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Walker S, Arsuaga J, Hiltner L, Calderer MC, Vázquez M. Fine structure of viral dsDNA encapsidation. Phys Rev E 2020; 101:022703. [PMID: 32168691 DOI: 10.1103/physreve.101.022703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
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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Skuridin SG, Vereshchagin FV, Salyanov VI, Chulkov DP, Kompanets ON, Yevdokimov YM. Ordering of double-stranded DNA molecules in a cholesteric liquid-crystalline phase and in dispersion particles of this phase. Mol Biol 2016. [DOI: 10.1134/s0026893316040129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yevdokimov YM, Skuridin SG, Salyanov VI, Volkov VV, Dadinova LA, Kompanets ON, Kats EI. About the spatial organization of double-stranded DNA molecules in the cholesteric liquid-crystalline phase and dispersion particles of this phase. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915050036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Michieletto D, Marenduzzo D, Orlandini E. Is the kinetoplast DNA a percolating network of linked rings at its critical point? Phys Biol 2015; 12:036001. [PMID: 25970016 DOI: 10.1088/1478-3975/12/3/036001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work we present a computational study of the kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is around three, as found experimentally for the kinetoplast DNA (kDNA). Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the kDNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.
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Affiliation(s)
- Davide Michieletto
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK
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Arsuaga J, Diao Y, Vazquez M. Mathematical Methods in Dna Topology: Applications to Chromosome Organization and Site-Specific Recombination. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4419-0670-0_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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6
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Livolant F, Leforestier A. DNA Mesophases: A Structural Analysis in Polarizing and Electron Microscopy. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/10587259208038510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Françoise Livolant
- a Centre de Biologie Cellulaire (CNRS) , 67, rue Maurice Günsbourg, 94200 , Ivry-sur-Seine , (FRANCE)
| | - Amélie Leforestier
- a Centre de Biologie Cellulaire (CNRS) , 67, rue Maurice Günsbourg, 94200 , Ivry-sur-Seine , (FRANCE)
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Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners DW, Roca J. DNA knots reveal a chiral organization of DNA in phage capsids. Proc Natl Acad Sci U S A 2005; 102:9165-9. [PMID: 15958528 PMCID: PMC1166588 DOI: 10.1073/pnas.0409323102] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. We present a different approach to the problems of randomness and chirality of the packed DNA. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid. Here, we show that these knots provide information about the global arrangement of the DNA inside the capsid. First, we analyze the distribution of the viral DNA knots by high-resolution gel electrophoresis. Next, we perform Monte Carlo computer simulations of random knotting for freely jointed polygons confined to spherical volumes. Comparison of the knot distributions obtained by both techniques produces a topological proof of nonrandom packaging of the viral DNA. Moreover, our simulations show that the scarcity of the achiral knot 4(1) and the predominance of the torus knot 5(1) over the twist knot 5(2) observed in the viral distribution of DNA knots cannot be obtained by confinement alone but must include writhe bias in the conformation sampling. These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed.
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Affiliation(s)
- Javier Arsuaga
- Departments of Mathematics, Molecular and Cell Biology, and Physics, University of California, Berkeley, CA 94720, USA.
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8
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Abstract
DNA packaging in bacteriophage P4 has been examined using a molecular mechanics model with a reduced representation containing one pseudoatom per turn of the double helix. The model is a discretized version of an elastic continuum model. The DNA is inserted piecewise into the model capsid, with the structure being reoptimized after each piece is inserted. Various optimization protocols were investigated, and it was found that molecular dynamics at a very low temperature (0.3 K) produces the optimal packaged structure. This structure is a concentric spool, rather than the coaxial spool that has been commonly accepted for so many years. This geometry, which was originally suggested by Hall and Schellman in 1982 (Biopolymers Vol. 21, pp. 2011-2031), produces a lower overall elastic energy than coaxial spooling.
