional space. Sci Rep 2021; 11:14721. [PMID: 34282179 PMCID: PMC8289874 DOI: 10.1038/s41598-021-94054-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022] Open
Abstract
A general ejection theory of polymer is developed in a two- and three-dimensional space. A polymer is confined initially in a cavity and ejects spontaneously to the outer space through a nanopore channel without the help of any external stimulus. A reflective wall boundary is set at the pore entrance to prevent the falling of the head monomer of chain into the cavity. Three stages are distinguished in a process: (1) an entering stage, in which the head monomer enters the pore to search for a way to traverse the pore channel, (2) a main ejection stage, in which the chain body is transported from the cavity to the outer space, (3) a leaving stage, in which the tail monomer passes through and leaves the pore channel. Depending on the number of the monomers remaining in the cavity, the main ejection stage can be divided into the confined and the non-confined stages. The non-confined stage can be further split into the thermal escape and the entropic pulling stages. The Onsager’s variational principle is applied to derive the kinetics equation of ejection. The escape time is calculated from the corresponding Kramers’ escape problem. Extensive molecular dynamics simulations are then performed in a quasi two-dimensional space to verify the theory. The variation of the ejection speed is carefully examined. The decreasing behavior of the number of monomers in the cavity is studied in details. The scaling properties of the spending time at each processing stage are investigated systematically by varying the chain length, the cavity diameter, and the initial volume fraction of chain. The results of simulation support firmly the predictions of the theory, cross-checked in the studies of various topics. In combining with the previous investigations in the three-dimensional space, the generalized theory is very robust, able to explain the two seemly different phenomena, polymer ejection and polymer translocation, together under the same theoretical framework in the two space dimensions.
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Affiliation(s)
- Pai-Yi Hsiao
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China. .,Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.
| | - Wei-Yei Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
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3
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Liu P, Arsuaga J, Calderer MC, Golovaty D, Vazquez M, Walker S. Ion-dependent DNA configuration in bacteriophage capsids. Biophys J 2021; 120:3292-3302. [PMID: 34265262 DOI: 10.1016/j.bpj.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/01/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteriophages densely pack their long double-stranded DNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy that combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and with molecular dynamics simulations for small capsids.
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Affiliation(s)
- Pei Liu
- School of Mathematics, University of Minnesota, Twin Cities, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California Davis, Davis, California; Department of Molecular and Cellular Biology, University of California Davis, Davis, California.
| | - M Carme Calderer
- School of Mathematics, University of Minnesota, Twin Cities, Minneapolis, Minnesota
| | - Dmitry Golovaty
- Department of Mathematics, The University of Akron, Akron, Ohio.
| | - Mariel Vazquez
- Department of Mathematics, University of California Davis, Davis, California; Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California
| | - Shawn Walker
- Department of Mathematics, Louisiana State University, Baton Rouge, Louisiana
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4
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Cruz B, Zhu Z, Calderer C, Arsuaga J, Vazquez M. Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor. Biophys J 2020; 118:2103-2116. [PMID: 32353255 PMCID: PMC7203069 DOI: 10.1016/j.bpj.2020.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/04/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.
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Affiliation(s)
- Brian Cruz
- Department of Mathematics, University of California, Berkeley, California
| | - Zihao Zhu
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California
| | - Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California at Davis, Davis, California; Department of Molecular and Cellular Biology, University of California at Davis, Davis, California.
| | - Mariel Vazquez
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California; Department of Mathematics, University of California at Davis, Davis, California.
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5
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Abstract
Unraveling the mechanisms of packing of DNA inside viral capsids is of fundamental importance to understanding the spread of viruses. It could also help develop new applications to targeted drug delivery devices for a large range of therapies. In this article, we present a robust, predictive mathematical model and its numerical implementation to aid the study and design of bacteriophage viruses for application purposes. Exploiting the analogies between the columnar hexagonal chromonic phases of encapsidated viral DNA and chromonic aggregates formed by plank-shaped molecular compounds, we develop a first-principles effective mechanical model of DNA packing in a viral capsid. The proposed expression of the packing energy, which combines relevant aspects of the liquid crystal theory, is developed from the model of hexagonal columnar phases, together with that describing configurations of polymeric liquid crystals. The method also outlines a parameter selection strategy that uses available data for a collection of viruses, aimed at applications to viral design. The outcome of the work is a mathematical model and its numerical algorithm, based on the method of finite elements, and computer simulations to identify and label the ordered and disordered regions of the capsid and calculate the inner pressure. It also presents the tools for the local reconstruction of the DNA "scaffolding" and the center curve of the filament within the capsid.
