
Welcome to Chemical Biology Lab
We are interested in the chemical biology of nucleic acids. Using the tools of organic chemistry, molecular biology and physical chemistry, we explore the chemical principles underlying the recognition, reactivity and structure of nucleic acids.
We certainly believe
that our group is one of the most active laboratories in the world. Please visit our Research
and Publication sections to learn more about our scientific activities. Also, you can see our
lab menbers and staff profiles to learn more about us!

2022.11
平島 眞吾さん(D3)が第49回国際核酸化学シンポジウム(ISNAC2022)でポスター発表を行い、優秀ポスター賞(ISNAC Outstanding Poster Award 2022)を受賞しました。
http://kuchem.kyoto-u.ac.jp/chembio/news.html2022.3
杉山 弘教授が最終講義を行いました。
https://ocw.kyoto-u.ac.jp/course/1072/2021.12
日高拓也さんの井上研究奨励賞の受賞が決まりました。
http://kuchem.kyoto-u.ac.jp/chembio/news.html2021.10
平島 眞吾さん(D2)が第43回日本光医学・光生物学会で口頭発表を行い奨励賞を受賞しました。
http://kuchem.kyoto-u.ac.jp/chembio/news.html2021.09
がん免疫療法の効果を高めるポリアミドを開発しました。
https://www.icems.kyoto-u.ac.jp/news/4468/2021.09
ミトコンドリアの変異DNAを減らす化合物を開発しました。
https://www.icems.kyoto-u.ac.jp/news/44212021.04
掲示板を更新しました。“Web of Science Top 10% Papers”
http://kuchem.kyoto-u.ac.jp/chembio/news.html-
2021.02
平島 眞吾さん(D1)が第4回A3若手研究者ミーティングで発表しA3北京大会へ選抜されました。
http://asianprobe.jp/news/the-fourth-a3-young-scientist-meeting/ -
2020.11
453. A Near-Infrared Fluorogenic Pyrrole-Imidazole Polyamide Probe for Live-Cell Imaging of Telomeres
Tsubono, Y.; Kawamoto, Y.; Hidaka, T.; Pandian, G.; Hashiya, K.; Bando, T.; Sugiyama, H.
J. Am. Chem. Soc. 2020, 142, 17356-17363.
の内容が紹介されました。
https://www.icems.kyoto-u.ac.jp/en/news/5646 -
2020.10
436. DNA Nanostructures as a Tool for Targeted Antimicrobial Delivery
Mela, I.; Vallejo-Raminez, P. P.; Makarchuk, S.; Christie, G.; Bailey D.; Henderson, R. M.; Sugiyama, H, Endo, M.; Kaminski, C. F.
Angew Chem. 2020, 59, 12698-12702.
の内容がYoutubeの記事になりました。 -
2020.07
朴 先生(助教)が旭硝子財団からの研究助成金を受けました。
“生物化学、DNAとアミノ酸を融合した機能性バイオハイプリッド分子の開発と応用"
- 523. Identification of Genes Responsible for the Social Skill in the Earthworm, Eudrilus Eugeniae.
Lathakumari, S.; Seenipandian, S.; Balakrishnan, S.; Raj, A. P. M. S.; Sugiyama, H.; Pandian, G. N.; Sivasubramaniam, S.
Gene Reports, 2023, 31, 101774 (1-19). - 522. Artificial Genetic Switches and DNA Origami: Current Landscape and Prospects as Designer Therapeutics and Visualization Tools.
Pandian, G. N.; Mishra, S.; Sugiyama, H.
in Handbook of Chemical Biology of Nucleic Acids, Eriks Rozners, Naoki Sugimoto, Ed. Springer Nature, in press - 521. Pyrrole-Imidazole Polyamides- A Frontrunner in Nucleic Acid-Based Small Molecule Drugs.
Vaijayanthi, T.; Pandian, G. N.; Sugiyama, H.
Advanced Therapeutics, 2023, 2300022 (1-8). - 520. Substitution to Hydrophobic Linker and Formation of Host–guest Complex Enhanced the Effect of Synthetic Transcription Factor.
Hatanaka, J.; Hashiya, K.; Bando, T.; Sugiyama, H.
