DNA is often depicted as a tidy double helix, but inside cells, it bends, loops, and knots. These tangles are regulated by enzymes, and when that regulation fails, the disruptions can contribute to conditions such as cancer and neurodegenerative disease. Studying these structural changes, known as DNA topology, has traditionally required time-consuming manual analysis.
A team led by the University of Sheffield has now automated this process, combining atomic force microscopy (AFM) with advanced image analysis and AI. AFM uses a nanoscale probe to trace physical features, making it well-suited to capture DNA’s three-dimensional arrangements. By integrating custom software, the researchers can determine in seconds what previously took hours.
“This is the first time we have been able to determine the structure of individual complex DNA structures found in cells with nanometre precision,” said Alice Pyne, professor of biophysics at Sheffield.
“This will allow us to look at what complex structures may be formed in the cell during normal and abnormal cellular processes, such as DNA replication and understand their implications.”
The approach is so precise that it can distinguish whether one strand of DNA passes over or under another, a feature that even enables the identification of mirror-image knots. “If we want to study the processes in cells that lead to DNA knotting, as well as the action of topoisomerases to remove the knotting, we need to be able to determine exactly how the DNA is tangled,” said Sean Colloms of the University of Glasgow.
The work, carried out with collaborators in Slovakia and France, highlights how nanoscale imaging paired with computational modeling can expand the study of DNA topology and protein interactions that influence genome regulation.
Publication Details
Holmes, E.P., Gamill, M.C., Provan, J.I. et al. Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy. Nat Commun 16, 5482 (2025). https://doi.org/10.1038/s41467-025-60559-x
A team led by the University of Sheffield has now automated this process, combining atomic force microscopy (AFM) with advanced image analysis and AI. AFM uses a nanoscale probe to trace physical features, making it well-suited to capture DNA’s three-dimensional arrangements. By integrating custom software, the researchers can determine in seconds what previously took hours.
“This is the first time we have been able to determine the structure of individual complex DNA structures found in cells with nanometre precision,” said Alice Pyne, professor of biophysics at Sheffield.
“This will allow us to look at what complex structures may be formed in the cell during normal and abnormal cellular processes, such as DNA replication and understand their implications.”
The approach is so precise that it can distinguish whether one strand of DNA passes over or under another, a feature that even enables the identification of mirror-image knots. “If we want to study the processes in cells that lead to DNA knotting, as well as the action of topoisomerases to remove the knotting, we need to be able to determine exactly how the DNA is tangled,” said Sean Colloms of the University of Glasgow.
The work, carried out with collaborators in Slovakia and France, highlights how nanoscale imaging paired with computational modeling can expand the study of DNA topology and protein interactions that influence genome regulation.
Publication Details
Holmes, E.P., Gamill, M.C., Provan, J.I. et al. Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy. Nat Commun 16, 5482 (2025). https://doi.org/10.1038/s41467-025-60559-x