Development of Novel Chemical Tools, Materials and Devices for Precise and Digital Analysis of Single Cell

2008 Fiscal Year Final Research Report

• Project/Area Number: 17066005
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Kyoto University
• Principal Investigator: HAMACHI Itaru Kyoto University, 大学院・工学研究科, 教授 (90202259)
• Co-Investigator(Kenkyū-buntansha): MIHARA Hisakazu 東京工業大学, 生命理工学研究科, 教授 (30183966) ; SUGIMOTO Naoki 甲南大学, 理工学部, 教授 (60206430) ; YOHDA Masafumi 東京農工大学, 共生科学技術研究部, 教授 (50250105) ; KINBARA Kazushi 東北大学, 多元物質科学研究所, 准教授 (30282578)
• Project Period (FY): 2005 – 2008
• Keywords: バイオセンサー / DNA構造変化 / 分子クラウディング / ペプチドアレイ / 化合物ライブラリー / 分子認識 / 化学センサー / 機能性タンパク質

Research Abstract

細胞機能を制御する生体機能シグナルは、物理シグナルだけでなく分子が担う化学シグナルが重要な位置を占める。具体的には、局所的な電位や温度、pHから金属イオン、アニオン種、有機小分子、糖類や核酸、脂質、ペプチド、タンパク質などが色々な局面で生体機能のデジタル情報を担っている。細胞内外の機能情報を網羅的に解析するために、このような非常に多様で複雑かつ微量な分析対象それぞれをハイスループットに検出・分析できるセンサーやプローブ、種々の材料を、人工小分子から核酸、ペプチド、タンパク質、ナノ構造体を基盤として開発することに成功した。