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Affiliation(s)
- Shawn Walker
- Department of Mathematics, 303 Lockett Hall, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Javier Arsuaga
- Department of Cellular and Molecular Biology, Briggs Hall 09, and Department of Mathematics, MSB 2115, University of California Davis, Davis, California 95616, USA
| | - Lindsey Hiltner
- School of Mathematics, 507 Vincent Hall, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - M Carme Calderer
- School of Mathematics, 507 Vincent Hall, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mariel Vázquez
- Department of Microbiology and Molecular Genetics, Briggs Hall 09, and Department of Mathematics, MSB 2150, University of California Davis, Davis, California 95616, USA
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6
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Milrot E, Shimoni E, Dadosh T, Rechav K, Unger T, Van Etten JL, Minsky A. Structural studies demonstrating a bacteriophage-like replication cycle of the eukaryote-infecting Paramecium bursaria chlorella virus-1. PLoS Pathog 2017; 13:e1006562. [PMID: 28850602 PMCID: PMC5593192 DOI: 10.1371/journal.ppat.1006562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/11/2017] [Accepted: 07/31/2017] [Indexed: 11/18/2022] Open
Abstract
A fundamental stage in viral infection is the internalization of viral genomes in host cells. Although extensively studied, the mechanisms and factors responsible for the genome internalization process remain poorly understood. Here we report our observations, derived from diverse imaging methods on genome internalization of the large dsDNA Paramecium bursaria chlorella virus-1 (PBCV-1). Our studies reveal that early infection stages of this eukaryotic-infecting virus occurs by a bacteriophage-like pathway, whereby PBCV-1 generates a hole in the host cell wall and ejects its dsDNA genome in a linear, base-pair-by-base-pair process, through a membrane tunnel generated by the fusion of the virus internal membrane with the host membrane. Furthermore, our results imply that PBCV-1 DNA condensation that occurs shortly after infection probably plays a role in genome internalization, as hypothesized for the infection of some bacteriophages. The subsequent perforation of the host photosynthetic membranes presumably enables trafficking of viral genomes towards host nuclei. Previous studies established that at late infection stages PBCV-1 generates cytoplasmic organelles, termed viral factories, where viral assembly takes place, a feature characteristic of many large dsDNA viruses that infect eukaryotic organisms. PBCV-1 thus appears to combine a bacteriophage-like mechanism during early infection stages with a eukaryotic-like infection pathway in its late replication cycle. Although extensively studied, the mechanisms responsible for internalization of viral genomes into their host cells remain unclear. A particularly interesting case of genome release and internalization is provided by the large Paramecium bursaria chlorella virus-1 (PBCV-1), which infects unicellular eukaryotic photosynthetic chlorella cells. In order to release its long dsDNA genome and to enable its translocation to the host nucleus, PBCV-1 must overcome multiple hurdles, including a thick host cell wall and multilayered chloroplast membranes that surround the host cytoplasm. Our observations indicate that these obstacles are dealt with perforations of the host wall, the host cellular membrane, and the host photosynthetic membranes by viral-encoded proteins. Furthermore, our results highlight a bacteriophage-like nature of early PBCV-1 infection stages, thus implying that this virus uniquely combines bacteriophage-like and eukaryotic-like pathways to accomplish its replication cycle.
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Affiliation(s)
- Elad Milrot
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Proteomics, The Weizmann Institute of Science, Rehovot, Israel
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
| | - Abraham Minsky
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
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7
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Keller N, Berndsen ZT, Jardine PJ, Smith DE. Experimental comparison of forces resisting viral DNA packaging and driving DNA ejection. Phys Rev E 2017; 95:052408. [PMID: 28618627 DOI: 10.1103/physreve.95.052408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Indexed: 11/07/2022]
Abstract
We compare forces resisting DNA packaging and forces driving DNA ejection in bacteriophage phi29 with theoretical predictions. Ejection of DNA from prohead-motor complexes is triggered by heating complexes after in vitro packaging and force is inferred from the suppression of ejection by applied osmotic pressure. Ejection force from 0% to 80% filling is found to be in quantitative agreement with predictions of a continuum mechanics model that assumes a repulsive DNA-DNA interaction potential based on DNA condensation studies and predicts an inverse-spool conformation. Force resisting DNA packaging from ∼80% to 100% filling inferred from optical tweezers studies is also consistent with the predictions of this model. The striking agreement with these two different measurements suggests that the overall energetics of DNA packaging is well described by the model. However, since electron microscopy studies of phi29 do not reveal a spool conformation, our findings suggest that the spool model overestimates the role of bending rigidity and underestimates the role of intrastrand repulsion. Below ∼80% filling the inferred forces resisting packaging are unexpectedly lower than the inferred ejection forces, suggesting that in this filling range the forces are less accurately determined or strongly temperature dependent.
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Affiliation(s)
- Nicholas Keller
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zachary T Berndsen
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, 515 Delaware Street SE, Minneapolis, Minnesota 55455, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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8
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Zhou LQ, Yu WC, Chen YH, Luo KF. Ejection dynamics of semiflexible polymers out of a nanochannel. Chin J Polym Sci 2016. [DOI: 10.1007/s10118-016-1842-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Affiliation(s)
- Rudolf Podgornik
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department
of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - M. Alphan Aksoyoglu
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Selcuk Yasar
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Daniel Svenšek
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - V. Adrian Parsegian
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
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10
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Goldfain AM, Garmann RF, Jin Y, Lahini Y, Manoharan VN. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages. J Phys Chem B 2016; 120:6130-8. [DOI: 10.1021/acs.jpcb.6b02153] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Yan Jin
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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11
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Hollenbeck EC, Douarche C, Allain JM, Roger P, Regeard C, Cegelski L, Fuller GG, Raspaud E. Mechanical Behavior of a Bacillus subtilis Pellicle. J Phys Chem B 2016; 120:6080-8. [PMID: 27046510 DOI: 10.1021/acs.jpcb.6b02074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacterial biofilms consist of a complex network of biopolymers embedded with microorganisms, and together these components form a physically robust structure that enables bacteria to grow in a protected environment. This structure can help unwanted biofilms persist in situations ranging from chronic infection to the biofouling of industrial equipment, but under certain circumstances it can allow the biofilm to disperse and colonize new niches. Mechanical properties are therefore a key aspect of biofilm life. In light of the recently discovered growth-induced compressive stress present within a biofilm, we studied the mechanical behavior of Bacillus subtilis pellicles, or biofilms at the air-liquid interface, and tracked simultaneously the force response and macroscopic structural changes during elongational deformations. We observed that pellicles behaved viscoelastically in response to small deformations, such that the growth-induced compressive stress was still present, and viscoplastically at large deformations, when the pellicles were under tension. In addition, by using particle imaging velocimetry we found that the pellicle deformations were nonaffine, indicating heterogeneous mechanical properties with the pellicle being more pliable near attachment surfaces. Overall, our results indicate that we must consider not only the viscoelastic but also the viscoplastic and mechanically heterogeneous nature of these structures to understand biofilm dispersal and removal.