Bioorg. Med. Chem. in press - 519. Nanoparticle-Based Artificial Mitochondrial DNA Transcription Regulator: MitoScript.
Yang, L.; Rathnam, C.; Hidaka, T.; Hou, Y.; Conklin, B.; Pandian, G. N.; Sugiyama, H.; Lee, K. B.
Nano Letter, 2023, 23, 2046-2055. - 518. Thiophene-extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions.
Kumagai, T.; Kinoshita, B.; Hirashima, S.; Sugiyama, H.; Park, S.
ACS Sensors, 2023, 8, 923-932. - 517. Evaluation by Experimentation and Simulation of a FRET Pair Comprising Fluorescent Nucleobase Analogs in Nucleosomes.
Hirashima, S.; Park, S.; Sugiyama, H.
Chem. Eur. J., 2023, e20220396 (1-8). - 516. Photocontrolled DNA Nanotubes as Stiffness Tunable Matrices for Controlling Cellular Behavior.
Sethi, S.; Emura, T.; Hidaka, K.; Sugiyama, H.; Endo, M.
Nanoscale, 2023, 15, 2904-2910. - 515. RNA G-quadruplex Organizes Stress Granule Assembly through DNAPTP6 in Neurons.
Asamitsu, S.; Yabuki, Y.; Matsuo, K.; Kawasaki, M.; Hirose, Y.; Kashiwazaki, G.; Chandran, A.; Bando, T.; Wang, D. O.; Sugiyama, H.; Shioda, N.
Science Advances, 2023, 9, eade2035 (1-15). - 514. Sequece-Specific Chromosomal DNA Binders: An Unfulfilled Promise?
Yu, Z.; Pandian, G. N.; Sugiyama, H.
Medicinal Chemistry and Chemical Biology: Drug Development and Clinical Applications, 2023, Chapter 5, 132-156. - 513. Mitochondria and G-quadruplex Evolution: An Intertwined Relationship
Sahayasheela, V. J.; Yu, Z.; Hidaka, T.; Pandian, G. N.; Sugiyama, H.
Trends in Genetics, 2023, 39, 15–30. - 512. Catalytic RNA Oligomers Formed by Co-Oligomerization of a Pair of Bimolecular RNase P Ribozymes
Siddika, M. A.; Yamada, T.; Aoyama, R.; Hidaka, K.; Sugiyama, H.; Endo, M.; Matsumura, S.; Ikawa, Y.
Molecules, 2022, 27, 8298. - 511. Twelve Colors of Streptavidin-Fluorescent Proteins (SA-FPs): A Versatile Tool to Visualize Genetic Information in Single-Molecule DNA
Jin, Y.; Bae, J.; Kim, T.; Hwang, H.; Kim, T.; Yu, M.; Oh, H.; Hashiya, K.; Bando, T.; Sugiyama, H.; Jo, K.
Analytical Chemistry, 2022, 94, 16927-16935. - 510. Chemical Probe-based Nanopore Sequencing to Selectively Assess the RNA Modifications
Ramasamy, S.; Sahayasheela, V. J.; Sharma, S.; Yu, Z.; Hidaka, T.; Cai, L.; Thangavel, V.; Sugiyama, H.; Pandian, G. N.
ACS Chem. Biol., 2022, 17, 2704-2709. - 509. A RUNX-targeted Gene Switch-off Approach Modulates the BIRC5/PIF1-p21 Pathway and Reduces Glioblastoma Growth in Mice
Hattori, E. Y.; Arakawa, Y.; Mineharu, Y.; Mikami, M.; Terada, Y.; Matsui, Y.; Masuda, T.; Kubota, H.; Hidemasa Matsuo, H.; Masahiro Hirata, M.; Kataoka, T. R.; Nakahata, T.; Ikeda, S.; Sugiyama, H.; Souichi Adachi, S.; Miyamoto, S.; Kamikubo, Y.
Communications Biology, 2022, 5, 939 - 508. Artificial Intelligence in Microbial Natural Product Drug Discovery: Current and Emerging Role
Sahayasheela, V. J.; Lankadasari, M. B.; Dan, V. M.; Dastager, S. G.; Pandian, G. N.; Sugiyama, H.
