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Department of Chemistry, Graduate School of Science, Kyoto University

Sugiyama Hiroshi (Professor)

Field of Expertise:
Chemical Biology, Bioorganic Chemistry
Research Interests:
  1. Chemistry of nucleic acid structure and function
  2. Development of tailor made antitumor agent
  3. Development of artificial genetic switch
  4. Development of DNA origami for single molecule analysis
Recent Papers:
    301. Tandem Trimer Pyrrole-Imidazole Polyamide Probes Targeting 18 Base Pairs in Human Telomere Sequence
    Kawamoto, Y.; Sasaki, A.; Hashiya, K.; Ide, S; Toshikazu, B.; Maeshima, K; Sugiyama, H.
    Chem. Sci. In Press.

    300. Rational Design of Specific Binding Hairpin Py-Im Polyamides Targeting Human Telomere Sequences
    Guo, C, X .; Kawamoto, Y.; Asamitsu, S.; Sawatani, Y.; Hashiya, K.; Toshikazu, B.; Sugiyama, H.
    Bioorg. Med. Chem. 2015, 23, 855-860.

    299. Advancing Small-Molecule-Based Chemical Biology With Next-Generation Sequencing Technologies
    Anandhakumar, C.; Kizaki, S.; Bando, T.; Pandian, G. N.; Sugiyama, H.
    ChemBioChem. 2015, 16, 20-38.

    298. Synthetic Strategies to Identify and Regulate Noncoding RNAs
    Pandian, G, N.; Syed, J.; Sugiyama, H.
    Long Noncoding RNAs: Structure and Function. In Press.

    297. Locating the 2'-Deoxyuridin-5-yl Radical Formed Upon Photoirradiation of 5-bromouracil-substituted DNA
    Hashiya, F.; Saha, A.; Kizaki, S.; Li, Y.; Sugiyama, H.
    Nucleic Acids Res. 2014, 42, 13469-13473.

    296. Identification of a Small Molecule that Turns `ON` the Pluripotency Gene Circuitry in Human Fibroblasts
    Pandian, G, N.; Sato, S.; Anandhakumar, C.; Taniguchi, J.; Takashima, K.; Syed, J; Han, L.; Saha, A.; Bando, T.; Nagase, H.; Sugiyama, H.
    ACS Chem. Biol. 2014, 9, 2729-2736.

    295. Direct Quantification of Loop Interaction and π-π Stacking for G-quadruplex Stability at the Sub-molecular Level
    Ghimire, C.; Park, S.; Iida, K.; Yangyuoru, P.; Otomo, H.; Yu, Z.; Nagasawa, K.; Sugiyama, H.; Mao, H.
    J. Am. Chem. Soc. 2014, 136, 15537-15544.

    294. Preparation of Chemically Modified RNA Origami Nanostructures
    Endo, M.; Takeuchi, Y.; Emura, T.; Hidaka, K.; Sugiyama, H.
    Chem. Eur. J. 2014, 20, 15330-15333.

    293. Development of DNA-based Hybrid Catalysts Through Direct Ligand Incorpororation: Towards Understanding of DNA-based Asymmetric Catalysis
    Park, S.; Zheng, L, J.; Kumakiri, S.; Sakashita, S.; Otomo, H.; Ikehata, K.; Sugiyama, H.
    ACS Catalysis. 2014, 4, 4070-4073.

    292. Next-Generation Sequencing Studies Guide the Design of Pyrrole-Imidazole Polyamides with Improved Binding Specifictiy by the Addition of β-alanine
    Anandhakumar, C.; Li, Y.; Kizaki, S.; Pandian, G, N.; Hashiya, K.; Bando, T.; Sugiyama, H.
    ChemBioChem. 2014, 15, 2647-2651.

    291. Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials
    Takenaka, T.; Endo, M.; Suzuki, Y.; Yang, Y.; Emura, T.; Hidaka, K.; Kato, T.; Mitata, T.; Namba, K.; Sugiyama, H.
    Chem. Eur. J. 2014, 20, 14951-14954.

    290. NanoScript: A Nanoparticle-Based Artificial Transcription Factor for Effective Gene Regulation
    Patel, S.; Jung, D.; Yin, P.; Carlton, P.; Yamamoto, M.; Bando, T.; Sugiyama, H.; Lee, K, B.
    ACS Nano. 2014, 8, 8959-8967.