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Affiliation(s)
- Emily C Hollenbeck
- Department of Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | - Carine Douarche
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay , Orsay, France
| | - Jean-Marc Allain
- Laboratoire de Mécanique des Solides, École Polytechnique, CNRS, Université Paris-Saclay , Palaiseau, France
| | - Philippe Roger
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Sud, Université Paris-Saclay , Orsay, France
| | - Christophe Regeard
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif sur Yvette, France
| | - Lynette Cegelski
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Gerald G Fuller
- Department of Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay , Orsay, France
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12
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Potestio R, Tubiana L. Discretized knot motion on a tensioned fiber induced by transverse waves. Soft Matter 2016; 12:669-673. [PMID: 26510521 DOI: 10.1039/c5sm01766a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Topological entanglement is a ubiquitous feature of many biological as well as artificial polymers and fibers. While the equilibrium properties of entangled chains have been the subject of several studies, little is known about their out-of-equilibrium behavior. Here, we address the problem of a stretched knotted fiber driven by a periodic force applied to one of its termini. We show that the onset of standing waves kinetically traps the knot in spatially localized states where the amplitude of the oscillations is maximal, while the knot normal diffusive dynamics is replaced by a discrete jump dynamics.
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Affiliation(s)
- Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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13
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Sung B, Leforestier A, Livolant F. Coexistence of coil and globule domains within a single confined DNA chain. Nucleic Acids Res 2015; 44:1421-7. [PMID: 26704970 PMCID: PMC4756835 DOI: 10.1093/nar/gkv1494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/09/2015] [Indexed: 11/17/2022] Open
Abstract
The highly charged DNA chain may be either in an extended conformation, the coil, or condensed into a highly dense and ordered structure, the toroid. The transition, also called collapse of the chain, can be triggered in different ways, for example by changing the ionic conditions of the solution. We observe individual DNA molecules one by one, kept separated and confined inside a protein shell (the envelope of a bacterial virus, 80 nm in diameter). For subcritical concentrations of spermine (4+), part of the DNA is condensed and organized in a toroid and the other part of the chain remains uncondensed around. Two states coexist along the same DNA chain. These ‘hairy’ globules are imaged by cryo-electron microscopy. We describe the global conformation of the chain and the local ordering of DNA segments inside the toroid.
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Affiliation(s)
- Baeckkyoung Sung
- Laboratoire de Physique des Solides, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
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14
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Bauer DW, Evilevitch A. Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ. J Mol Biol 2015; 427:3189-3200. [PMID: 26254570 DOI: 10.1016/j.jmb.2015.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/22/2015] [Accepted: 07/26/2015] [Indexed: 11/27/2022]
Abstract
Viruses must remain infectious while in harsh extracellular environments. An important aspect of viral particle stability for double-stranded DNA viruses is the energetically unfavorable state of the tightly confined DNA chain within the virus capsid creating pressures of tens of atmospheres. Here, we study the influence of internal genome pressure on the thermal stability of viral particles. Using differential scanning calorimetry to monitor genome loss upon heating, we find that internal pressure destabilizes the virion, resulting in a smaller activation energy barrier to trigger DNA release. These experiments are complemented by plaque assay and electron microscopy measurements to determine the influence of intra-capsid DNA pressure on the rates of viral infectivity loss. At higher temperatures (65-75°C), failure to retain the packaged genome is the dominant mechanism of viral inactivation. Conversely, at lower temperatures (40-55°C), a separate inactivation mechanism dominates, which results in non-infectious particles that still retain their packaged DNA. Most significantly, both mechanisms of infectivity loss are directly influenced by internal DNA pressure, with higher pressure resulting in a more rapid rate of inactivation at all temperatures.
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Affiliation(s)
- D W Bauer
- Carnegie Mellon University Department of Physics, Pittsburgh, PA 15213, USA
| | - A Evilevitch
- Carnegie Mellon University Department of Physics, Pittsburgh, PA 15213, USA; Lund University Department of Biochemistry and Structural Biology, 221 00 Lund, Sweden.