Research Products

• [Journal Article] Fluorescent BODIPY-Based Zn(II)-Complex as a Molecular Probe for Selective Detection of Neurofibrillary Tangles in the Brains of Alzheimer's Disease Patients. (2009)
  • Author(s): Ojida A, Sakamoto T, Inoue M, Fujishima S, Lippens G, Hamachi I.
  • Journal Title: J. Am. Chem. Soc., (ASAP Article)
  • Peer Reviewed
• [Journal Article] Ligand-directed tosyl chemistry for protein labeling in vivo. (2009)
  • Author(s): Tsukiji S, Miyagawa M, Takaoka Y, Tamura T, Hamachi I.
  • Journal Title: Nature Chemical Biology 5 Pages: 341-343
  • Peer Reviewed
• [Journal Article] MCM-Enzyme-Supramolecular Hydrogel Hybrid as a Fluorescence Sensing Material for Poly-anions of Biological Significance. (2009)
  • Author(s): Wada A, Tamaru S, Ikeda M, Hamachi I.
  • Journal Title: J.Am.Chem.Soc. 131(ASAP Article)
  • Peer Reviewed
• [Journal Article] Poly(amidoamine)dendrimermodified gold surfaces for anomalous reflection of gold (AR) method to detect biomolecular interactions. (2009)
  • Author(s): Syahir A, Tomizaki K -Y, Kajikawa K, Mihara H.
  • Journal Title: Langmuir 25 Pages: 3667-3674
  • Peer Reviewed
• [Journal Article] Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. (2009)
  • Author(s): Miyoshi D, Nakamura K, Tateishi-Karimata H, Ohmichi T, Sugimoto N.
  • Journal Title: J Am Chem Soc 131 Pages: 3522-3531
  • Peer Reviewed
• [Journal Article] Molecular Glues Carrying Multiple Guanidinium Ion Pendants via an Oligoether Spacer : Stabilization of Microtubules against Depolymerization. (2009)
  • Author(s): Okuro K, Kinbara K, Tsumoto, Ishii N, Aida T
  • Journal Title: J. Am. Chem. Soc. 131 Pages: 1626-1627
  • Peer Reviewed
• [Journal Article] A Tubular Biocontainer : Metal Ion-Induced 1D Assembly of a Molecularly Engineered Chaperonin (2009)
  • Author(s): Biswas S, Kinbara K, Oya N, Ishii N, Taguchi H, Aida T
  • Journal Title: J. Am. Chem. Soc. (in press)
  • Peer Reviewed
• [Journal Article] Turn-on Fluorescence Sensing of Nucleside Polyphosphates Using a Xanthene-Based Zn(II) ComplexChemosensor. (2008)
  • Author(s): Ojida A, Takashima I, Kohira T, Nonaka H, Hamachi I.
  • Journal Title: J.Am.Chem.Soc. 130 Pages: 12095-12101
  • Peer Reviewed
• [Journal Article] Regulation of telomerase activity by the thermodynamic stability of a DNA x RNA hybrid. (2008)
  • Author(s): Yu H.-Q, Zhang D.-H, Gu X.-B, Miyoshi D, Sugimoto N.
  • Journal Title: Angew Chem Int Ed 47 Pages: 9034-9038
  • Peer Reviewed
• [Journal Article] Structure and molecular dynamics simulation of archaeal prefoldin : the molecular mechanism for binding and recognition of nonnative substrate proteins. (2008)
  • Author(s): Ohtaki A, Kida H, Miyata Y, Ide N, Yonezawa A, Arakawa T, Iizuka R, Noguchi K, Kita A, Odaka M, Miki K, Yohda M.
  • Journal Title: J Mol Biol 376 Pages: 1130-1141
  • Peer Reviewed
• [Journal Article] Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1. (2008)
  • Author(s): Kida H, Sugano Y, Iizuka R, Fujihashi M, Yohda M, Miki, K.
  • Journal Title: J Mol Biol 383 Pages: 465-474
  • Peer Reviewed
• [Journal Article] Functional characterization of recombinant prefoldin complexes from a hyperthermophilic archaeon, Thermococcus sp. strain KS-1. (2008)
  • Author(s): Iizuka R, Sugano Y, Ide N, Ohtaki A, Yoshida T, Fujiwara S, Imanaka T, Yohda M.
  • Journal Title: J Mol Biol 377 Pages: 972-983
  • Peer Reviewed
• [Journal Article] Toward Long-Distance Mechanical Communication : Studies on a Ternary Complex Interconnected by a Bridging Rotary Module. (2008)
  • Author(s): Kai H, Nara S, Kinbara K, Aida T
  • Journal Title: J. Am. Chem. Soc. 130 Pages: 6725-6727
  • Peer Reviewed
• [Journal Article] Phosphate-Mediated Molecular Memory Driven by Two Different Protein Kinases as Information Input Elements. (2007)
  • Author(s): Tomizaki K -Y, Mihara H.
  • Journal Title: J. Am. Chem. Soc. 129 Pages: 8345-8352
  • Peer Reviewed
• [Journal Article] Localization of prefoldin interaction sites in the hyperthermophilic group II chaperonin and correlations between binding rate and protein transfer rate. (2007)
  • Author(s): Zako T, Murase Y, Iizuka R, Yoshida T, Kanzaki T, Ide N, Maeda M, Funatsu T, Yohda M.
  • Journal Title: J Mol Biol 364 Pages: 110-120
  • Peer Reviewed
• [Journal Article] (2007)
  • Author(s): Horiuchi H, Iwamia N, Tachibana F, Ohtaki A, Iizuka R, Zako T, Oda M, Yohda M, Tani T. Yohda M, Tani T.
  • Journal Title: J Luminescence 127 Pages: 192-197
  • Peer Reviewed
• [Journal Article] A Novel Peptide Microarray for Protein Detection and Analysis Utilizing a Dry Peptide Array System. (2006)
  • Author(s): Usui K, Tomizaki K -Y, Ohyama T, Nokihara K, Mihara H.
  • Journal Title: Mol. BioSyst. 2 Pages: 113-121
  • Peer Reviewed
• [Journal Article] Protein-fingerprint data mining of a designed a-helical peptide array (2006)
  • Author(s): Usui K, Tomizaki K -Y, Mihara H.
  • Journal Title: Mol. BioSyst. 2 Pages: 417-420
  • Peer Reviewed
• [Journal Article] DNA Logic Gates Based on Structural Polymorphism of Telomere DNA Molecules Responding to Chemical Input Signals. (2006)
  • Author(s): Miyoshi D, Inoue M, Sugimoto N.
  • Journal Title: Angew Chem Int Ed 45 Pages: 7716-7719
  • Peer Reviewed
• [Journal Article] Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. (2006)
  • Author(s): Miyoshi D, Karimata H, Sugimoto N.
  • Journal Title: J Am Chem Soc 128 Pages: 7957-7963
  • Peer Reviewed
• [Journal Article] Mechanical Twisting of a Guest by a Photoresponsive Host. (2006)
  • Author(s): Muraoka T, Kinbara K, Aida T
  • Journal Title: Nature 440 Pages: 512-515
  • Peer Reviewed
• [Journal Article] Semibiological Molecular Machine with an Implemented "AND" Logic Gate for Regulation of Protein Folding. (2006)
  • Author(s): Muramatsu S, Kinbara K, Taguchi, H, Ishii N, Aida T
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 3764-3769
  • Peer Reviewed
• [Journal Article] Double-Modification of Lectin Using Two Distinct Chemistries for Fluorescent Ratiometric Sensing and Imaging Saccharides in Test Tube or in Cell. (2005)
  • Author(s): Nakata E, Kosh Y, Koga E, Katayama Y, Hamachi I.
  • Journal Title: J.Am.Chem.Soc. 127(38) Pages: 13253-13261
  • Peer Reviewed
• [Journal Article] Protein-Detecting Microarrays : Current Accomplishments and Requirements. (2005)
  • Author(s): Tomizaki K -Y, Usui K, Mihara H.
  • Journal Title: ChemBioChem 6 Pages: 782-799
  • Peer Reviewed
• [Journal Article] Site-selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside. (2005)
  • Author(s): Nakano S, Uotani Y, Uenishi K, Fujii M, Sugimoto N.
  • Journal Title: J Am Chem Soc 127 Pages: 4350-4353
  • Peer Reviewed