    289. Engineering RNA-Protein Complexes with Different Shapes for Imaging and Therapeutic Applications
    Osada, E.; Suzuki, Y.; Hidaka, K.; Ohno, H.; Sugiyama, H.; Endo, M.; Saito, H.
    ACS Nano. 2014, 8, 8130-8140.

    288. Structure Evaluation of Tandem Hairpin Pyrrole-Imidazole Polyamides Recoginzing Human Telomeres
    Hirata, A.; Nokihara, K.; Kawamoto, Y.; Bando, T.; Sasaki, A.; Ide, S.; Maeshima, K.; Kasama, T.; Sugiyama, H.
    J. Am. Chem. Soc. 2014, 136, 11546-11554.

    287. Targeted Suppression of EVI1 Oncogene Expression by Sequence-specific Pyrrole-imidazole Polyamide
    Junetha, S.; Pandian, G, N.; Sato, S.; Taniguchi, J.; Anandhakumar, C.; Hashiya, K.; Bando, T.; Sugiyama, H.
    Chem. Bio. 2014, 23, 1370-1380.

    286. Amplification of Fluorescent DNA through Enzymatic Incorporation of a Highly Emissive Deoxyguanosine Analogue
    Otomo, H.; Park, S.; Yamamoto, S.; Sugiyama, H.
    RSC Adv. 2014, 4, 31341-31344.

    285. Sequence-Specific DNA Alkylation and Transcriptional Inhibition by Long-Chain Hairpin Pyrrole-Imidazole Polyamide-Chlorambucil Conjugates Targeting CAG/CTG Trinucleotide Repeats.
    Asamitsu, S.; Kawamoto, Y.; Hashiya, F.; Hashiya, K.; Yamamoto, M.; Kizaki, S.; Bando, T.; Sugiyama, H.
    Bioorg. Med. Chem 2014, 22, 4646-4657.

    284. AFM Analysis of Changes in Nucleosome Wrapping Induced by DNA Epigenetic Modification
    Kizaki, S.; Suzuki, Y.; Takenaka, T.; Endo, M.; Sugiyama, H.
    Biomater. Sci. 2014, 2, 1399-1403.

    283. Chemically Modified Synthetic Small Molecule Boosts its Biological Efficacy against Pluripotency Genes in Mouse Fibroblast
    Saha, A.; Pandian, G. N.; Sato, S.; Taniguchi, J.; Kawamoto, Y.; Hashiya, K.; Bando, T.; Sugiyama, H.
    ChemMedChem 2014, 9, 2374-2380.

    282. Single Molecule Mechanochemical Sensing Using DNA Origami Nanostructures
    Koirala, D.; Shrestha, P.; Emura, T; Hidaka, K.; Mandal, S.; Endo, M,; Sugiyama, H.; Mao, H.
    Angew. Chem. Int. Ed. 2014, 126, 8275-8279.

    281. Helical DNA Origami Tubular Structures with Various Sizes and Arrangements
    Endo, M.; Yamamoto, S.; Emura, T; Hidaka, Kumi.; Morone, N.; Heuser, J, E.; Sugiyama, H.
    Angew. Chem. Int. Ed. 2014, 53, 7484-7490.

    280. Sequence-specific DNA Alkylation by Tandem Py-Im Polyamide Conjugates
    Taylor, R, D.; Kawamoto, Y.; Hashiya, K.; Bando, T.; Sugiyama, H.
    Chem. Asian J. 2014, 9, 2527-2533.

    279. Lock-and-Key Mechanism for the Controllable Fabrication of DNA Origami Structures
    Rajendran, A.; Endo, M.; Hidaka, K.; Shimada, N.; Maruyama, A.; Sugiyama, H.
    Chem. Comm. 2014, 50, 8743-8746.

    278. Alteration of Epigenetic Program to Recover Memory and Alleviate Neurodegeneration: Prospects of Multi-target Molecules
    Pandian, G. N.; Taylor, R. D.; Junetha, S.; Saha, A.; Anandhakumar, C.; Vaijayanthi, T.; Sugiyama, H.
    Biomater. Sci. 2014, 2, 1043-1056.