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15
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Jin Y, Knobler CM, Gelbart WM. Controlling the extent of viral genome release by a combination of osmotic stress and polyvalent cations. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:022708. [PMID: 26382433 DOI: 10.1103/physreve.92.022708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Indexed: 06/05/2023]
Abstract
While several in vitro experiments on viral genome release have specifically studied the effects of external osmotic pressure and of the presence of polyvalent cations on the ejection of DNA from bacteriophages, few have systematically investigated how the extent of ejection is controlled by a combination of these effects. In this work we quantify the effect of osmotic pressure on the extent of DNA ejection from bacteriophage lambda as a function of polyvalent cation concentration (in particular, the tetravalent polyamine spermine). We find that the pressure required to completely inhibit ejection decreases from 38 to 17 atm as the spermine concentration is increased from 0 to 1.5 mM. Further, incubation of the phage particles in spermine concentrations as low as 0.15 mM--the threshold for DNA condensation in bulk solution-is sufficient to significantly limit the extent of ejection in the absence of osmolyte; for spermine concentrations below this threshold, the ejection is complete. In accord with recent investigations on the packaging of DNA in the presence of a condensing agent, we observe that the self-attraction induced by the polyvalent cation affects the ordering of the genome, causing it to get stuck in a broad range of nonequilibrated structures.
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Affiliation(s)
- Yan Jin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute (MBI), University of California, Los Angeles, California 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, California 90095, USA
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16
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Jin Y, Sdao SM, Dover JA, Porcek NB, Knobler CM, Gelbart WM, Parent KN. Bacteriophage P22 ejects all of its internal proteins before its genome. Virology 2015; 485:128-34. [PMID: 26245366 DOI: 10.1016/j.virol.2015.07.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/22/2015] [Accepted: 07/07/2015] [Indexed: 12/11/2022]
Abstract
Double-stranded DNA bacteriophages are highly pressurized, providing a force driving ejection of a significant fraction of the genome from its capsid. In P22-like Podoviridae, internal proteins ("E proteins") are packaged into the capsid along with the genome, and without them the virus is not infectious. However, little is known about how and when these proteins come out of the virus. We employed an in vitro osmotic suppression system with high-molecular-weight polyethylene glycol to study P22 E protein release. While slow ejection of the DNA can be triggered by lipopolysaccharide (LPS), the rate is significantly enhanced by the membrane protein OmpA from Salmonella. In contrast, E proteins are not ejected unless both OmpA and LPS are present and their ejection when OmpA is present is largely complete before any genome is ejected, suggesting that E proteins play a key role in the early stage of transferring P22 DNA into the host.
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Affiliation(s)
- Yan Jin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Sophia M Sdao
- Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA
| | - John A Dover
- Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA
| | - Natalia B Porcek
- Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA; Michigan State University, Department of Microbiology and Molecular Genetics, East Lansing, MI 48824, USA
| | - Charles M Knobler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.
| | - Kristin N Parent
- Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824, USA.
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17
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Mutsafi Y, Fridmann-sirkis Y, Milrot E, Hevroni L, Minsky A. Infection cycles of large DNA viruses: Emerging themes and underlying questions. Virology 2014; 466-467:3-14. [DOI: 10.1016/j.virol.2014.05.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/20/2022]
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18
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Sae-Ueng U, Li D, Zuo X, Huffman JB, Homa FL, Rau D, Evilevitch A. Solid-to-fluid DNA transition inside HSV-1 capsid close to the temperature of infection. Nat Chem Biol 2014; 10:861-7. [PMID: 25195012 DOI: 10.1038/nchembio.1628] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/31/2014] [Indexed: 01/06/2023]
Abstract
DNA in the human Herpes simplex virus type 1 (HSV-1) capsid is packaged to a tight density. This leads to tens of atmospheres of internal pressure responsible for the delivery of the herpes genome into the cell nucleus. In this study we show that, despite its liquid crystalline state inside the capsid, the DNA is fluid-like, which facilitates its ejection into the cell nucleus during infection. We found that the sliding friction between closely packaged DNA strands, caused by interstrand repulsive interactions, is reduced by the ionic environment of epithelial cells and neurons susceptible to herpes infection. However, variations in the ionic conditions corresponding to neuronal activity can restrict DNA mobility in the capsid, making it more solid-like. This can inhibit intranuclear DNA release and interfere with viral replication. In addition, the temperature of the human host (37 °C) induces a disordering transition of the encapsidated herpes genome, which reduces interstrand interactions and provides genome mobility required for infection.
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19
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Sae-Ueng U, Liu T, Catalano CE, Huffman JB, Homa FL, Evilevitch A. Major capsid reinforcement by a minor protein in herpesviruses and phage. Nucleic Acids Res 2014; 42:9096-107. [PMID: 25053840 PMCID: PMC4132744 DOI: 10.1093/nar/gku634] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Herpes simplex type 1 virus (HSV-1) and bacteriophage λ capsids undergo considerable structural changes during self-assembly and DNA packaging. The initial steps of viral capsid self-assembly require weak, non-covalent interactions between the capsid subunits to ensure free energy minimization and error-free assembly. In the final stages of DNA packaging, however, the internal genome pressure dramatically increases, requiring significant capsid strength to withstand high internal genome pressures of tens of atmospheres. Our data reveal that the loosely formed capsid structure is reinforced post-assembly by the minor capsid protein UL25 in HSV-1 and gpD in bacteriophage λ. Using atomic force microscopy nano-indentation analysis, we show that the capsid becomes stiffer upon binding of UL25 and gpD due to increased structural stability. At the same time the force required to break the capsid increases by ∼70% for both herpes and phage. This demonstrates a universal and evolutionarily conserved function of the minor capsid protein: facilitating the retention of the pressurized viral genome in the capsid. Since all eight human herpesviruses have UL25 orthologs, this discovery offers new opportunities to interfere with herpes replication by disrupting the precise force balance between the encapsidated DNA and the capsid proteins crucial for viral replication.
