Effect of molecular architecture on ring polymer dynamics in semidilute linear polymer solutions

Zhou, Yuecheng; Hsiao, Kai Wen; Regan, Kathryn; Kong, Dejie; McKenna, Gregory B.; Robertson‐Anderson, Rae M.; Schroeder, Charles M.

doi:10.1038/s41467-019-09627-7

Cited by 58 publications

(83 citation statements)

References 49 publications

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“…Indeed, ring DNA tracers embedded in solutions of entangled linear DNA have been reported to have diffusion coefficients up to an order of magnitude lower than their linear DNA equivalents (34,46,50), a phenomenon which has been attributed to threading events. Simulations have also shown that threading leads to anomalous diffusion and swelling of DNA coils (47)(48)(49)54) similar to our results. Finally, large fluctuations in the relaxation dynamics of ring DNA embedded in semidilute linear DNA solutions have recently been observed and attributed to threading events (49).…”

Section: Discussionsupporting

confidence: 90%

“…Simulations have shown that these multiple diffusive modes, and the interconversion between them, leads to heterogeneous transport and conformations of rings (54)(55)(56). However, experimental evidence for these varied transport modes and conformations is sparse (49,50,57). Further, how these idealized models translate to complex biological systems, such as DNA diffusion through the cytoskeleton, remains unknown.…”

Section: Introductionmentioning

confidence: 99%

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Topology-dependent anomalous dynamics of ring and linear DNA are sensitive to cytoskeleton crosslinking

et al. 2019

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Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection, and gene therapy. Here we elucidate the transport properties and conformational dynamics of linear and ring DNA molecules diffusing through entangled and crosslinked composite networks of actin and microtubules. We couple single-molecule conformational tracking with differential dynamic microscopy to reveal that ring and linear DNA exhibit surprisingly distinct transport properties that are influenced differently by cytoskeleton crosslinking. Ring DNA coils are swollen and undergo heterogeneous and biphasic subdiffusion that is hindered by crosslinking. Conversely, crosslinking actually facilitates the single-mode subdiffusion that compacted linear chains exhibit. Our collective results demonstrate that transient threading by cytoskeleton filaments plays a key role in the dynamics of ring DNA, whereas the mobility of the cytoskeleton dictates transport of linear DNA.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Topology-dependent anomalous dynamics of ring and linear DNA are sensitive to cytoskeleton crosslinking

et al. 2019

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“…The ring topology is also important for stabilizing links. Unlike the recently observed transient hooking of rings by linear chains [11], ring-ring links cannot be destroyed by convective-constraint release because rings lack ends. Figure 5(a) plots the fraction of topologically linked rings φ top at the terminal strain for all W i of the N = 400 melt.…”

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confidence: 57%

“…Microscopic measures of ring entropy directly relate the nonlinear rise in stress to elongated supramolecular clusters. Unlike the transient "hooking" of rings by linear chains [11], these new ring-ring links are pulled tight and stabilized by the flow. Thus, supramolecules can persist even if W i is changed.…”

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confidence: 95%

Topological Linking Drives Anomalous Thickening of Ring Polymers in Weak Extensional Flows

O'Connor

Rubinstein

et al. 2020

Phys. Rev. Lett.

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Molecular dynamics simulations confirm recent extensional flow experiments showing ring polymer melts exhibit strong extension-rate thickening of the viscosity at Weissenberg numbers W i << 1. Thickening coincides with the extreme elongation of a minority population of rings that grows with W i. The large susceptibility of some rings to extend is due to a flow-driven formation of topological links that connect multiple rings into supramolecular chains. Links form spontaneously with a longer delay at lower W i and are pulled tight and stabilized by the flow. Once linked, these composite objects experience larger drag forces than individual rings, driving their strong elongation. The fraction of linked rings depends non-monotonically on W i, increasing to a maximum when W i ∼ 1 before rapidly decreasing when the strain rate approaches 1/τe. arXiv:1910.14666v1 [cond-mat.soft]

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“…Most experimental studies on entangled polymers to date have focused on linear chains, although there is growing interest in more complex topologies, such as circular chains [24][25][26]. Recently, our group performed single-molecule experiments to compress and induce self-entanglements in circular DNA with electric fields, with self-entanglements serving as a minimal system for studying chain entanglements [27].…”

Section: Introductionmentioning

confidence: 99%

Self-entanglement of a tumbled circular chain

Soh

Gengaro

Klotz

et al. 2019

Phys. Rev. Research

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The spontaneous knotting of linear chains has been well studied, but little attention has been given to the self-entanglement of chains with more complex topologies. In this work, we perform experiments with granular chains that undergo tumbling motion to investigate the self-entanglement of circular chains, which lack the chain ends essential for forming knots. We study the entanglement probability and types of self-entanglements formed on linear and circular chains, using the well-studied self-entanglements on a linear chain to frame our understanding of self-entanglements on a circular chain. We describe a characterization method that views a self-entangled circular chain as a link of two components and use it to characterize the self-entanglements on circular chains with known topological descriptors from knot theory. Our experimental results show that an increase in circular chain length leads to an increase in entanglement probability and entanglement complexity until a plateau is reached, similar to the trends observed with linear chains. By examining the formation pathway of several self-entanglements, we infer a general mechanism for the self-entanglement of circular chains.

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Effect of molecular architecture on ring polymer dynamics in semidilute linear polymer solutions

Cited by 58 publications

References 49 publications

Topology-dependent anomalous dynamics of ring and linear DNA are sensitive to cytoskeleton crosslinking

Topology-dependent anomalous dynamics of ring and linear DNA are sensitive to cytoskeleton crosslinking

Topological Linking Drives Anomalous Thickening of Ring Polymers in Weak Extensional Flows

Self-entanglement of a tumbled circular chain

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