Kanazawa University Research: Scientists Discover How Ring Proteins Capture and Gather DNA Chains

High-speed nanoscale imaging reveals how a protein structure changes shape to capture and compress DNA more tightly.

Researchers from Kanazawa University in Japan and the National Institute of Genetics used high-speed atomic force microscopes to observe how a group of proteins known as Smc5 /6 interact with DNA. The images show how this structure opens and closes, captures DNA, and pulls the separated fragments together. The researchers also observed that Smc5 /6 fixes twisted DNA fragments in place, thereby forming a tighter arrangement. The research results provide new insights into the molecular processes involved in maintaining and repairing genetic material.

Observe how protein structures change shape

Every living cell must protect and maintain its own DNA. This genetic material contains the instructions necessary for life, but it is constantly subjected to pressures that may damage its structure. During cell division, the DNA must also be accurately replicated. To accomplish these tasks, cells rely on proteins that interact with DNA, regulate their arrangement, and support the maintenance of integrity.

Smc5 /6 is one of them; it is composed of various proteins that together form a structure. It belongs to a family of proteins that are involved in maintaining chromosomes, which are structures within cells that carry DNA. Although scientists have long known that Smc5 /6 is very important for the maintenance and repair of DNA, it has always been difficult to directly observe how it captures and processes DNA.

The research team used a high-speed atomic force microscope ( HS-AFM ). This technology utilizes extremely precise probes to track movements and structural changes at the nanoscale. Unlike traditional imaging methods that mainly provide static views, HS-AFM can record a series of images to demonstrate the behavior of individual molecular structures over time.

Under controlled experimental conditions, the research team studied Smc5 /6, which was purified from budding yeast, observing its movement and its interaction with DNA.

They discovered that Smc5 /6 can assume two different forms. In one form, its two long arms are close to each other, resembling the letter I; in the other form, the two long arms are separated, forming an open structure similar to the letter O.

The conversion between these two forms is influenced by adenosine triphosphate ( ATP ). ATP is a molecule that provides energy for many cellular processes. The binding of ATP promotes an open conformation, while the subsequent changes related to ATP are associated with the protein holding DNA in a different manner.

Capture DNA and pull it together.

As shown in the image, Smc5 /6 can interact with DNA at different parts of its structure. In some conformations, DNA is fixed in a region near one end of the protein assembly; in other conformations, DNA is located within the structure formed by its arms, which provides evidence for how Smc5 /6 captures DNA.

Researchers also observed that Smc5 /6 is capable of simultaneously contacting two different fragments of DNA. This allows the protein assembly to fix these fragments together, a process known as DNA retention.

Another important observation relates to the DNA distortion. When Smc5 /6 interacts with the distorted DNA structure, the area occupied by DNA is smaller than when there is no protein assembly. The results indicate that Smc5 /6 can help compress DNA by pulling together the DNA fragments and stabilizing the distorted conformation.

Understanding how cells maintain genetic material

This study more clearly demonstrates how Smc5 /6 interacts with DNA through coordinated shape changes. Protein assemblies do not simply attach at a certain location in DNA; instead, they can adopt different conformations, which helps to fix and reposition genetic material.

These characteristics are related to the broader biological functions of Smc5 /6, including its involvement in chromosome maintenance and DNA repair.

The experiment was conducted outside of cells using purified proteins and DNA. Therefore, these results reveal molecular interactions under controlled conditions, rather than directly demonstrating how this entire process functions within cells.

Potential meaning

This research has advanced our understanding of how proteins physically process DNA. By revealing the movements of Smc5 /6 and demonstrating how these movements are related to the capture, retention, and compression by DNA, this study provides new information on the molecular mechanisms that maintain chromosomes.

A deeper understanding of these mechanisms may in the future contribute to the study of issues arising from the failure to maintain and repair DNA. However, this research focuses on basic molecular biology and has not demonstrated any medical treatments or clinical applications.

The Umeda Kenichi from Kanazawa University said, "By observing how individual Smc5 /6 structures interact with DNA, we can see how their shape changes are related to the different ways in which they capture and fix DNA. These observations bring us one step closer to understanding how this protein assembly carries out its function of maintaining chromosomes."

Research Limitations

This study examines purified Smc5 /6 and DNA in a controlled experiment. The images do not directly prove every step of the activity of Smc5 /6 within living cells.

References

Kenichi Umeda, Yumiko Kurokawa, Noriyuki Kodera, and Yasuto Murayama: "Submolecular Video Imaging of the Topological Combination of Smc5 /6 Complex with DNA". Nature Communications 17, 10398 (2026). DOI: 10.1038/ s41467-026-77122-x

Funding

This research was supported by the Japan Science and Technology Agency (JST) through PRESTO (including JPMJPR20E3, JPMJPR23J2, and JPMJPR19KB), as well as CREST (including JPMJCR1762); by the Japan Society for the Promotion of Science through projects 19K15409, 21K04849, 26119003, 20H00327, 24H00402, 23K23814, and 24H02282 under KAKENHI; by the Takeda Science Foundation; and by the support of the World-Class International Research Center Program (WPI) of the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT).

Media Contact

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About the Institute of Nanobiological Sciences at Kanazawa University ( WPI-NanoLSI )

The Institute of Nanobiological Sciences at Kanazawa University has developed advanced nanoprobe technology for directly imaging, analyzing, and manipulating biomolecules in living systems. By exploring phenomena at the nanoscale that were previously unreachable, the institute aims to reveal the fundamental principles of life and disease.

About the World's Top International Research Center Program ( WPI )

The WPI project was initiated by the Japanese Ministry of Education, Culture, Sports, Science and Technology in 2007, with the aim of establishing a research center that has global influence, boasts an excellent research environment, and enjoys a high degree of autonomy. This project is managed by the Japan Society for the Promotion of Science ( JSPS ).

About Kanazawa University

Kanazawa University was founded in 1862 and is located in Ishikawa Prefecture. It is one of Japan's leading comprehensive national universities. The university promotes interdisciplinary research and international cooperation in fields such as science, medicine, engineering, humanities, and social sciences.

SOURCE Kanazawa University