High-speed atomic force microscopy reveals how enzymes find and break apart vulnerable regions of DNA while tightly packed structures resist degradation
Researchers at the Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University have directly visualized how enzymes find and break DNA molecules in real time. Using high-speed atomic force microscopy, the team followed individual enzymes as they moved along DNA and found that they repeatedly returned to vulnerable regions before breaking them apart. The findings reveal how the structure of DNA influences its vulnerability to enzymatic breakdown.
The research was led by Richard Wong and his team was Jingge Yang, Yujia Qiu, Keesiang Lim and Toshio Ando.
Watching DNA degradation molecule by molecule
DNA is a long molecule that carries the genetic information of living organisms. It is constantly exposed to processes that can damage or break it. Some enzymes—proteins that carry out specific tasks in living organisms—can deliberately break down DNA. These enzymes, called nucleases, play important roles in maintaining cells and clearing unwanted DNA.
One of the best-known of these enzymes is DNase I. It helps remove DNA released from damaged or dying cells. Problems with this clearance process have been associated with inflammatory and autoimmune diseases.
Although scientists know a great deal about the chemistry of DNase I, it has been difficult to see exactly how individual enzyme molecules approach DNA, where they remain and what happens immediately before and after the DNA is cut.
The Kanazawa University researchers addressed this problem using high-speed atomic force microscopy (HS-AFM), a technique that can record nanoscale changes in biological molecules in liquid without requiring them to be fixed, stained or crystallized. This allowed the researchers to observe in real time how individual nuclease enzymes interacted with and gradually broke apart DNA.
DNA has vulnerable regions
The HS-AFM movies revealed that DNase I did not interact with every part of a DNA molecule in the same way. The enzyme was frequently found near exposed DNA ends and regions where the DNA was curved or locally bent. Individual DNase I molecules could repeatedly return to restricted regions before visible fragmentation occurred.
Longer-lasting interactions were also more common around curved regions where DNA was more likely to be cut. Together, these observations showed that the shape of DNA influenced where the enzymes interacted with it.
Importantly, the HS-AFM cannot directly show the chemical reaction occurring at the enzyme’s active site. The researchers therefore describe the relationship between DNA shape, repeated enzyme engagement and subsequent cleavage as a spatial and temporal correlation rather than direct observation of the catalytic reaction.
Five stages of DNA degradation
Based on these recurring patterns of interaction, the researchers developed a conceptual framework called STORM: Scan – Target – Occupy – Rupture – Mobilize.
In this framework, an enzyme samples the DNA, becomes localized at a particular region, remains associated with it, fragmentation occurs and the resulting pieces are redistributed.
The researchers emphasize that STORM is a framework for describing the interaction patterns revealed by the experiments rather than a fixed sequence through which every enzyme molecule must pass.
The team also examined another DNA-cutting enzyme, micrococcal nuclease (MNase). Despite differences between DNase I and MNase, the researchers observed similar patterns of DNA sampling, localized interaction, repeated association, disruption and fragment redistribution. This suggests that STORM-like behavior may reflect broader physical principles governing how different nucleases interact with DNA.
Tightly packed DNA resists attack
The experiments also revealed how the physical organization of DNA can protect it from degradation.
The researchers examined DNA condensed by protamine, a small protein that binds strongly to DNA. Protamines are particularly important in sperm cells, where they help package the paternal genome into an extremely compact form.
Under the experimental conditions, protamine caused DNA to form mainly two compact structures: elongated rod-like structures and ring-shaped structures called toroids.
High-speed microscopy showed that DNase I molecules could gather around these condensed structures without destroying them. The toroidal structures were particularly compact. DNase I rarely penetrated their central regions, and the structures remained intact during continuous observation for more than six minutes despite the presence of the enzyme.
When the condensed structures were partially loosened, however, exposed regions again became susceptible to degradation.
The results suggest that protection does not arise simply from the electrical interaction between protamine and DNA. Instead, tightly packing DNA into particular three-dimensional structures creates a physical barrier that limits the enzyme’s access.
A possible framework for understanding DNA protection and clearance
The study provides a dynamic view of a fundamental biological problem: why some DNA is accessible to enzymes while other DNA remains protected.
The findings could contribute to understanding how compact structures help preserve genetic information, including the exceptionally dense packaging found in sperm cells. They could also be relevant to extracellular DNA released from damaged or dying cells, which can stimulate immune responses if it is not efficiently removed.
The results may additionally be useful for the development of DNA-based therapeutics and gene-delivery systems. Packaging genetic material into structures that restrict nuclease access could potentially increase its resistance to degradation.
“Our high-speed AFM imaging allows us to follow the interaction between individual nuclease enzymes and DNA as it happens,” says Jingge Yang. “We can see that DNA is not simply a passive target. Its local shape and higher-order organization strongly influence where enzymes interact and whether degradation can proceed.” says Richard Wong.
Putting the findings in perspective
The study directly visualizes nuclease-DNA interactions and DNA fragmentation in a purified experimental system under liquid imaging conditions. It also shows that protamine-condensed DNA can strongly resist DNase I attack and that susceptibility returns when compact structures loosen.
HS-AFM does not directly resolve the enzyme’s active-site chemistry or distinguish every productive binding event from a nonproductive one. The proposed STORM framework should therefore be understood as a probabilistic description of reproducible interaction patterns rather than direct visualization of individual catalytic intermediates.
Despite these limitations, the work provides a nanoscale framework linking DNA shape, structural accessibility and enzymatic degradation in real time.
Key findings
●HS-AFM captured individual nuclease enzymes interacting with and fragmenting DNA in real time.
●DNase I interactions were enriched around exposed DNA ends and curved or locally bent regions.
●Enzymes repeatedly visited some regions before detectable fragmentation occurred.
●The researchers summarize the observed interaction pattern with the STORM framework: Scan, Target, Occupy, Rupture and Mobilize.
●A second nuclease, MNase, showed similar behavior, suggesting that these physical principles may extend beyond DNase I.
●Protamine condensed DNA into rod-like and toroidal structures that were strongly resistant to DNase I.
●DNA became more susceptible to degradation when these compact structures loosened.
Glossary
Article
- Title
- Shield Strike Shatter in DNA Topology and Nuclease Interactions
- Author
- Jingge Yang, Yujia Qiu, Keesiang Lim, Toshio Ando and Richard W. Wong.
- Journal
- Nature Communications
- Publication date
- Sep 24, 2026
- DOI
- 10.1038/s41467-026-77354-x
- URL
- https://www.nature.com/articles/s41467-026-77354-x