Outline of Research
Our body is made up of 60 trillion cells, which are replaced periodically (3-4 months) by metabolism. This metabolism is based on the genetic information in DNA, the "blueprint of life" in the cell nucleus. This DNA is damaged by various factors and is repeatedly repaired. Understanding of DNA damage and its repair would lead to a better treatment and a more effective prevention of "cancer," which is derived from an abnormal cell growth.
1. Analysis of DNA damage induced by lasers and laser-driven quantum beams
We are investigating how DNA damage, which is considered to be the cause of biological effects, is produced and the mechanism of its generation by irradiating lasers and even laser-driven quantum beams.
Figure 1. Analysis of laser-induced DNA damage generation
Figure 2. DNA damage generation by laser-driven quantum beam and analysis of biological effect
2. Analysis of DNA damage repair
With advanced technology utilizing fluorescence resonance energy transfer or atomic force microscopy, we are conducting research to clarify the process of DNA damage formation, its form and structure, as well as the repair process. In addition, we are also working to elucidate the mechanisms of how DNA damage leads to mutagenesis. The results obtained from these studies are expected to be useful in the treatment and prevention of cancer.
Figure 3 Localization of DNA damage measured by fluorescence resonance energy transfer
Figure 4 Various forms of DNA damage visualized using atomic force microscopy
Member
| AKAMATSU Ken | Project Leader |
| OKA Kiyoshi | Senior Principal Researcher |
| NAKANO Toshiaki | Senior Principal Researcher |
| YONETANI Yoshiteru | Senior Principal Researcher |
| SHIKAZONO Naoya | Senior Staff |
| MORIBAYASHI Kengo | Senior Expert |
| AOKI Hiroyo | Assistant |
| TSUDA Kanae | Assistant |
List of Achievements (Papers, Awards, Press Releases, etc.)
2026
- Takeshi Seki, Kiyoshi Oka, Akihiro Naganawa, "Neural network–assisted optical temperature estimation using a composite–type optical fiberscope for transbronchial photothermal therapy", Optics and Lasers in Engineering, , 2026-01. Link
- Masanori Kobayashi, Osamu Okudaira, Naoya Shikazono, Kazuhiro Terasawa, Satoshi Kodaira, Nagaya Okada, "Quantitative analysis of Fe ion interactions with the negative pressure phase of ultrasound pulses in water", Jpn. J. Appl. Phys. 65 02SP20 2026. Link
2025
- Yoshiteru Yonetani, "Helical and antiparallel structures from truncated long-range interactions in water and dipolar spins", Chemical Physics 598 112854 2025. Link
- Kazuhi Terakawa, Susumu Fujiwara, Tomoko Mizuguchi, Hiroaki Nakamura, Ken Akamatsu, Naoya Shikazono, Yoshiteru Yonetani, "Molecular dynamics study on clustered DNA damage: AP sites on the same strand", Biophysical Chemistry 319 107394 2025. Link
- Masanori Kobayashi, Osamu Okudaira, Naoya Shikazono, Kazuhiro Terasawa, Satoshi Kodaira, Nagaya Okada, "Visualization of heavy ion particle Bragg peaks in water by ultrasound imaging", Jpn. J. Appl. Phys. 64 03SP26 (2025) Link
- Toshiaki Nakano, Ken Akamatsu, Masaoki Kohzaki, Masataka Tsuda, Ryoichi Hirayama, Akira Sassa, Manabu Yasui, Mahmoud I Shoulkamy, Takeshi Hiromoto, Taro Tamada, Hiroshi Ide, Naoya Shikazono, "Deciphering repair pathways of clustered DNA damage in human TK6 cells: insights from atomic force microscopy direct visualization", Nucleic Acids Res. 2025 53(1):gkae1077. Link
- Mahmoud I. Shoulkamy, Tareg Omer Mohammed, Hiroshi Ide, Toshiaki Nakano, "DNA-protein cross-links emerge as major contributors to chemotherapeutic cytotoxicity at physiological equitoxic doses", Scientific reports, 15, 23330, 2025. Link
- Kengo Moribayashi, "Role of photoelectrons and Auger electrons in X-ray ablation" 2025 J. Phys. B, 58, 165601/1-10 Link
2024
- Ryuta Kawanami, Susumu Fujiwara, Yoshiteru Yonetani, Tsukasa Aso, "Analyzing hydroxyl radical accessibility related to hydrogen abstraction in a DNA sugar moiety using molecular dynamics simulations", AIP Advances 14 105318 2024. Link
- Yoshiteru Yonetani, "Unsolved problem of long-range interactions: dipolar spin-ice study", Journal of Physics: Condensed Matter 36 175401 2024. Link
- Tomonari Kinoshita, Kiyoshi Oka, Takashi Ohtsuka, "How to approach and observe the peripheral airway of the resected lung using an ultra-thin fiberscope", Respiratory Endoscopy, 2(2), 93-96, 2024-07. Link
- S Kitamura, K Satoh, Y Hase, R Yoshihara, Y Oono, Naoya Shikazono, "Differential contributions of double-strand break repair pathways to DNA rearrangements following the irradiation of Arabidopsis seeds and seedlings with ion beams" Plant J. 2024 120(2):445-458. Link
- Naoya Shikazono, Ken Akamatsu, "The role of DNA polymerase I in tolerating single-strand breaks generated at clustered DNA damage in Escherichia coli", Scientific Report 2024 4(1):19124. Link
- Ken Akamatsu, K Satoh, Naoya Shikazono, T Saito, "Proximity Estimation and Quantification of Ionizing Radiation-induced DNA Lesions in Aqueous Media using Fluorescence Spectroscopy" Radiat Res. 2024 201(2):150-159. Link
- Ken Akamatsu, Tomoyuki Endo, Hiroshi Akagi, Hidetoshi Kono, Ryuji Itakura, "Specificity of DNA damage formation induced by femtosecond near-infrared laser filamentation in water", J Photochem Photobiol B. 2024 Sep;258:112994. Link
2023
- Yusuke Sato, Yoshihide Takaku, Toshiaki Nakano, Ken Akamatsu, Dai Inamura, and Seiichi Nishizawa, Synthetic DNA binders for fluorescence sensing of thymine glycol-containing DNA duplexes and inhibition of endonuclease activity, Chemical Communications, 59(40), 6088-6091
- Yusuke Matsuya, Yuji Yoshii, Tamon Kusumoto, Ken Akamatsu, Yuho Hirata, Tatsuhiko Sato, Takeshi Kai, A step-by-step simulation code for estimating yields of water radiolysis species based on electron track-structure mode in the PHITS code, Physics in Medicine & Biology, 69(3), ad199b
- Ken Akamatsu, Katsuya Satoh, Naoya Shikazono, and Takeshi Saito, Proximity estimation and quantification of ionizing radiation-induced DNA lesions in aqueous media using fluorescence spectroscopy, Radiation Research, 201(2), 150-159
- Kengo Moribayashi, Hiroki Matsubara, Yoshiteru Yonetani, Naoya Shikazono, Multi-Scale Simulations Aiming To Advance Heavy Ion Beam Cancer Therapy, API conference proceedings, 2756(1), 030001/1-8
- Toshiaki Nakano, Ken Akamatsu, Naoya Shikazono, Structural analysis and repair kinetics of radiation-induced DNA damage, Radiation Chemistry