Natural Product Reports, 2022, 39, 2215-2230 - 507. DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion
Yao, S.; Chang, Y.; Zhai, Z.; Sugiyama, H.; Endo, M.; Zhu, W.; Xu, Y.; Yang, Y.; Qian, X.
ACS Appl. Mater. Interfaces, 2022, 14, 20739-20748 - 506. RUNX1-Survivin Axis as a Novel Therapeutic Target for Malignant Rhabdoid Tumor
Mikami, M.; Masuda, T.; Kanatani, T.; Noura, M.; Umeda, K.; Hiramatsu, H.; Kubota, H.; Daifu, T.; Iwai, A.; Hattori, E.; Furuichi, K.; Takasaki, S.; Tanaka, S.; Matsui, Y.; Matsuo, H.; Hirata, M.; Kataoka, T. R.; Nakahata, T.; Kuwahara, Y.; Iehara, T.; Hosoi, H.; Takita, J.; Sugiyama, H.; Adachi, S.; Kamikubo, Y.
Molecules and Cells, 2022, 45, 886-895. - 505. Chlorambucil-conjugated PI-polyamides (Chb-M’), a Transcription Inhibitor of RUNX Family, Has an Anti-tumor Activity Against SHH-type Medulloblastoma with p53 Mutation
Matsui, Y.; Mineharu, Y.; Noguchi, Y.; Yamamoto-Hattori, E.; Kubota, H.; Hirata, M.; Miyamoto, S.; Sugiyama, H.; Kamikubo, Y.
BBRC., 2022, 620, 150-157. - 504. Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers
Islam, M. D.; Hidaka, K.; Suzuki, Y.; Sugiyama, H,; Endo, M.; Matsumura, S.; Ikawa, Y.
J. Biosci. Bioeng., 2022, 134, 195-202. - 503. N-terminal Cationic Modification of Linear Pyrrole-Imidazole Polyamide Improves its Binding
Hatanaka, J.; Hirose, Y.; Hashiya, K.; Bando, B.; Sugiyama, H.
ChemBioChem, 2022, 23, e202200124 - 502. Characterization of 2-Fluoro-2’-deoxyadenosine in Duplex, G-quadruplex and I-motif
Hirashima, S.; Sugiyama, H.; Park, S.
ChemBioChem, 2022, 23, e202200222 - 501. An Informatics Approach to Distinguish RNA Modifications in Nanopore Direct RNA Sequencing
Ramasamy, S.; Mishra, S.; Sharma, S.; Parimalam, S. S.; Thangavel, V.; Fujita, Y.; Kovi, B.; Sugiyama, H.; Pandian, G. N.
Genomics, 2022, 114, 110372. - 500. Targeting Chemoresistance in Xp11.2 Translocation Renal Cell Carcinoma using a Novel Polyamide-chlorambucil Conjugate.
Funasaki, S.; Mehanna, S.; Ma, W.; Nishizawa, H.; Kamikubo, Y.; Sugiyama, H.; Ikeda, S.; Motoshima, T.; Hasumi, H.; Linehan, W. M.; Schmit, L.S.; Ricketts, C.; Suda, T.; Oike, Y. Kamba, T.; Baba, M.
Cancer Science, 2022, 113, 2352-2367. - 499. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives
Yum, J. H.; Sugiyama, H.; Park, S.
Chemical Record, 2022, 22, e202100333. - 498. Inhibition of GLI-mediated Transcription by Cyclic Pyrrole-Imidazole Polyamide in Cancer Stem Cells.
Sahayasheela, V. J.; Yu, Z.; Hirose, Y.; Pandian, G. N.; Bando, T.; Sugiyama, H.
Bull. Chem. Soc. J., 2022, 95, 693-699. - 497. Tumor Accumulation of PIP-based KRAS Inhibitor KR12 Evaluated by the Use of a Simple, Versatile Chicken Egg Tumor Model.
Higashi, Y.; Ikeda, S.; Matsumoto, K.; Satoh, S.; Komatsu, A.; Sugiyama, H.; Tamanoi, F.
