Tuning the topology of a two-dimensional catenated DNA network

Yadav, Indresh; Sulaiman, Dana Al; Doyle, Patrick S.

doi:10.1103/physrevresearch.5.013141

Cited by 3 publications

(10 citation statements)

References 40 publications

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“…3). Intriguingly, this size change was not observed in confocal microscopy in the bulk [22]. On the contrary, we did not observe any significant shrinking in EcoRI treated samples.…”

Section: Discussioncontrasting

confidence: 79%

“…We note that similar kDNA structures have been recently prepared and analysed via confocal microscopy in a bulk solution by Yadav et al [22]. They reported that the digested kDNAs did not appear to assume a different size or shape, yet they displayed a different dynamical relaxation timescale, which they measured by computing correlations of the anisotropy vector.…”

Section: Discussionmentioning

confidence: 70%

“…Fig. 2c then suggests that cleaving both maxicircles and the minor class of minicircles (in total about 15% of the kDNA mass) has a compound effect in the network morphology likely due to a decrease in network connectivity [22, 34].…”

Section: Resultsmentioning

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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“…3). Intriguingly, this size change was not observed in confocal microscopy in the bulk [22]. On the contrary, we did not observe any significant shrinking in EcoRI treated samples.…”

Section: Discussioncontrasting

confidence: 79%

Section: Discussionmentioning

confidence: 70%

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Single-Molecule Morphology of Topologically Digested Olympic Networks

Ramakrishnan,

Chen,

Fosado

et al. 2023

Preprint

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“…6,7 Typically it is their planar rather than their catenated nature that serves in this capacity, and it is unclear how their catenated molecular topology affects their mechanical properties, although more recent studies have begun to investigate this relation. 8,9 Most of what is known about kinetoplast topology comes from experiments on Crithidia fasciculata (an insect parasite) kinetoplasts, in which minicircles were linearized with restriction enzymes and gel electrophoresis was used to determine the relative proportion of linear, circular, doubly-catenanted, and triply-catenated molecules. 10 It was concluded that each minicircle was connected to three others on average and that the regular lattice most consistent with the data was the honeycomb.…”

Section: Introductionmentioning

confidence: 99%

“…While the main reason for their study is to better understand and disrupt the parasite life cycle, in recent years they have seen use as a model system for two‐dimensional polymer physics 6,7 . Typically it is their planar rather than their catenated nature that serves in this capacity, and it is unclear how their catenated molecular topology affects their mechanical properties, although more recent studies have begun to investigate this relation 8,9 …”

Section: Introductionmentioning

confidence: 99%

The effect of the kinetoplast edge loop on network percolation

Ragotskie,

Morrison,

Stackhouse

et al. 2023

Journal of Polymer Science

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We use graph theory simulations and single molecule experiments to investigate percolation properties of kinetoplasts, the topologically linked mitochondrial DNA from trypanosome parasites. The edges of some kinetoplast networks contain a fiber of redundantly catenated DNA loops, but previous investigations of kinetoplast topology did not take this into account. Our graph simulations track the size of connected components in lattices as nodes are removed, analogous to the removal of minicircles from kinetoplasts. We find that when the edge loop is taken into account, the largest component after the network de‐percolates is a remnant of the edge loop, before it undergoes a second percolation transition and breaks apart. This implies that stochastically removing minicircles from kinetoplast DNA would isolate large polycatenanes, which is observed in experiments that use photonicking to stochastically destroy kinetoplasts from Crithidia fasciculata. Our results imply kinetoplasts may be used as a source of linear polycatenanes for future experiments.

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