    277. Direct Analysis of Holliday Junction Resolving Enzyme in a DNA Origami Nanostructurecolor
    Suzuki, Y.; Endo, M.; Canas, C.; Ayora, S.; Alonso, J. C.; Sugiyama, H.; Takeyasu, K.
    Nucleic Acids Res. 2014, 42, 7421-7428.

    276. Single Molecule Visualization and Characterization of Sox2-Pax6 Complex Formation on a Regulatory DNA Element Using a DNA Origami Frame
    Yamamoto, S.; De, D.; Hidaka, K.; Kim, K. K.; Endo, M.; Sugiyama, H.
    Nano Lett. 2014, 14, 2286-2292.

    275. The Origin of Enantioselectivity for Intramolecular Friedel-Crafts Reaction Catalyzed by Supramolecular Cu/DNA catalyst Complex
    Petrova, G. P.; Ke, Z.; Park, S.; Sugiyama, H.; Morokuma, K.
    Chem. Phys. Lett. 2014, 600, 87-95.

    274. Cellular Reprogramming for Pancreatic beta Cell Regeneration: Clinical Potential of Small-Molecule Control
    Pandian, G. N.; Taniguchi, J.; Sugiyama, H.
    Clin. Transl. Med. 2014, 3: 6.

    273. Investigation of B-Z Transitions with DNA Oligonucleotides Containing 8-Methylguanine
    Chen, Y-H.; Park, S.; Otomo, H.; Sakashita, S.; Sugiyama, H.
    Artificial DNA: PNA & XNA. 2014, 5, e28226-1-e28226-7.

    272. Direct Observation of the Dual-Switching Behaviours Corresponding to the State Transition in a DNA Origami
    Yang, Y.; Endo, M.; Suzuki, Y.; Hidaka, K.; Sugiyama, H.
    Chem. Comm. 2014, 50, 4211-4213.

    271. Targeted Editing of Therapeutic Genes using DNA-based Transcriptional Activators: Scope and Challenges
    Pandian, G. N.; Sugiyama, H.
    Chemical Biology of Nucleic Acids:Fundamentals and Clinical Applications (Springer Book) 2014,347-365.

    270. Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates
    Rajendran, A.; Endo, M.; Hidaka, K.; Sugiyama, H.
    Angew. Chem. Int. Ed. 2014, 126, 4191-4196.

    269. Single-Molecule Imaging of Dynamic Motions of Biomolecules in DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy
    Endo, M.; Sugiyama, H.
    Acc. Chem. Res. 2014, 47, 1645-1653.

    268. Specific Alkylation of Human Telomere Repeat Sequences by a Tandem-Hairpin Motif of Pyrrole-Imidazole Polyamides with Indole-Seco-CBI
    Yamamoto, M.; Bando, T.; Kawamoto, Y.; Taylor, R.; Hashiya, K.; Sugiyama, H.
    Bioconjugate Chem. 2014, 25, 552-559.

    267. Direct Observation of G-Quadruplexes using DNA Origami Nanoscaffold
    Rajendran, A.; Li, Y.; Endo,M.; Sugiyama, H.
    E. Book Chapter:DNA G-quadruplexes as new anticancer targets, (Ed. Ryan De Vooght-Johnson), Future Science Ltd, London. 2014

    266. Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface
    Suzuki, Y.; Endo, M.; Yang, Y.; Sugiyama, H.
    J. Am. Chem. Soc. 2014, 136, 1714-1717.

    265. Distinct DNA-based Epigenetic Switches Trigger Transcriptional Activation of Silent Genes in Human Dermal Fibroblasts
    Pandian, G. N.; Taniguchi, J.; Junetha, S.; Sato, S.; Han, L.; Saha, A.; Anandhkumar, C.; Bando, T.; Nagase, H.; Thangavel, V.; Taylor, R. D.; Sugiyama, H.
    Sci. Rep. 2014, 4, 3843.

    264. G-quadruplex-binding Ligand-induced DNA Synapsis Inside a DNA Origami Frame
    Rajendran, A.; Endo, M.; Hidaka, K.;Tran, P.L.T.; Teulade-Fichou, M-P.; Mergny, J-L.; Sugiyama, H.
    RSC. Adv. 2014, 4, 6346-6355.

    263. DNA Origami Based Visualization System for Studying Site-Specific Recombination Events
    Suzuki, Y.; Endo, M.; Katsuda, Y.;Ou, K.; Hidaka, K.; Sugiyama, H.
    J. Am. Chem. Soc. 2014, 136, 211-218.

