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A model for the formation of folded DNA toroids within bacteriophage heads. (A) The first DNA to enter the phage head forms the initial loop of the toroid. (B) In the presence of a condensing environment, successive loops of DNA are deposited onto the initial loop, and the toroid develops as described by the constant radius of curvature model (Hud et al., 1995). The condensation of DNA, as it enters into the phage head, results in the gyration of the toroid such that the point of DNA deposition onto the toroid is always near the proximal vertex. (C) When the toroid has grown to a point at which it becomes constrained by the maximally expanded protein capsid, it begins to collapse upon itself. Head filling will continue
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Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have...
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... models for the structure and formation of DNA toroids, the calculated diameters of the putative T2 and T7 DNA toroid-loops, and the size of their respective heads suggest a possible origin of the folded toroid packaging motif. In this model, the first DNA to enter the phage head forms the initial loop of the toroid (Fig. 1 A) (Serwer, 1986). As head filling proceeds, the outside diameter of the toroid will eventually become equal to the inside diameter of the maximally expanded phage head (Fig. 1 B). Continued condensation of DNA onto the toroid is then expected to cause the toroid to assume a bifolded close-packed state (Fig. 1 C). Head filling will ...
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... respective heads suggest a possible origin of the folded toroid packaging motif. In this model, the first DNA to enter the phage head forms the initial loop of the toroid (Fig. 1 A) (Serwer, 1986). As head filling proceeds, the outside diameter of the toroid will eventually become equal to the inside diameter of the maximally expanded phage head (Fig. 1 B). Continued condensation of DNA onto the toroid is then expected to cause the toroid to assume a bifolded close-packed state (Fig. 1 C). Head filling will continue until the folded toroid is too large to rotate and take on additional DNA or until endonuclease cleavage of the entering DNA is triggered or both ...
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... forms the initial loop of the toroid (Fig. 1 A) (Serwer, 1986). As head filling proceeds, the outside diameter of the toroid will eventually become equal to the inside diameter of the maximally expanded phage head (Fig. 1 B). Continued condensation of DNA onto the toroid is then expected to cause the toroid to assume a bifolded close-packed state (Fig. 1 C). Head filling will continue until the folded toroid is too large to rotate and take on additional DNA or until endonuclease cleavage of the entering DNA is triggered or both ...
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Citations
... Models for the organization of DNA inside icosahedral bacteriophages started in the early 1970s, when Richards and colleagues proposed the ball of yarn model and the coaxial spooling model as two potential packaging geometries for DNA (72). These models were later followed by other models such as the coaxial and longitudinal spooling model (11)(12)(13)(14)73), the spiral-fold model (74), the liquid-crystal model (75,76), and the folded toroid model (76,77). Computer simulations have been key in understanding these models and have provided biophysical arguments favoring some models over others (Table 2). ...
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... The discrete transition of the DNA coil to a globule results in a very tight packaging of DNA similar to the DNA packaging in bacteriophage heads (90) and causes a complete inhibition of DNA transcriptional activity (91). In this regard, DNA binding with only 20% of HO compared to the saturation amount leads to a change in DNA compaction scenario that may allow for a more flexible regulation of DNA genetic activity in eukaryotic cells. ...
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... [Color figure can be viewed at wileyonlinelibrary.com] spacing in phages without need to invoke highly ordered spooled conformations. Other authors have previously noted [50] that a possible over-interpretation [1] of the X-ray scattering data may have led to the assumption of spooled structures. ...
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... The conformation of the DNA rope there is knotted, which can be most easily detected by removing the confinement once the minimal shape is found and letting it relax -a prototypical trefoil knot appears, with three-fold symmetry and maximally extended loops so that their curvature is minimal. The writhe of the relaxed shape drops by one, to ≈ 3. The knotted shapes cannot thus be unfolded to a toroid once the capsid is destroyed -this is a situation quite different from the one discussed by Hud 14 and applies also to the shape shown in Fig. 2l, representative for the knotted shapes in the large region of parameter space when f = 2 (see below). ...
... They thus interlink the previous studies (e.g. Hud's folded toroid 14 13,32 ), showing that different shapes of confined DNA condensates may be understood in a unifying model. ...
