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Takumi Ishizuka

Current position:
 Assistant Professor, Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki
Academic degree:
 Ph.D
Biography:
 2006  School of Bioscience and Biotechnology, Tokyo Institute of Technology
2008  Department of Bioengineering, Graduate School of Engineering, The University of Tokyo
2008  Visiting Researcher, University of Parma in Italy
2009  JSPS Research Fellow (DC2), The University of Tokyo
2011  Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
2011  JSPS Research Fellow (PD), RIKEN
2013  Project Assistant Professor, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki
2016  Assistant Professor, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki
2021  Assistant Professor, Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki
2022  Lecturer, Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki
Specialty:
 Nucleic acids chemistry
Society:
 The Chemical Society of Japan, The Japan Society of Nucleic Acids Chemistry, Japanese Society for Photomedicine and Photobiology, Japan Society of Histochemistry and Cytochemistry, The Japanese Association of Anatomists
Research interest:
Publication:
 Ikenoue M, Choijookhuu N, Yano K, Fidya, Takahashi N, Ishizuka T, Shirouzu S, Yamaguma Y, Kai K, Higuchi K, Sawaguchi A, Nanashima A, Hishikawa Y. The crucial role of SETDB1 in structural and functional transformation of epithelial cells during regeneration after intestinal ischemia reperfusion injury. Histochem Cell Biol. 2024 Jan 13. doi: 10.1007/s00418-023-02263-9.

Fidya, Choijookhuu N, Ikenoue M, Yano K, Yamaguma Y, Shirouzu S, Kai K, Ishizuka T, Hishikawa Y. Protective role of estrogen through G-protein coupled receptor 30 in a colitis mouse model. Histochem Cell Biol. 2023 Oct 12. doi: 10.1007/s00418-023-02235-z.

Shirouzu S, Sugita N, Choijookhuu N, Yamaguma Y, Takeguchi K, Ishizuka T, Tanaka M, Fidya, Kai K, Chosa E, Yamashita Y, Koshimoto C and Hishikawa Y. Pivotal role of High-Mobility Group Box 2 in ovarian folliculogenesis and fertility. J Ovarian Res. 2022, 15, 133. doi: 10.1186/s13048-022-01071-4.

He Z, Ishizuka T, Hishikawa Y, Xu Y. Click chemistry for fluorescence imaging via combination of a BODIPY-based ‘turn-on’ probe and a norbornene glucosamine. Chem. Commun. 2022, 58, 12479-12482. doi:10.1039/D2CC05359D.

Choijookhuu N, Shibata Y, Ishizuka T, Xu Y, Koji T, Hishikawa Y. An advanced detection system for in situ hybridization using a fluorescence resonance energy transfer–based molecular beacon probe. Acta Histochem. Cytochem. 2022, 55, 119-128. doi: 10.1267/ahc.22-00075.

Yamaguma Y, Sugita N, Choijookhuu N, Yano K, Lee D, Ikenoue M, Fidya, Shirouzu S, Ishizuka T, Tanaka M, Yamashita Y, Chosa E, Taniguchi N, Hishikawa Y.  Crucial role of high-mobility group box 2 in mouse ovarian follicular development through estrogen receptor beta. Histochem. Cell Biol. 2022, 157, 359-369. doi: 10.1007/s00418-022-02074-4.

Yum J H, Ishizuka T, Fukumoto K, Hori D, Bao H L, Xu Y, Sugiyama H, Park S: Systematic Approach to DNA Aptamer Design Using Amino Acid-Nucleic Acid Hybrids (ANHs) Targeting Thrombin. ACS Biomater. Sci. Eng. 2021, 7, 1338-1343. doi:10.1021/acsbiomaterials.1c00060.

Bao H L, Ishizuka T, Yamashita A, Furukoji E, Asada Y, Xu Y: Improving thermodynamic stability and anticoagulant activity of a thrombin binding aptamer by incorporation of 8-trifluoromethyl-2′-deoxyguanosine. J. Med. Chem. 2021, 64, 711-718. doi:10.1021/acs.jmedchem.0c01711.

Sasaki S, Ma Y, Ishizuka T, Bao H-L, Hirokawa T, Xu Y, Tera M, Nagasawa K: Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex. RSC Advances 2020, 10, 43319-43323. doi:10.1039/d0ra09413g.

Hayasaka K, Shibata T, Sugahara A, Momotake A, Matsui T, Neya S, Ishizuka T, Xu Y, Yamamoto Y: Characterization of structure and catalytic activity of a complex between heme and an all parallel-stranded tetrameric G-quadruplex formed from DNA/RNA chimera sequence d(TTA)r(GGG)dT. Bull. Chem. Soc. Jpn. 2020, 93, 621-629. doi:10.1246/bcsj.20200013.