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Affiliation(s)
- Udom Sae-Ueng
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ting Liu
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Carlos Enrique Catalano
- Department of Medicinal Chemistry, University of Washington School of Pharmacy, H172 Health Sciences Building, Box 357610, Seattle, WA 98195, USA
| | - Jamie B Huffman
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Fred L Homa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Alex Evilevitch
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA Department of Biochemistry and Structural Biology, Lund University, Box 124, Lund, Sweden
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20
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DE FRUTOS M, LEFORESTIER A, LIVOLANT F. RELATIONSHIP BETWEEN THE GENOME PACKING IN THE BACTERIOPHAGE CAPSID AND THE KINETICS OF DNA EJECTION. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013500069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present a general survey of experimental and theoretical observations of DNA structure and in vitro ejection kinetics for different bacteriophage species. In some species, like T5, the ejection may present pauses and arrests that have not been detected in others species like Lambda. We propose hypotheses to explain such differences and we discuss how the experimental conditions may be important for their detection. Our work highlights the role of DNA organization inside the bacteriophage capsid on the stochastic and out of equilibrium nature of the ejection process.
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Affiliation(s)
- M. DE FRUTOS
- Institut de Biologie et Biochimie Moléculaire et Cellulaire, UMR CNRS 8619, Bât 430, Université Paris Sud, 91405 Orsay cedex, France
| | - A. LEFORESTIER
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris-Sud, Bât 510, Orsay 91405, France
| | - F. LIVOLANT
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris-Sud, Bât 510, Orsay 91405, France
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21
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22
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Abstract
Herpes simplex virus type 1 (HSV-1) packages its micrometers-long double-stranded DNA genome into a nanometer-scale protein shell, termed the capsid. Upon confinement within the capsid, neighboring DNA strands experience repulsive electrostatic and hydration forces as well as bending stress associated with the tight curvature required of packaged DNA. By osmotically suppressing DNA release from HSV-1 capsids, we provide the first experimental evidence of a high internal pressure of tens of atmospheres within a eukaryotic human virus, resulting from the confined genome. Furthermore, the ejection is progressively suppressed by increasing external osmotic pressures, which reveals that internal pressure is capable of powering ejection of the entire genome from the viral capsid. Despite billions of years of evolution separating eukaryotic viruses and bacteriophages, pressure-driven DNA ejection has been conserved. This suggests it is a key mechanism for viral infection and thus presents a new target for antiviral therapies.
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Affiliation(s)
- David W Bauer
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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23
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Mahalik JP, Hildebrandt B, Muthukumar M. Langevin dynamics simulation of DNA ejection from a phage. J Biol Phys 2013; 39:229-45. [PMID: 23860871 DOI: 10.1007/s10867-013-9316-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/22/2013] [Indexed: 11/30/2022] Open
Abstract
We have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from Φ29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages.
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Affiliation(s)
- J P Mahalik
- Department of Polymer Science and Engineering, Department of Physics, University of Massachusetts, Amherst, MA 01003, USA
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24
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Abstract
Double-stranded DNA bacteriophage genomes are packaged into their icosahedral capsids at the highest densities known so far (about 50 % w:v). How the molecule is folded at such density and how its conformation changes upon ejection or packaging are fascinating questions still largely open. We review cryo-TEM analyses of DNA conformation inside partially filled capsids as a function of the physico-chemical environment (ions, osmotic pressure, temperature). We show that there exists a wide variety of DNA conformations. Strikingly, the different observed structures can be described by some of the different models proposed over the years for DNA organisation inside bacteriophage capsids: either spool-like structures with axial or concentric symmetries, or liquid crystalline structures characterised by a DNA homogeneous density. The relevance of these conformations for the understanding of DNA folding and unfolding upon ejection and packaging in vivo is discussed.
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Affiliation(s)
- Amélie Leforestier
- Laboratoire de Physqiue des Solides, CNRS, UMR 8502, Université Paris Sud, Orsay, France.
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25
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Tomita N, Mohammad MM, Niedzwiecki DJ, Ohta M, Movileanu L. Does the lipid environment impact the open-state conductance of an engineered β-barrel protein nanopore? Biochim Biophys Acta 2013; 1828:1057-65. [PMID: 23246446 PMCID: PMC3560310 DOI: 10.1016/j.bbamem.2012.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 11/16/2012] [Accepted: 12/04/2012] [Indexed: 12/11/2022]
Abstract
Using rational membrane protein design, we were recently able to obtain a β-barrel protein nanopore that was robust under an unusually broad range of experimental circumstances. This protein nanopore was based upon the native scaffold of the bacterial ferric hydroxamate uptake component A (FhuA) of Escherichia coli. In this work, we expanded the examinations of the open-state current of this engineered protein nanopore, also called FhuA ΔC/Δ4L, employing an array of lipid bilayer systems that contained charged and uncharged as well as conical and cylindrical lipids. Remarkably, systematical single-channel analysis of FhuA ΔC/Δ4L indicated that most of its biophysical features, such as the unitary conductance and the stability of the open-state current, were not altered under the conditions tested in this work. However, electrical recordings at high transmembrane potentials revealed that the presence of conical phospholipids within the bilayer catalyzes the first, stepwise current transition of the FhuA ΔC/Δ4L protein nanopore to a lower-conductance open state. This study reinforces the stability of the open-state current of the engineered FhuA ΔC/Δ4L protein nanopore under various experimental conditions, paving the way for further critical developments in biosensing and molecular biomedical diagnosis.