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... The inverse spool Ansatz need not enter the de- scription of DNA ordering a priori. A continuum description 102,103 based on a minimal 33 or a full Landau- de Gennes free energy model with the continuity of the DNA chain properly taken into account 34,35 leads to more complicated and less symmetric packaging config- urations, such as the folded toroid configuration as ob- served in experiments 104 and simulations 105 ; in fact the chain connectivity is particularly important in all the cases when no a priori Ansatz for the symmetry of the chain packing is introduced. In the coarse-grained, con- tinuum description, the connectivity is taken into account by a constraint on the chain flux vector, linking the den- sity variations and the director deformations, enforced by a penalty potential as described in 34 . ...
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... In viruses and bacteriophages, the DNA or RNA is surrounded by a protein capsid, sometimes further enveloped by a lipid membrane. Double-stranded DNA is stored inside the capsid in the form of a spool, which can have different types of coiling (Hud, 1995) leading to different types of liquid-crystalline packing (Earnshaw and Harrison, 1977;Hud and Downing, 2001;Knobler and Gelbart, 2009;Leforestier and Livolant, 2009). This packing can change from hexagonal to cholesteric to isotropic at different stages of the phage functioning (Leforestier and Livolant, 2010). ...
DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.
... DNA condensation has been shown to produce a variety of DNA structures (toroids, rod and spherical globules) [11][12][13][14][15][16][17][18][19] . Of all these, the toroidal structures have aroused great curiosity; the reason for such an interest being the most favorable morphology used by nature for high density DNA packaging in a cell [20][21][22][23] . Cobalt hexamine trichloride is an inorganic polyamine known to induce toroidal DNA condensation 24 . ...
The bacterial cell division protein, FtsZ, polymerizes to form a cytoicinetic Z-ring at the midcell, which engineers bacterial cell division. Herein, we have examined the effects of an inorganic polyamine, cobalt hexamine trichloride, on the assembly of FtsZ in vitro. Cobalt hexamine trichloride strongly enhances FtsZ assembly, suppresses its GTPase activity and stabilizes FtsZ polymers. However, CoCl(2) and MnCl(2) have no detectable effect on the assembly of FtsZ in vitro. Interestingly, FtsZ is found to assemble into toroidal structures in the presence of low concentrations of cobalt hexamine trichloride. The Z-ring in bacterial cells appears to be a toroidal-like structure, suggesting that the use of cobalt hexamine trichloride may help to understand the assembly of FtsZ into toroidal structure. The toroidal structures may also serve as templates to build toroidal resonators for electrical and thermal applications.
... During this last stage we also observed that the coaxial spooling motif becomes distorted. In a few analyzed trajectories ( Figure 3S, Supporting Material), the distortion was so pronounced that the global DNA conformation changed to a folded toroid (Hud, 1995;Petrov and Harvey, 2007). This is in agreement with the recent morphological analysis of the individual packaging conformations of T5 mutant (Leforestier and Livolant, 2010), in which locally ordered hexagonal structures organized into domains coexist with local defects, due to DNA bending or supertwisting. ...
Electrostatic interactions play an important role in both packaging of DNA inside bacteriophages and its release into bacterial cells. While at physiological conditions DNA strands repel each other, the presence of polyvalent cations such as spermine and spermidine in solutions leads to the formation of DNA condensates. In this study, we discuss packaging of DNA into bacteriophages P4 and Lambda under repulsive and attractive conditions using a coarse-grained model of DNA and capsids. Packaging under repulsive conditions leads to the appearance of the coaxial spooling conformations; DNA occupies all available space inside the capsid. Under the attractive potential both packed systems reveal toroidal conformations, leaving the central part of the capsids empty. We also present a detailed thermodynamic analysis of packaging and show that the forces required to pack the genomes in the presence of polyamines are significantly lower than those observed under repulsive conditions. The analysis reveals that in both the repulsive and attractive regimes the entropic penalty of DNA confinement has a significant non-negligible contribution into the total energy of packaging. Additionally we report the results of simulations of DNA condensation inside partially packed Lambda. We found that at low densities DNA behaves as free unconfined polymer and condenses into the toroidal structures; at higher densities rearrangement of the genome into toroids becomes hindered, and condensation results in the formation of non-equilibrium structures. In all cases packaging in a specific conformation occurs as a result of interplay between bending stresses experienced by the confined polymer and interactions between the strands.
