Single-Molecule Structure and Topology of Kinetoplast DNA Networks

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 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 characterize 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. Finally, we estimate the 2D Young modulus of the network to be orders of magnitude smaller than that of other 2D materials. Our findings explain outstanding questions in the field and offer single-molecule insights into the properties of a unique topological material.
Original languageEnglish
Article number021010
Pages (from-to)1-13
Number of pages13
JournalPhysical Review X
Volume13
Issue number2
DOIs
Publication statusPublished - 19 Apr 2023

Keywords / Materials (for Non-textual outputs)

  • cond-mat.soft
  • physics.bio-ph

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