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Affiliation(s)
- Jaclyn C LaMarque
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Singh PB, Huskisson NS. Chromatin complexes as aperiodic microcrystalline arrays that regulate genome organisation and expression. DEVELOPMENTAL GENETICS 2000; 22:85-99. [PMID: 9499583 DOI: 10.1002/(sici)1520-6408(1998)22:1<85::aid-dvg9>3.0.co;2-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The current understanding of chromatin-mediated repression in Metazoa stems largely from work on two systems in Drosophila: heterochromatin-induced position-effect variegation and repression of the homeotic genes by the Polycomb-group of genes. A common feature of these two systems is the cooperative assembly of multimeric complexes which can epigenetically silence gene activity. Moreover, both older and more recent work has suggested that these complexes can themselves associate to give rise to larger complexes: The specificity of the association is likely to be determined by complementarity of the structural components of the complexes. Here, we aim to accommodate these, and other, features of chromatin-mediated repression in a single hypothesis, namely the crystallisation hypothesis. This hypothesis views the nucleus as being an environment that favours the formation of chromatin complexes which behave as aperiodic microcrystalline arrays constructed through the cooperative assembly of different types of lattice unit. The lattice units possess regions of structural complementarity that allow interactions between complexes. Aperiodicity confers specificity on the complexes and is a key feature of the model which, we suggest, provides a gene with a "chromosomal address." The chromosomal address allows the side-by-side alignment of homologous chromosomal regions, a properly that may be important in a variety of biologically relevant situations. Aperiodicity is also a feature of the hypothesis that is directly testable.
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Affiliation(s)
- P B Singh
- Department of Development and Genetics, Babraham Institute, Cambridge, England
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Kellenberger E, Arnold-Schulz-Gahmen B. Chromatins of low-protein content: Special features of their compaction and condensation. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05727.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Spurio R, Dürrenberger M, Falconi M, La Teana A, Pon CL, Gualerzi CO. Lethal overproduction of the Escherichia coli nucleoid protein H-NS: ultramicroscopic and molecular autopsy. MOLECULAR & GENERAL GENETICS : MGG 1992; 231:201-11. [PMID: 1310520 DOI: 10.1007/bf00279792] [Citation(s) in RCA: 124] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Escherichia coli hns gene, which encodes the nucleoid protein H-NS, was deprived of its natural promoter and placed under the control of the inducible lambda PL promoter. An hns mutant yielding a protein (H-NS delta 12) with a deletion of four amino acids (Gly112-Arg-Thr-Pro115) was also obtained. Overproduction of wild-type (wt) H-NS, but not of H-NS delta 12, resulted in a drastic loss of cell viability. The molecular events and the morphological alterations eventually leading to cell death were investigated. A strong and nearly immediate inhibition of both RNA and protein synthesis were among the main effects of overproduction of wt H-NS, while synthesis of DNA and cell wall material was inhibited to a lesser extent and at a later time. Upon cryofixation of the cells, part of the overproduced protein was found in inclusion bodies, while the rest was localized by immunoelectron microscopy to the nucleoids. The nucleoids appeared condensed in cells expressing both forms of H-NS, but the morphological alterations were particularly dramatic in those overproducing wt H-NS; their nucleoids appeared very dense, compact and almost perfectly spherical. These results provide direct evidence for involvement of H-NS in control of the organization and compaction of the bacterial nucleoid in vivo and suggest that it may function, either directly or indirectly, as transcriptional repressor and translational inhibitor.
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Affiliation(s)
- R Spurio
- Dept. of Biology, University of Camerino, Italy
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Rill RL, Livolant F, Aldrich HC, Davidson MW. Electron microscopy of liquid crystalline DNA: direct evidence for cholesteric-like organization of DNA in dinoflagellate chromosomes. Chromosoma 1989; 98:280-6. [PMID: 2612287 DOI: 10.1007/bf00327314] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Freeze-fracture-etch replicas of concentrated DNA solutions which appeared, by polarized light microscopy, to be in a cholesteric-like liquid crystalline state were examined by high resolution transmission electron microscopy (TEM). Individual DNA molecules were resolvable, and the microscopic morphologies observed for such replicas confirmed the cholesteric organization of DNA molecules in this liquid crystalline state. Furthermore, replica morphologies were strikingly similar to TEM images of dinoflagellate chromosomes in both thin section and freeze-etch replicas, providing strong support for the cholesteric DNA packing model proposed for the organization of DNA in these chromosomes by Bouligand and Livolant.
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Affiliation(s)
- R L Rill
- Department of Chemistry, Florida State University, Tallahassee 32306
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