Is the kinetoplast DNA a percolating network of linked rings at its critical point?

  title={Is the kinetoplast DNA a percolating network of linked rings at its critical point?},
  author={Davide Michieletto and Davide Marenduzzo and Enzo Orlandini},
  journal={Physical biology},
  volume={12 3},
In this work we present a computational study of the kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is… 
Topology Regulation during Replication of the Kinetoplast DNA
The model describes a self-regulating system capable of full replication that reproduces several previous experimental studies of Kinetoplast DNA and finds the topological state to be that of a marginally linked network structure in which the fraction of mini- circles linked to the largest connected component approaches unity as R=A decreases.
Estimating properties of kinetoplast DNA by fragmentation reactions
The mitochondrial DNA of trypanosomes, called kinetoplast DNA (kDNA) contains thousands of minicircles that are topologically linked into a single structure that resembles a medieval chainmail. This
Equilibrium structure and deformation response of 2D kinetoplast sheets
The equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail, are studied, finding that kinetoplasts adopt a hemispherical configuration with strong intrinsic curvature.
Synergy of Topoisomerase and Structural-Maintenance-of-Chromosomes Proteins Creates a Universal Pathway to Simplify Genome Topology
Computational evidence is reported that Structural Maintenance of Chromosomes (SMC) proteins – such as cohesins and condensins – can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements, arguing that this synergy may be at work across organisms and throughout the cell cycle.
Phase Transition of Catenated DNA Networks in Poly(ethylene glycol) Solutions
Conformational phase transitions of macromolecules are an important class of problems in fundamental polymer physics. While the conformational phase transitions of linear DNA have been extensively
Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology
Computational evidence is reported that structural-maintenance-of-chromosomes proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements.
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
It is shown that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc, which implies that the timescale of topological Relaxation is virtually independent of the substrate length.
Linking of Ring Polymers in Slit-Like Confinement
Stochastic simulations are used to study the linking properties of solutions of circular polymers in slit confinement. Specifically, we consider dispersions of semiflexible rings at various densities
A Bio-Physical Model for the Kinetoplast DNA
The Kinetoplast DNA (or KDNA) (Simpson 1967) is one of the most complex and singular forms of DNA in nature. It is uniquely found in the mitochondrion of a group of unicellular eukaryotic organisms
On the tree-like structure of rings in dense solutions.
This work shows how to characterise local tree-like structures in rings by measuring the local writhing of the rings' segments and by identifying the patterns of intra-chain contacts, and shows that one can identify hierarchically looped structures whose degree increases linearly with the size of a ring.


The topology of the kinetoplast DNA network
It is concluded that each minicircle is linked on average to three other minicircles of the Crithidia fasciculata network, which has implications for the assembly, structure, and function of kDNA networks.
Changes in network topology during the replication of kinetoplast DNA.
Measurements of minicircle valence and density, and the network's surface area, revealed striking changes in network topology during replication ofinetoplast DNA of Crithidia fasciculata.
Isolation of proteins associated with kinetoplast DNA networks in vivo.
  • C. Xu, D. Ray
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1993
It is suggested that basic proteins may play a role in the condensation of kDNA in the kinetoplast and that these proteins are imported into the kinEToplast by a mechanism involving a cleavable presequence.
The effects of density on the topological structure of the mitochondrial DNA from trypanosomes
A simple mathematical model in which a collection of randomly oriented minicircles are spread over a rectangular grid is introduced and predicts the existence of a percolation density and that the distribution of minicircle valences is more heterogeneous than initially thought.
The attachment of minicircles to kinetoplast DNA networks during replication
Using electron microscopy autoradiography, it is found that newly synthesized 3H-labeled minicircles, after short labeling periods, are concentrated in two peripheral zones on opposite sides of the network.
The structure and replication of kinetoplast DNA.
The mitochondrial DNA of trypanosomatid protozoa, termed kinetoplast DNA (kDNA), is unique in its structure, function, and mode of replication. kDNA is a massive network, composed of thousands of
Organized packaging of kinetoplast DNA networks
This work has developed two assays to examine the structure of kDNA networks compacted in vitro with spermidine and suggests that minicircles are arranged into a regular structure with an exposeddomain which is DNAase I- and restriction-sensitive and a protected domain which is resistant to restriction endonucleases and DNAase II.
Network news: the replication of kinetoplast DNA.
Recent studies on kDNA structure and replication are discussed, emphasizing recent developments on replication enzymes, how the timing of kDNA synthesis is controlled during the cell cycle, and the machinery for segregating daughter networks after replication.
The Crithidia fasciculata KAP1 gene encodes a highly basic protein associated with kinetoplast DNA.
The Crithidia fasciculata KAP1 gene encodes a small basic protein (p21) associated with kinetoplast DNA. The p21 protein has a nine amino acid cleavable presequence closely related to those of
Fellowship of the rings: the replication of kinetoplast DNA.
The replication of the kDNA network is more complex than previously thought, and the discovery of new proteins involved in this process is currently the best approach for illuminating the replication mechanism.