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Affiliation(s)
- Noriko Tomita
- Department of Physics, Syracuse University, Syracuse, New York 13244-1130, USA
- Institute of Fluid Science, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | | | | | - Makoto Ohta
- Institute of Fluid Science, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Liviu Movileanu
- Department of Physics, Syracuse University, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, Syracuse, New York 13244-4100, USA
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York 13244, USA
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26
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Abstract
Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo.
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Affiliation(s)
- Ian J Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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27
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Lemay SG, Panja D, Molineux IJ. Role of osmotic and hydrostatic pressures in bacteriophage genome ejection. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 87:022714. [PMID: 23496555 DOI: 10.1103/physreve.87.022714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 06/01/2023]
Abstract
A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly in vitro, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution or culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection in vivo; the mechanism is perfectly consistent with phage genome ejection in vitro.
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Affiliation(s)
- Serge G Lemay
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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28
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Hernando-Pérez M, Miranda R, Aznar M, Carrascosa JL, Schaap IAT, Reguera D, de Pablo PJ. Direct measurement of phage phi29 stiffness provides evidence of internal pressure. Small 2012; 8:2366-70. [PMID: 22648860 DOI: 10.1002/smll.201200664] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Indexed: 05/18/2023]
Abstract
Using AFM nanoindentation experiments, DNA-full phi29 phage capsids are shown to be stiffer than when empty. The presence of counterions softens full viruses in a reversible manner, indicating that pressure originates from the confined DNA. A finite element analysis of the experiments provides an estimate of the pressure of ∼40 atm inside the capsid, which is similar to theoretical predictions.
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29
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Abstract
Tailed dsDNA bacteriophage virions bind to susceptible cells with the tips of their tails and then deliver their DNA through the tail into the cells to initiate infection. This chapter discusses what is known about this process in the short-tailed phages (Podoviridae). Their short tails require that many of these virions adsorb to the outer layers of the cell and work their way down to the outer membrane surface before releasing their DNA. Interestingly, the receptor-binding protein of many short-tailed phages (and some with long tails) has an enzymatic activity that cleaves their polysaccharide receptors. Reversible adsorption and irreversible adsorption to primary and secondary receptors are discussed, including how sequence divergence in tail fiber and tailspike proteins leads to different host specificities. Upon reaching the outer membrane of Gram-negative cells, some podoviral tail machines release virion proteins into the cell that help the DNA efficiently traverse the outer layers of the cell and/or prepare the cell cytoplasm for phage genome arrival. Podoviruses utilize several rather different variations on this theme. The virion DNA is then released into the cell; the energetics of this process is discussed. Phages like T7 and N4 deliver their DNA relatively slowly, using enzymes to pull the genome into the cell. At least in part this mechanism ensures that genes in late-entering DNA are not expressed at early times. On the other hand, phages like P22 probably deliver their DNA more rapidly so that it can be circularized before the cascade of gene expression begins.
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Affiliation(s)
- Sherwood R Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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30
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Leforestier A, Siber A, Livolant F, Podgornik R. Protein-DNA interactions determine the shapes of DNA toroids condensed in virus capsids. Biophys J 2011; 100:2209-16. [PMID: 21539789 DOI: 10.1016/j.bpj.2011.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/10/2011] [Accepted: 03/14/2011] [Indexed: 11/29/2022] Open
Abstract
DNA toroids that form inside the bacteriophage capsid present different shapes according to whether they are formed by the addition of spermine or polyethylene glycol to the bathing solution. Spermine-DNA toroids present a convex, faceted section with no or minor distortions of the DNA interstrand spacing with respect to those observed in the bulk, whereas polyethylene glycol-induced toroids are flattened to the capsid inner surface and show a crescent-like, nonconvex shape. By modeling the energetics of the DNA toroid using a free-energy functional composed of energy contributions related to the elasticity of the wound DNA, exposed surface DNA energy, and adhesion between the DNA and the capsid, we established that the crescent shape of the toroidal DNA section comes from attractive interactions between DNA and the capsid. Such attractive interactions seem to be specific to the PEG condensation process and are not observed in the case of spermine-induced DNA condensation.
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Affiliation(s)
- Amélie Leforestier
- Laboratoire de Physique des Solides, Centre National de la Recherche Scientifique UMR 8502, Université Paris-Sud, Orsay, France
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31
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Abstract
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ∼500 mg ml(-1). This high density requires substantial compression of the normal B-form helix, leading to the conjecture that DNA in mature phage virions is under significant pressure, and that pressure is used to eject the DNA during infection. A large number of theoretical, computer simulation and in vitro experimental studies surrounding this conjecture have revealed many--though often isolated and/or contradictory--aspects of packaged DNA. This prompts us to present a unified view of the statistical physics and thermodynamics of DNA packaged in phage capsids. We argue that the DNA in a mature phage is in a (meta)stable state, wherein electrostatic self-repulsion is balanced by curvature stress due to confinement in the capsid. We show that in addition to the osmotic pressure associated with the packaged DNA and its counterions, there are four different pressures within the capsid: pressure on the DNA, hydrostatic pressure, the pressure experienced by the capsid and the pressure associated with the chemical potential of DNA ejection. Significantly, we analyze the mechanism of force transmission in the packaged DNA and demonstrate that the pressure on DNA is not important for ejection. We derive equations showing a strong hydrostatic pressure difference across the capsid shell. We propose that when a phage is triggered to eject by interaction with its receptor in vitro, the (thermodynamic) incentive of water molecules to enter the phage capsid flushes the DNA out of the capsid. In vivo, the difference between the osmotic pressures in the bacterial cell cytoplasm and the culture medium similarly results in a water flow that drags the DNA out of the capsid and into the bacterial cell.
