Holmes, E.P., Gamill, M.C. orcid.org/0009-0007-3250-5299, Provan, J.I. et al. (12 more authors) (2025) Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy. Nature Communications, 16 (1). 5482. ISSN 2041-1723
Abstract
DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Microscopy (AFM) with a new high-throughput automated pipeline, we can quantify the length, conformation, and topology of individual complex DNA molecules with sub-molecular resolution. Our pipeline uses deep-learning methods to trace the backbone of individual DNA molecules and identify crossing points, efficiently determining which segment passes over which. We use this pipeline to determine the structure of stalled replication intermediates from Xenopus egg extracts, including theta structures and late replication products, and the topology of plasmids, knots and catenanes from the E. coli Xer recombination system. We use coarse-grained simulations to quantify the effect of surface immobilisation on twist-writhe partitioning. Our pipeline opens avenues for understanding how fundamental biological processes are regulated by DNA topology.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © The Author(s) 2025. Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
Keywords: | Biophysics; Molecular biology; Physics |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Engineering (Sheffield) > School of Chemical, Materials and Biological Engineering The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > School of Medicine and Population Health The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Computer Science (Sheffield) The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Materials Science and Engineering (Sheffield) |
Funding Information: | Funder Grant number Engineering and Physical Sciences Research Council EP/P02470X/1 Engineering and Physical Sciences Research Council EP/P025285/1 Engineering and Physical Sciences Research Council EP/S019367/1 Engineering and Physical Sciences Research Council EP/R00661X/1 UK RESEARCH AND INNOVATION MR/W00738X/1 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 09 Jul 2025 11:51 |
Last Modified: | 09 Jul 2025 11:51 |
Status: | Published |
Publisher: | Springer Science and Business Media LLC |
Refereed: | Yes |
Identification Number: | 10.1038/s41467-025-60559-x |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:228836 |