Is the Kinetoplast DNA a Percolating Network of Linked Rings at its Critical Point?

TL;DR

This study models Kinetoplast DNA as a network of linked loops near a percolation transition, explaining experimental observations and suggesting biological significance of its critical state.

Contribution

The paper introduces a computational model of Kinetoplast DNA as linked loops near percolation, aligning with experimental data with minimal assumptions.

Findings

Percolation transition occurs at DNA densities matching experimental conditions.

Mean valency of linked loops is approximately 3, consistent with experimental data.

Distribution of oligomers after enzymatic digestion matches experimental gel electrophoresis results.

Abstract

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 around 3 as found experimentally for the Kinetoplast DNA. Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the Kinetoplast DNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.