Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

Kang, Hongsuk; Yoon, Young-Gui; Thirumalai, D.; Hyeon, Changbong

doi:10.1103/physrevlett.115.198102

Cited by 78 publications

(99 citation statements)

References 43 publications

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“…These findings are a strong signature that rings display longlasting intercoil correlations that are present even after they have traveled beyond their own size, in agreement with previous numerical and experimental findings (5,8). In addition, this is clear evidence that the exchange dynamics of the rings becomes slower, more glass-like (16,36), as the polymerization M increases. The increasingly stretched decay of φ nc also implies that the relaxation dynamics of the chains becomes more heterogeneous, i.e., some parts of the chains are much slower to separate from one another than other parts.…”

Section: Contiguity Is Persistent For Longer Chainssupporting

confidence: 90%

A topologically driven glass in ring polymers

Michieletto

Turner

2016

Proc. Natl. Acad. Sci. U.S.A.

108

185

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The static and dynamic properties of ring polymers in concentrated solutions remains one of the last deep unsolved questions in polymer physics. At the same time, the nature of the glass transition in polymeric systems is also not well understood. In this work, we study a novel glass transition in systems made of circular polymers by exploiting the topological constraints that are conjectured to populate concentrated solutions of rings. We show that such rings strongly interpenetrate through one another, generating an extensive network of topological interactions that dramatically affects their dynamics. We show that a kinetically arrested state can be induced by randomly pinning a small fraction of the rings. This occurs well above the classical glass transition temperature at which microscopic mobility is lost. Our work both demonstrates the existence of long-lived inter-ring penetrations and realizes a novel, topologically induced, glass transition.glass transition | ring polymers | topology | topological glass | molecular dynamics T he physics of ring polymers remains one of the last big mysteries in polymer physics (1). Concentrated systems of ring polymers have been observed, in both simulations and experiments, to display unique features that are not easily reconciled with the standard reptation theory of linear polymers (2-6). The main reason for this is that ring polymers do not possess free terminal segments, or ends, essential for end-directed curvilinear diffusion. In contrast, ring polymers possess a closed contour, which leads to markedly different relaxation and diffusion mechanisms. Recently, there has been much improvement in the production of purified systems of rings (6-8), with the consequent result that more and more experimental puzzling evidence requires a deeper understanding of their motion in concentrated solutions and melts from a theoretical point of view.Recently, it has been conjectured that ring polymers assume crumpled, segregated conformations in concentrated solution or the melt (5). On the other hand, numerical and experimental findings (5, 6) suggest that rings exhibit strong intercoil correlations, which have proved difficult to address in simplified theoretical models (9-12). Because of this, there have been many recent attempts to rigorously characterize these interchains' interactions (13-16), although a precise definition and unambiguous identification of these "threadings" in concentrated solutions of rings remains elusive. The primary reason for this is that the rings are assumed to remain strictly topologically unlinked from one another throughout if synthesized in this state.In the case of concentrated solutions of rings embedded in a gel, a method to identify these interpenetrating threadings has recently been proposed (13). Here it was shown that the number of threadings scales extensively in the polymer length (or mass) and can therefore be numerous for long rings, creating a hierarchical sequence of constraints that can span the entire system. It has also been con...

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Section: Contiguity Is Persistent For Longer Chainssupporting

confidence: 90%

A topologically driven glass in ring polymers

Michieletto

Turner

2016

Proc. Natl. Acad. Sci. U.S.A.

108

185

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“…S1). Together with the exponent of stretch-exponential β less than 1, which is a quintessential marker of glassy dynamics [56], the non-monotonic dependence of τ on q should be noted (Fig. 8c).…”

Section: Brownian Dynamics Simulationsmentioning

confidence: 95%

Heterogeneous Morphology and Dynamics of Polyelectrolyte Brush Condensates in Trivalent Counterion Solution