Zhang T, Yin C, Boyd D F, Quarato G, Ingram J P, Shubina M, Ragan K B, Ishizuka T, Crawford J C, Tummers B, Rodriguez D A, Xue J, Peri S, Kaiser W J, López C B, Xu Y, Upton J W, Thomas P G, Green D R, Balachandran S: Influenza virus Z-RNAs induce ZBP1-mediated necroptosis. Cell 2020, 180, 1115-1129.e1113. doi:10.1016/j.cell.2020.02.050.

Liu H S, Ishizuka T, Kawaguchi M, Nishii R, Kataoka H, Xu Y: A nucleoside derivative 5-vinyluridine (VrU) for imaging RNA in cells and animals. Bioconjug. Chem. 2019, 30, 2958-2966. doi:10.1021/acs.bioconjchem.9b00643.

Ishizuka T, Bao H L, Xu Y: 19F NMR spectroscopy for the analysis of DNA G-quadruplex structures using 19F-labeled nucleobase. Methods Mol. Biol. 2019, 2035, 407-433. doi:10.1007/978-1-4939-9666-7_26.

Balasubramaniyam T, Ishizuka T, Xu Y: Stability and properties of Z-DNA containing artificial nucleobase 2′-O-methyl-8-methyl guanosine. Bioorg. Med. Chem. 2019, 27, 364-369. doi:10.1016/j.bmc.2018.12.005.

Balasubramaniyam T, Ishizuka T, Xiao C D, Bao H L, Xu Y: 2’-O-methyl-8-methylguanosine as a Z-form RNA stabilizer for structural and functional study of Z-RNA. Molecules 2018, 23, 10.3390/molecules23102572.

Ishizuka T, Yamashita A, Asada Y, Xu Y: Studying DNA G-quadruplex aptamer by 19F NMR. ACS Omega 2017, 2, 8843-8848. doi:10.1021/acsomega.7b01405.

Ishizuka T, Zhao P Y, Bao H L, Xu Y: A multi-functional guanine derivative for studying the DNA G-quadruplex structure. Analyst 2017, 142, 4083-4088. doi:10.1039/c7an00941k.

Xiao C D, Ishizuka T, Xu Y: Antiparallel RNA G-quadruplex formed by human telomere RNA containing 8-bromoguanosine. Sci. Rep. 2017, 7, 6695. doi:10.1038/s41598-017-07050-w.

Liu X, Ishizuka T, Bao H L, Wada K, Takeda Y, Iida K, Nagasawa K, Yang D, Xu Y: Structure-dependent binding of hnRNPA1 to telomere RNA. J. Am. Chem. Soc. 2017, 139, 7533-7539. doi:10.1021/jacs.7b01599.

Bao H L, Ishizuka T, Iwanami A, Oyoshi T, Xu Y: A simple and sensitive 19F NMR approach for studying the interaction of RNA G‐quadruplex with ligand molecule and protein. ChemistrySelect 2017, 2, 4170-4175. doi:10.1002/slct.201700711.

Xiao C D, Ishizuka T, Zhu X Q, Li Y, Sugiyama H, Xu Y: Unusual topological RNA architecture with an eight-stranded helical fragment containing A-, G-, and U-tetrads. J. Am. Chem. Soc. 2017, 139, 2565-2568. doi:10.1021/jacs.6b12274.

Bao H L, Ishizuka T, Sakamoto T, Fujimoto K, Uechi T, Kenmochi N, Xu Y: Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy. Nucleic Acids Res. 2017, 45, 5501-5511. doi:10.1093/nar/gkx109.

Ishizuka T, Xu Y: Click chemistry takes a snapshot of DNA-RNA hybrid G-quadruplex in living cells. J. Nat. Sci. 2016, 2, e237.

Ishizuka T, Liu H S, Ito K, Xu Y: Fluorescence imaging of chromosomal DNA using click chemistry. Sci. Rep. 2016, 6, 33217. doi:10.1038/srep33217.

Ishizuka T, Xu Y, Komiyama M: Clipping of telomere from human chromosomes using a chemistry-based artificial restriction DNA cutter. Curr. Protoc. Nucleic Acid Chem. 2015, 61, 6.13.11-16.13.13. doi:10.1002/0471142700.nc0613s61.