    262. Highly Emissive Deoxyguanine Analogue Capable of Direct Visualization of B-Z Transition
    Park, S.; Otomo, H.; Zheng, L.; Sugiyama, H.
    Chem. Comm. 2014, 50, 1573-1575.

    261. Sequence-specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole-Imidazole Polyamide Seco-CBI Conjugates
    Taylor, R. D.; Asamitsu, S.; Takenaka, T.; Yamamoto, M.; Hashiya, K.; Kawamoto, Y.; Bando, T.; Nagase, H.; Sugiyama, H.
    Chem. Eur. J. 2014, 20, 1310-1317.

    260. Controlling Electron Rebound Within Four-Base π-Stacks in Z-DNA by Changing Sugar Moiety from Deoxy- to Ribonucleotide
    Sannohe, Y.; Kizaki, S.; Kanesato, S.; Fujiwara, A.; Morinaga, H.; Tashiro, R.; Sugiyama, H.
    Chem. Eur. J. 2014, 20, 1223-1225.

    259. Conjugation of Peptide Nucleic Acid with Pyrrole-Imidazole Polyamide to Specifically Recognize and Cleave DNA
    Kameshima, W.; Ishizuka, T.; Minoshima, M.; Yamamoto, M.; Sugiyama, H.; Xu, Y.; Komiyama, M.
    Angew. Chem. Int. Ed. 2013, 52, 13681-13684.

    258. Sequence-Specific DNA Recognition by Dimerized Cysteine Cyclic Pyrrole-Imidazole Polyamides
    Yamamoto, M.; Bando, T.; Morinaga, N.; Kawamoto, Y.; Hashiya, K.; Sugiyama, H.
    Chem. Eur. J. 2014, 20, 752-759.

    257. Construction and Characterization of Cy3- or Cy5-Conjugated Hairpin Pyrrole/Imidazole Polyamide Binding to DNA in the Nucleosome
    Han, Y-W.; Tsunaka, Y.; Yokota, H.; Matsumoto, T.; Kashiwazaki, G.; Morinaga, H.; Hashiya, K.; Bando, T.; Sugiyama, H.; Harada, Y.
    Biomater. Sci. 2014, 2, 297-307.

    256. State-of-the Art High Speed Atomic Force Microscopy for the Investigation of Single-Molecular Dynamics of Proteins
    Rajendran, A.; Endo, M.; Sugiyama, H.
    Chem. Rev. 2014, 114, 1493-1520.

    255. CGmCGCG is a Versatile Substrate with Which to Evaluate Tet Protein Activity
    Kizaki, S.; Sugiyama, H.
    Org. Biomol. Chem. 2014, 12, 104-107.

1979 B.S. Kyoto Univ. Department of Synthetic Chemistry.
1981 M.S. Kyoto Univ. Department of Synthetic Chemistry.
1984 Ph.D. Kyoto Univ. Department of Synthetic Chemistry.
1984 Research Associate at University of Virginia (USA).
1986 Research Associate at Kyoto University.
1987 Assistant Professor, Kyoto Univ. Department of Synthetic Chemistry.
1993 Associate Professor, Kyoto Univ. Department of Synthetic Chem. & Biological Chem.
1996 Professor, Tokyo Medical & Dental Univ. Institute of Biomaterials & Bioengineering.
2003 Professor, Kyoto Univ. Graduate School of Science, Department of Chemistry.
2008 Principal Investigator, Institute for Integrated Cell-Material Sciences (iCeMS).
IBM Japan Science Award (1999)
The CSJ Award for Creative Work (2005)
Editorial Advisory Board of ChemBioChem. (2005)
Editorial Advisory Board of J. Am. Chem. Soc. (2009)
Editional Board of J. Nucleic Acids. (2009)
Editorial Advisory Board of J. Med. Chem. (2011)
Editorial Board of The Chemical Record (2011)
Associate Editor of Biomaterials Science (2012)
Contact Information:
Phone: 81(Japan)-75-753-4047
Fax: 81(Japan)- 75-753-4050
E-mail: hs + @kuchem.kyoto-u.ac.jp
Chemical biology laboratory (internal link)
Sugiyama Research Group web site

This page was last modified on 05 April 2018.

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