Research topics

A review article on the design of nucleic acid enzymes using artificial intelligence (AI) by a joint research group comprising Associate Professor Shuntaro Takahashi, Associate Professor Hisae Tateishi-Karimata, and Distinguished Professor Naoki Sugimoto from Frontier Institute for Biomolecular Engineering Research Konan University (FIBER) collaborated with the research group from Waseda University has been published in RSC Chemical Biology. The article was selected for the journal’s Inside Front Cover.

Nucleic acids (DNA and RNA) not only function as molecules that store and express genetic information, but can also exhibit enzymatic activity like proteins. Such nucleic acid enzymes, called DNAzymes and RNAzymes, are expected to be applied in pharmaceuticals that manipulate intracellular nucleic acids, as well as in the detection of ions and heavy metals. On the other hand, a problem arises because the activity of these nucleic acid enzymes is highly dependent on the surrounding environment, meaning the designed nucleic acid enzymes may not fully exhibit the expected functions.

The FIBER research group has developed methods to predict the structural stability of DNA and RNA within cells based on their sequences. In this newly published review, we explain how these unique structural stability predictions serve as an important and promising tool for designing nucleic acid enzymes capable of exhibiting desired activity within cells. Furthermore, in collaboration with Professor Michiaki Hamada of Waseda University, a co-researcher in Konan New Century Strategy Project and an expert in nucleic acid bioinformatics, we also discussed how the AI-driven application of these structural predictions can enable the effective design of nucleic acid enzymes. The content of this review is expected to provide important guidance for future developments in the pharmaceutical and analytical fields.

This presentation reports research findings related to Konan New Century Strategy Project. It was conducted with support from the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (21K05283, 22H04975, 24K01631), the Japan Society for the Promotion of Science Core-to-Core Program, Chubei Itoh Foundation, and The Asahi Glass Foundation.

【RSC Chemical Biology (electronic edition)】Click here for the link to the published page.

【Published Articles】

“Fitness landscapes and thermodynamic approaches to development of nucleic acids enzymes: from classical methods to AI integration”

S. Takahashi, M. Hamada, H. Tateishi-Karimata, and N. Sugimoto, RSC Chemical Biology, 6, 1667-1685 (2025)

【Paper Cover】

Frontier Institute for Biomolecular Engineering Research Konan University (FIBER) will continue to contribute to the advancement of science and technology and to the society through the application of research outcomes in the field of biochemistry.