Cancers, 2022, 14, 951. - 496. A Hexameric Ribozyme Nanostructure Formed by Double-Decker Assembly of a Pair of Triangular Ribozyme Trimers
Yu, K.; Hidaka, K.; Sugiyama, H.; Endo, M.; Matsumura, S.; Ikawa, Y.
ChemBioChem., 2022, 23, e202100573. - 495. Photo-Cross-Linking between BrU and Pyrene Residues in an RNA/DNA Hybrid
Tashiro, R.; Yum, J. H.; Park, S.; Sugiyama, H.
ChemBioChem., 2022, 23, e202100626. - 494. Single Base-Modification Reports and Locates Z-DNA Conformation on a Z-B-Chimera Formed by Topological Constraint
Liu, M.; Cui, Y.; Zhang, Y.; An, R.; Li, L.; Park, S.; Sugiyama, H.; Liang, X.
Bull. Chem. Soc. J., 2022, 95, 433-439. - 493. Dissection of Nanoconfinement and Proximity Effects on the Binding Events in DNA Origami Nanocavity.
Jonchhe, S.; Pandey, S.; Beneze, C.; Emura, T.; Sugiyama, H.; Endo, M.; Mao, H.
Nucleic Acids Res., 2022, 50, 697-703. - 492. Enhanced Immunostimulatory Activity of Covalent DNA Dendrons
Kawamoto, Y.; Liu, W.; Yum, J. H.; Park, S.; Sugiyama, H.; Takahashi, Y.; Takakura, Y.
ChemBioChem., 2022, 23, e202100583. - 491. RUNX1 Transactivates BCR-ABL1 Expression in Philadelphia Chromosome Positive Acute Lymphoblastic Leukemia
Masuda, T.; Maeda, S.; Shimada, S. ; Sakuramoto, N.; Morita, K.; Koyama, A.; Suzuki, K.; Mitsuda, Y.; Matsuo, H.; Kubota, H.; Kato, I.; Tanaka, K.; Takita, J.; Hirata, M.; Karaoke, T.; Nakahata, T.; Adachi, S.; Hirai, H.; Mizuta, S.; Naka, K.; Imai, Y.; Kimura, S.; Sugiyama, H.; Kamikubo, Y.
Cancer Science, 2022, 113, 529-539. - 490. Strong and Specific Recognition of CAG/CTG Repeat DNA (5’-dWGCWGCW-3’) by a Cyclic Pyrrole–Imidazole Polyamide
Hirose, Y.; Ohno, T.; Asamitsu, S.; Hashiya, K.; Bando, T.; Sugiyama, H.
ChemBioChem., 2022, 23, e202100533 (1-5). - 489. Biomimetic DNA Nanotechnology to Understand and Control Cellular Responses
Sethi, S.; Sugiyama, H.; Endo, M.
ChemBioChem., 2022, 23, e202100446. - 488. Single-Molecule Visualization of B-Z Transition in DNA Origami using High-Speed AFM
Endo, M; Sugiyama H.
Z-DNA Methods and Protocols. Methods in Molecular Biology K. Kim and V. Subramani Ed., in press - 487. Photoreaction of DNA Containing 5-Halouracil and its Products
Tashiro, R.; Sugiyama, H.
Photochemistry and Photobiology, 2022, 98, 532-545. - 486. Targeted Epigenetic Induction of Mitochondrial Biogenesis Enhances Antitumor Immunity in Mouse Model
Matinee M.; Pandian, G. N.; Sugiyama, H.
Cell Chem. Biol., 2022, 29, 463-475. - 485. Targeted Elimination of Mutated Mitochondrial DNA by a Multi-functional Conjugate Capable of Sequence-specific Adenine Alkylation
Hidaka, T.; Hashiya, K.; Bando, T.; Pandian, G. N.; Sugiyama, H.
Cell Chem. Biol., 2022, 29, 1-6.
〒 606-8502
Department of Chemistry,
Graduate School of Science Kyoto University
Kitashirakawa-Oiwakecho, Sakyo-Ku, kyoto, Japan
TEL +81-75-753-4002
FAX +81-75-753-3670