2017

Self Cite

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Recent experiments have shown that trivalent ion, spermidine 3+ , can provoke lateral microphase segregation in DNA brushes. Using molecular simulations and simple theoretical arguments, we explore the effects of trivalent counterions on polyelectrolyte brushes. At a proper range of grafting density, polymer size, and ion concentration, the brush polymers collapse heterogeneously into octopus-like surface micelles. Remarkably, the heterogeneity in brush morphology is maximized and the relaxation dynamics of chain and condensed ion are the slowest at the 1:3 stoichiometric concentration of trivalent ions to polyelectrolyte charge. A further increase of trivalent ion concentration conducive to a charge inversion elicits modest reswelling and homogenizes the morphology of brush condensate. Our study provides a new insight into the origin of the diversity in DNA organization in cell nuclei as well as the ion-dependent morphological variation in polyelectrolyte brush layer of biological membranes.Polyelectrolyte brushes are ubiquitous in biological systems. As the main component of outer membrane in Gram-negative bacteria, lipopolysaccharides, consisting of charged O-polysaccharides side chains, form a brush layer and mediate the interaction of bacteria with their environment [1]. For vertebrates, negatively charged polysaccharide hyaluronic acids play a vital role in the organization of pericellular matrix [2,3]. Double-stranded DNA brushes on a biochip [4] at a cell-like density (∼ 10 4 kb/µm 3 ) have been developed as a platform to study cell-free gene expression [5]. Due to the negative charges along the backbone, this synthetic system behaves like a well-defined strong polyelectrolyte brush [5], the height of which can be varied by modulating the ionic strength of monovalent salt (NaCl) solution and the grafting density [6]. Recently, it has been reported that trivalent counterions, spermidine 3+ (Spd 3+ ), can induce a collapse transition of DNA brush into fractal-like dendritic macroscopic domains [7]. The heterogeneous morphology of DNA condensate points to polyamine-mediated regulation of local DNA configuration and gene expression [8,9], underscoring the importance of understanding the effects of multivalent counterions on polyelectrolyte brush [10,11]. Compared with uncharged polymer brushes in good or poor solvent, the electrostatic interaction and osmotic pressure, which are readily controlled by the salt concentration and pH, yield additional flexibilities in manipulating polyelectrolyte brushes, and thus holding promise for its wide applications [12,13].Conventional theoretical approaches, successful in explaining the behaviors of polyelectrolytes in monovalent salt solutions [11,14,15], are of limited use, particularly, when multivalent counterions are at work. For example, the solution to the mean-field PoissonBoltzmann theory [16] fails to account for phenomena such as ion condensation, charge over-compensation, and collapse of like-charged polymers [17][18][19][20]. A prediction from a nonlocal den...

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“…Stretching is significant for a pore with a critical diameter <3 mm, but of course such a large pore is also constricting many nearby chromosomes within a crowded nucleoplasm. Potentially, chromatin compaction by small constrictions increases the volume fraction to a critical value, thus decreasing the accessible space within the nucleus (20) and, in turn, increasing the chromatin stretching. Importantly, the integrity of the stretched and cleaved locus is always maintained, which strongly indicates that constrictions are unlikely to provide sufficient stress to mechanically break the covalent bonds in both strands of DNA.…”

mentioning

confidence: 99%

As a Nucleus Enters a Small Pore, Chromatin Stretches and Maintains Integrity, Even with DNA Breaks

Irianto

Xia

Pfeifer

et al. 2017

Biophysical Journal

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As a cell pushes or pulls its nucleus through a small constriction, the chromatin must distort and somehow maintain genomic stability despite ever-present double-strand breaks in the DNA. Here we visualize within a living cell the pore-size dependent deformation of a specific locus engineered into chromosome-1 and cleaved. An mCherrytagged nuclease targets the submicron locus, causing DNA cleavage and recruiting repair factors such as GFP-53BP1 to a large region around the locus. Aspiration of a cell and its nucleus into a micropipette shows that chromatin aligns and stretches parallel to the pore. Extension is largest in small pores, increasing >10-fold but remaining 30-fold shorter than the DNA contour length in the locus. Brochard and de Gennes' blob model for tube geometry fits the data, with a simple modification for chromatin crowding. Continuity of the highly extended, cleaved chromatin is also maintained, consistent with folding and cross bridging of the DNA. Surprisingly, extensional integrity is unaffected by an inhibitor of the DNA repair scaffold.

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Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

Cited by 78 publications

References 43 publications

A topologically driven glass in ring polymers

A topologically driven glass in ring polymers

Heterogeneous Morphology and Dynamics of Polyelectrolyte Brush Condensates in Trivalent Counterion Solution

As a Nucleus Enters a Small Pore, Chromatin Stretches and Maintains Integrity, Even with DNA Breaks

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