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!





  • 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