Single-Molecule Structure and Topology of Kinetoplast DNA Networks

TL;DR

This study provides the first high-resolution analysis of kinetoplast DNA networks, revealing their heterogeneous topology, density distribution, and buckling behavior, which advances understanding of their self-assembly and potential synthetic applications.

Contribution

First single-molecule AFM and simulation study revealing detailed topology, density, and buckling properties of kinetoplast DNA networks.

Findings

Heterogeneous distribution of minicircle density and valence.

Identification of DNA hubs causing buckling transition.

Insights into the self-assembly and topology of kDNA networks.

Abstract

The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials. Here we report the first high-resolution, single-molecule study of kDNA network topology using AFM and steered molecular dynamics simulations. We map out the DNA density within the network and the distribution of linking number and valence of the minicircles. We also characterise the DNA hubs that surround the network and show that they cause a buckling transition akin to that of a 2D elastic thermal sheet in the bulk. Intriguingly, we observe a broad distribution of density and valence of the minicircles, indicating heterogeneous network structure and individualism of different kDNA structures. Our findings explain outstanding questions in the field and offer single-molecule insights into the properties of a unique topological material.