Xu Y, Suzuki Y, Ishizuka T, Xiao C D, Liu X, Hayashi T, Komiyama M: Finding a human telomere DNA-RNA hybrid G-quadruplex formed by human telomeric 6-mer RNA and 16-mer DNA using click chemistry: a protective structure for telomere end. Bioorg. Med. Chem. 2014, 22, 4419-4421. doi:10.1016/j.bmc.2014.05.053.

Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M: Conjugation of peptide nucleic acid with a pyrrole/imidazole polyamide to specifically recognize and cleave DNA. Angew. Chem. Int. Ed. 2013, 52, 13681-13684. doi:10.1002/anie.201305489.

Ishizuka T, Xu Y, Komiyama M: A chemistry-based method to detect individual telomere length at a single chromosome terminus. J. Am. Chem. Soc. 2013, 135, 14-17. doi:10.1021/ja308481c.

Xu Y, Ishizuka T, Yang J, Ito K, Katada H, Komiyama M, Hayashi T: Oligonucleotide models of telomeric DNA and RNA form a hybrid G-quadruplex structure as a potential component of telomeres. J. Biol. Chem. 2012, 287, 41787-41796. doi:10.1074/jbc.M112.342030.

Ishizuka T, Kimoto M, Sato A, Hirao I: Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry. Chem. Commun. 2012, 48, 10835-10837. doi:10.1039/c2cc36293g.

Ishizuka T, Yang J, Komiyama M, Xu Y: G-rich sequence-specific recognition and scission of human genome by PNA/DNA hybrid G-quadruplex formation. Angew. Chem. Int. Ed. 2012, 51, 7198-7202. doi:10.1002/anie.201201176.

Xu Y, Ishizuka T, Kimura T, Komiyama M: A U-tetrad stabilizes human telomeric RNA G-quadruplex structure. J. Am. Chem. Soc. 2010, 132, 7231-7233. doi:10.1021/ja909708a.

Ishizuka T, Tedeschi T, Corradini R, Komiyama M, Sforza S, Marchelli R: SSB-assisted duplex invasion of preorganized PNA into double-stranded DNA. ChemBioChem 2009, 10, 2607-2612. doi:10.1002/cbic.200900381.

Xu Y, Ishizuka T, Kurabayashi K, Komiyama M: Consecutive formation of G-quadruplexes in human telomeric-overhang DNA: a protective capping structure for telomere ends. Angew. Chem. Int. Ed. 2009, 48, 7833-7836. doi:10.1002/anie.200903858.

Miyajima Y, Ishizuka T, Yamamoto Y, Sumaoka J, Komiyama M: Origin of high fidelity in target-sequence recognition by PNA-Ce(IV)/EDTA combinations as site-selective DNA cutters. J. Am. Chem. Soc. 2009, 131, 2657-2662. doi:10.1021/ja808290e.

Ishizuka T, Sforza S, Komiyama M: Promotion of strand invasion by utilizing entropically-favored PNA. Nucleic Acids Symp. Ser. 2009, 161-162. doi:10.1093/nass/nrp081.

Ishizuka T, Otani K, Sumaoka J, Komiyama M: Strand invasion of conventional PNA to arbitrary sequence in DNA assisted by single-stranded DNA binding protein. Chem. Commun. 2009, 1225-1227. doi:10.1039/b813975j.

Komiyama M, Aiba Y, Ishizuka T, Sumaoka J: Solid-phase synthesis of pseudo-complementary peptide nucleic acids. Nat. Protoc. 2008, 3, 646-654. doi:10.1038/nprot.2008.6.

Ishizuka T, Komiyama M: Single-strand binding protein enhances invasion of a PNA strand to double-stranded DNA. Nucleic Acids Symp. Ser. 2008, 141-142. doi:10.1093/nass/nrn072.

Miyajima Y, Ishizuka T, Komiyama M: Mismatch recognition in PNA double-duplex invasion. Nucleic Acids Symp. Ser. 2008, 125-126. doi:10.1093/nass/nrn064.

Ishizuka T, Yoshida J, Yamamoto Y, Sumaoka J, Tedeschi T, Corradini R, Sforza S, Komiyama M: Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Res. 2008, 36, 1464-1471. doi:10.1093/nar/gkm1154.

Okada S, Arayama K, Murayama R, Ishizuka T, Hara K, Hirone N, Hata T, Urabe H: Iron-catalyst-switched selective conjugate addition of grignard reagents: α,β,γ,δ-unsaturated amides as versatile templates for asymmetric three-component coupling processes. Angew. Chem. Int. Ed. 2008, 47, 6860-6864. doi:10.1002/anie.200801928.