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Affiliation(s)
- Debabrata Panja
- Institute for Theoretical Physics, Universiteit van Amsterdam, Science Park 904, Postbus 94485, 1090 GL Amsterdam, The Netherlands.
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32
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Wu D, Van Valen D, Hu Q, Phillips R. Ion-dependent dynamics of DNA ejections for bacteriophage lambda. Biophys J 2010; 99:1101-9. [PMID: 20712993 DOI: 10.1016/j.bpj.2010.06.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 10/19/2022] Open
Abstract
We studied the control parameters that govern the dynamics of in vitro DNA ejection in bacteriophage lambda. Previous work demonstrated that bacteriophage DNA is highly pressurized, and this pressure has been hypothesized to help drive DNA ejection. Ions influence this process by screening charges on DNA; however, a systematic variation of salt concentrations to explore these effects has not been undertaken. To study the nature of the forces driving DNA ejection, we performed in vitro measurements of DNA ejection in bulk and at the single-phage level. We present measurements on the dynamics of ejection and on the self-repulsion force driving ejection. We examine the role of ion concentration and identity in both measurements, and show that the charge of counterions is an important control parameter. These measurements show that the mobility of ejecting DNA is independent of ionic concentrations for a given amount of DNA in the capsid. We also present evidence that phage DNA forms loops during ejection, and confirm that this effect occurs using optical tweezers.
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Affiliation(s)
- David Wu
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California, USA
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33
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Chiaruttini N, de Frutos M, Augarde E, Boulanger P, Letellier L, Viasnoff V. Is the in vitro ejection of bacteriophage DNA quasistatic? A bulk to single virus study. Biophys J 2010; 99:447-55. [PMID: 20643062 DOI: 10.1016/j.bpj.2010.04.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/24/2010] [Accepted: 04/12/2010] [Indexed: 01/03/2023] Open
Abstract
Bacteriophage T5 DNA ejection is a complex process that occurs on several timescales in vitro. By using a combination of bulk and single phage measurements, we quantitatively study the three steps of the ejection-binding to the host receptor, channel-opening, and DNA release. Each step is separately addressed and its kinetics parameters evaluated. We reconstruct the bulk kinetics from the distribution of single phage events by following individual DNA molecules with unprecedented time resolution. We show that, at the single phage level, the ejection kinetics of the DNA happens by rapid transient bursts that are not correlated to any genome sequence defects. We speculate that these transient pauses are due to local phase transitions of the DNA inside the capsid. We predict that such pauses should be seen for other phages with similar DNA packing ratios.
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34
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Abstract
Biopolymers in vivo are typically subject to spatial restraints, either as a result of molecular crowding in the cellular medium or of direct spatial confinement. DNA in living organisms provides a prototypical example of a confined biopolymer. Confinement prompts a number of biophysics questions. For instance, how can the high level of packing be compatible with the necessity to access and process the genomic material? What mechanisms can be adopted in vivo to avoid the excessive geometrical and topological entanglement of dense phases of biopolymers? These and other fundamental questions have been addressed in recent years by both experimental and theoretical means. A review of the results, particularly of those obtained by numerical studies, is presented here. The review is mostly devoted to DNA packaging inside bacteriophages, which is the best studied example both experimentally and theoretically. Recent selected biophysical studies of the bacterial genome organization and of chromosome segregation in eukaryotes are also covered.
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Affiliation(s)
- D Marenduzzo
- SUPA, School of Physics, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK
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35
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Svensek D, Veble G, Podgornik R. Confined nematic polymers: order and packing in a nematic drop. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:011708. [PMID: 20866636 DOI: 10.1103/physreve.82.011708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Indexed: 05/29/2023]
Abstract
We investigate the tight packing of nematic polymers inside a confining hard sphere. We model the polymer via the continuum Frank elastic free energy augmented by a simple density dependent part as well as by taking proper care of the connectivity of the polymer chains when compared with simple nematics. The free energy ansatz is capable of describing an orientational ordering transition within the sample between an isotropic polymer solution and a polymer nematic phase. We solve the Euler-Lagrange equations numerically with the appropriate boundary conditions for the director and density field and investigate the orientation and density profile within a sphere. Two important parameters of the solution are the exact locations of the beginning and the end of the polymer chain. Pending on their spatial distribution and the actual size of the hard sphere enclosure we can get a plethora of various configurations of the chain exhibiting different defect geometry.
