Single-Molecule Structure and Topology of Kinetoplast DNA Networks

He, Pinyao; Katan, Allard J.; Tubiana, Luca; Dekker, Cees; Michieletto, Davide

doi:10.1103/physrevx.13.021010

Cited by 9 publications

(9 citation statements)

References 55 publications

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“…4e). We note that even for the control case, the average height is smaller than the one expected for several (possibly tens) of DNA strands overlapping each other at the hub [53] – each around 2 nm thick in the hydrated DNA structure – due to (i) imaging dehydrated DNA and (ii) the compression of the DNA by the AFM tip [36]. Nevertheless, the qualitative and quantitative disruption in the EcoRI treated samples is clear and points to the fact that hubs are mostly made by essential crossings between minicircles rather than maxicircles.…”

Section: Resultsmentioning

confidence: 99%

“…We then used ImageJ to manually compute the area of each kDNA, distance between hubs and pore size using morphological segmentation via MorphoLibJ [60] as previously described (Ref. [36]). The heights of the hubs in Figure 4e were quantified using Gwyddion software.…”

Section: Methodsmentioning

confidence: 99%

“…Simulations of polymer rings with tunable linking degree suggest that a mean linking degree, or valence, of 3 – similar to that found in kDNA structures [34–36] – may reflect the fact that these networks are poised at the percolation point, where a random graph starts displaying a system-spanning component [30, 31, 37]. In fact, a random graph with valence 3 is optimally connected, i.e.…”

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confidence: 91%

“…it displays percolation but without redundant links between circles, thus ensuring integrity of the structure whilst optimising the rate of replication, which in C. fasciculata occurs through decatenation of minicircles from the network [4, 31]. At the same time, whilst the material and elastic properties of kDNA networks are still largely unknown, recent work has estimated the bending stiffness to be in the range of κ ≃ 10 − 21 − 10 − 19 J [21, 36] and in-plane Young modulus Y ≃ 0.1 pN/ μ m [36]. Since the elasticity of an Olympic network correlates with the mean linking number [25, 37, 38], we expect that the kDNA elasticity will strongly depend on its underlying topology.…”

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confidence: 99%

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Single-Molecule Morphology of Topologically Digested Olympic Networks

Ramakrishnan,

Chen,

Fosado

et al. 2023

Preprint

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The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure are fascinating open questions in biology that can also inform us how to realise synthetic Olympic networks in vitro. To obtain a deeper understanding of the structure and assembly of kDNA networks, we sequenced the Crithidia fasciculata kDNA genome and performed high-resolution Atomic Force Microscopy (AFM) and analysis of kDNA networks that had been partially digested by selected restriction enzymes. We discovered that these topological perturbations lead to networks with significantly different geometrical features and morphologies with respect to the unperturbed kDNA, and that these changes are strongly dependent on the class of DNA circles targeted by the restriction enzymes. Specifically, cleaving maxicircles leads to a dramatic reduction in network size once adsorbed onto the surface, whilst cleaving both maxicircles and a minor class of minicircles yields non-circular and deformed structures. We argue that our results are a consequence of a precise positioning of the maxicircles at the boundary of the network, and we discuss our findings in the context of kDNA biogenesis, design of artificial Olympic networks and detection of in vivo perturbations.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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confidence: 91%

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confidence: 99%

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Single-Molecule Morphology of Topologically Digested Olympic Networks

Ramakrishnan,

Chen,

Fosado

et al. 2023

Preprint

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“…The key observable for studying the wetting behavior is the contact angle θ given by Young's equation 114 (44) where γ sv , γ sl , and γ lv are the interfacial tensions between the solid and the "vapor" phase, between the solid and the "liquid" phase, and between "liquid" and "vapor" phases. In order to calculate the two solid−fluid tensions, one sets the boundary condition far away from the wall to the corresponding bulk densities and computes the inhomogeneous density profiles ρ i (z) from DFT as described above.…”

Section: Correlations and Response Functionsmentioning

confidence: 99%

Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior

Staňo,

Likos,

Egorov

2023

Macromolecules

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We derive and parameterize effective interaction potentials between a multitude of different types of ring polymers and linear chains, varying the bending rigidity and solvent quality for the former species. We further develop and apply a density functional treatment for mixtures of both disconnected (chain–ring) and connected (chain-polycatenane) mixtures of the same, drawing coexistence binodals and exploring the ensuing response functions as well as the interface and wetting behavior of the mixtures. We show that worsening of the solvent quality for the rings brings about a stronger propensity for macroscopic phase separation in the linear-polycatenane mixtures, which is predominantly of the demixing type between phases of similar overall particle density. We formulate a simple criterion based on the effective interactions, allowing us to determine whether any specific linear-ring mixture will undergo a demixing phase separation.

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Self-Organized States from Solutions of Active Ring Polymers in Bulk and under Confinement

Miranda,

Locatelli,

Valeriani

2023

J. Chem. Theory Comput.

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In the present work, we study, by means of numerical simulations, the structural and dynamical behavior of a suspension of active ring polymers in bulk and under lateral confinement. At high activity, when changing the distance between the confining planes and the polymers' density, we identify the emergence of a self-organized dynamical state, characterized by the coexistence of slowly diffusing clusters of rotating disks and faster rings moving in between them. We further assess that selforganization is robust in a range of polymer sizes, and we identify a critical value of the activity, necessary to trigger cluster formation. This system has distinctive features resembling at the same time polymers, liquid crystals, and active systems, where the interplay between activity, topology, and confinement leads to a spontaneous segregation in an initially one-component solution.

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Single-Molecule Structure and Topology of Kinetoplast DNA Networks

Cited by 9 publications

References 55 publications

Single-Molecule Morphology of Topologically Digested Olympic Networks

Single-Molecule Morphology of Topologically Digested Olympic Networks

Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior

Self-Organized States from Solutions of Active Ring Polymers in Bulk and under Confinement

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