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Affiliation(s)
- Daniel Svensek
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1111 Ljubljana, Slovenia
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36
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Chang CY, Kemp P, Molineux IJ. Gp15 and gp16 cooperate in translocating bacteriophage T7 DNA into the infected cell. Virology 2009; 398:176-86. [PMID: 20036409 DOI: 10.1016/j.virol.2009.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Revised: 10/16/2009] [Accepted: 12/01/2009] [Indexed: 10/20/2022]
Abstract
Loss of up to four amino acids from the C terminus of the 1318 residue bacteriophage T7 gp16 allows plaque formation at normal efficiencies. Loss of five residues results in non-infective virions, and loss of twelve prevents assembly of stable particles. However, replacing the C-terminal seven with nineteen non-native residues allows assembly of non-infective virions. The latter adsorb and eject internal core proteins into the cell envelope but no phage DNA enters the cytoplasm. Extragenic suppressors of the defective gene 16 lie in gene 15; the mutant gp15 proteins not only re-establish infectivity, they fully restore the kinetics of genome internalization to those exhibited by wild-type phage. After ejection from the infecting particle, gp15 and gp16 thus function together in ratcheting the leading end of the T7 genome into the cytoplasm of the infected cell.
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Affiliation(s)
- Chung-Yu Chang
- Section of Molecular Genetics and Microbiology, and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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Marenduzzo D, Orlandini E, Stasiak A, Sumners de W, Tubiana L, Micheletti C. DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting. Proc Natl Acad Sci U S A 2009; 106:22269-74. [PMID: 20018693 DOI: 10.1073/pnas.0907524106] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids is both highly knotted and neatly structured. What is the physical basis of this organization? Here we show evidence from stochastic simulation techniques that suggests that a key element is the tendency of contacting DNA strands to order, as in cholesteric liquid crystals. This interaction favors their preferential juxtaposition at a small twist angle, thus promoting an approximately nematic (and apolar) local order. The ordering effect dramatically impacts the geometry and topology of DNA inside phages. Accounting for this local potential allows us to reproduce the main experimental data on DNA organization in phages, including the cryo-EM observations and detailed features of the spectrum of DNA knots formed inside viral capsids. The DNA knots we observe are strongly delocalized and, intriguingly, this is shown not to interfere with genome ejection out of the phage.
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Leforestier A, Livolant F. The bacteriophage genome undergoes a succession of intracapsid phase transitions upon DNA ejection. J Mol Biol 2010; 396:384-95. [PMID: 19944702 DOI: 10.1016/j.jmb.2009.11.047] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 11/24/2022]
Abstract
Double-stranded DNA bacteriophage genomes are densely packaged into capsids until the ejection is triggered upon interaction of the tail with the bacterial receptor. Using cryo-electron microscopy, we describe the organization of the genome in the full capsid of T5 and show how it undergoes a series of phase transitions upon progressive ejection when the encapsidated DNA length decreases. Monodomains of hexagonally crystallized DNA segments initially form a three-dimensional lattice of defects. The structure turns liquid crystalline (two-dimensional hexagonal and then cholesteric) and finally isotropic. These structures suggest a mechanism in which defects of the full capsid would initiate the ejection and introduce the necessary fluidity to relax the constrained mosaic crystal to let the genome start flowing out of the capsid.
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Duda RL, Ross PD, Cheng N, Firek BA, Hendrix RW, Conway JF, Steven AC. Structure and energetics of encapsidated DNA in bacteriophage HK97 studied by scanning calorimetry and cryo-electron microscopy. J Mol Biol 2009; 391:471-83. [PMID: 19540242 DOI: 10.1016/j.jmb.2009.06.035] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/12/2009] [Accepted: 06/15/2009] [Indexed: 11/22/2022]
Abstract
Encapsidation of duplex DNA by bacteriophages represents an extreme case of genome condensation, reaching near-crystalline concentrations of DNA. The HK97 system is well suited to study this phenomenon in view of the detailed knowledge of its capsid structure. To characterize the interactions involved, we combined calorimetry with cryo-electron microscopy and native gel electrophoresis. We found that, as in other phages, HK97 DNA is organized in coaxially wound nested shells. When DNA-filled capsids (heads) are scanned in buffer containing 1 mM Mg(2+), DNA melting and capsid denaturation both contribute to the complex thermal profile between 82 degrees C and 96 degrees C. In other conditions (absence of Mg(2+) and lower ionic strength), DNA melting shifts to lower temperatures and the two events are resolved. Heads release their DNA at temperatures well below the onset of DNA melting or capsid denaturation. We suggest that, on heating, the internal pressure increases, causing the DNA to exit-probably via the portal vertex-while the capsid, although largely intact, sustains local damage that leads to an earlier onset of thermal denaturation. Heads differ structurally from empty capsids in the curvature of their protein shell, a change attributable to outwards pressure exerted by the DNA. We propose that this transition is sensed by the portal that is embedded in the capsid wall, whereupon the structure of the portal and its interactions with terminase, the packaging enzyme, are altered, thus signaling that packaging is at or approaching completion.
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Abstract
The structure of DNA toroids made of individual DNA molecules of various lengths (3,000 to 55,000 bp) was studied, by using partially filled bacteriophage capsids in conjunction with cryoelectron microscopy. The tetravalent cation spermine was diffused through the capsid to condense the DNA under conditions that were chosen to produce a hexagonal packing. Our results demonstrate that the frustration arising between chirality and hexagonal packing leads to the formation of twist walls; the correlation between helices combined with their strong curvature impose variations of the DNA helical pitch.
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