Chemical Biology of DNA Structure and Functions

• Project/Area Number: 19205023
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Chemistry related to living body
• Research Institution: Kyoto University
• Principal Investigator: SUGIYAMA Hiroshi Kyoto University, 大学院・理学研究科, 教授 (50183843)
• Co-Investigator(Kenkyū-buntansha): BANDO Toshikazu 京都大学, 大学院・理学研究科, 准教授 (20345284) ; SHINOHARA Kenichi 京都大学, 大学院・理学研究科, 助教 (70378561)
• Project Period (FY): 2007 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥42,120,000 (Direct Cost: ¥32,400,000、Indirect Cost: ¥9,720,000); Fiscal Year 2010: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000); Fiscal Year 2009: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000); Fiscal Year 2008: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000); Fiscal Year 2007: ¥11,310,000 (Direct Cost: ¥8,700,000、Indirect Cost: ¥2,610,000)
• Keywords: 核酸 / 蛋白質 / 構造機能解析 / 光反応性 / 修飾塩基 / 5-ハロウラシル / DNA

Research Abstract

Our research group are utilizing photo-irradiation of BrU substituted DNA to investigate the DNA structure and reactivity relationship at a molecular level. These studies demonstrated the detailed relationships between the local DNA structures and the photochemical products of photoinduced hydrogen abstraction by the resulting uracil-5-yl radicals, and proposed that this photochemical method can be used to detect DNA structures. Dynamic DNA conformational change which directly relates to specific gene expression can chemically be understood.

Research Products

• [Journal Article] Chiral Wedge Moleculeinhibits Telomerase Activity. (2010)
  • Author(s): Shinohara, K., Sannohe,Y., Kaieda, S., Tanaka, K., Osuga, H., Xu, Y., Bando, T., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. 132 Pages: 3778-3782
• [Journal Article] Visualization of Dynamic Conformation Switching of the G-Quadruplex in a DNA Nanostructure. (2010)
  • Author(s): Sannohe, Y., Endo, M., Katsuda, Y., Hidaka, K., Sugiyama,H.
  • Journal Title: J.Am.Chem.Soc. 132 Pages: 16311-16313
• [Journal Article] Folding Pathways of Human Telomeric Type-1 and Type-2 G-Quadruplex Structures. (2010)
  • Author(s): Mashimo, T., Yagi, H., Sannohe, Y., Rajendran, A., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. 132 Pages: 14910-14918
• [Journal Article] The Distance between Donor and Acceptor Affects the Proportion of C1' and C2' Oxidation Products of DNA in a BrUcontaining Excess Electron Transfer System. (2010)
  • Author(s): Tashiro, R., Ohtsuki, A., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc 132 Pages: 14361-14363
• [Journal Article] Comparative Analysis of DNA Alkylation by Conjugates between Pyrrole-Imidazole Hairpin Polyamides and Chlorambucil or seco-CBI. (2010)
  • Author(s): Minoshima, M., Bando, T., Shinohara, K., Kashiwazaki, K., Nishijima, S., Sugiyama, H.
  • Journal Title: Bioorg.Med.Chem. 18 Pages: 1236-1243
  • NAID: 120001887644
• [Journal Article] Alkylation of a Human Telomere Sequence by Heterotrimeric Chlorambucil PI Polyamide Conjugates. (2010)
  • Author(s): Kashiwazaki, G., Bando, T., Shinohara, K., Mioshima, M., Kumamoto, H., Nishijima, S., Sugiyama, H.
  • Journal Title: Bioorg.Med.Chem. 18 Pages: 2887-2893
• [Journal Article] Chiral Wedge Molecule inhibits Telomerase Activity. (2010)
  • Author(s): Shinohara, K., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. Volume: 132 Pages: 3778-3782
  • Peer Reviewed
• [Journal Article] Visualization of Dynamic Conformation Switching of the G-Quadruplex in a DNA Nanostructure (2010)
  • Author(s): Sannohe, Y,; Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. Volume: 132 Pages: 16311-16313
  • Peer Reviewed
• [Journal Article] The Distance between Donor and Acceptor Affects the Proportion of C1' and C2' Oxidation Products of DNA in a BrU-containing Excess Electron Transfer System (2010)
  • Author(s): Tashiro, R.; Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. Volume: 132 Pages: 14361-14363
  • Peer Reviewed
• [Journal Article] The Orientation of the Ends of G-Quadruplex Structures Investigated using End-Extended Oligonucleotides. (2009)
  • Author(s): Sannohe, Y., Sato, K., Matsugami, A., Shinohara, K., Mashimo, T., Katahira, M., Sugiyama, H.
  • Journal Title: Bioorg.Med.Chem. 19 Pages: 1870-1875
• [Journal Article] Cooperative Alkylation of Double strand Human Telomere Repeat Sequences by PI Polyamides with 11-Base-pair Recognition Based on a Heterotrimeric Design. (2009)
  • Author(s): Kashiwazaki, G., Bando, T., Shinohara, K., Minoshima, M., Nishijima, S., Sugiyama, H.
  • Journal Title: Bioorg.Med.Chem. 17 Pages: 1393-1397
• [Journal Article] The Orientation of the Ends of G-Quadruplex Structures Investigated using End-Extended Oligonucleotides (2009)
  • Author(s): Sannohe, Y., Sato, K., Matsugami, A., Shinohara, K., Mashimo, T., Katahira, M., Sugiyama, H.
  • Journal Title: Bioorg. Med. Chem. 17 Pages: 1870-1875
  • Peer Reviewed
• [Journal Article] The Orientation of the Ends of G-Quadruplex Structures Investigated using End-Extended oligonucleotides. (2009)
  • Author(s): Sugiyama, H., et al.
  • Journal Title: Bioorg. Med. Chem. 17 Pages: 1870-1875
  • Peer Reviewed
• [Journal Article] Chemical Approaches to DNA Nanotechnology (2009)
  • Author(s): Sugiyama, H., et al.
  • Journal Title: ChemBioChem 10 Pages: 2420-2443
  • Peer Reviewed
• [Journal Article] DNA Prism Structures Constructed by Folding of Multiple Rectangular Arms (2009)
  • Author(s): Sugiyama, H., et al.
  • Journal Title: J.Am.Chem.Soc. 131 Pages: 15570-15571
  • Peer Reviewed
• [Journal Article] Stable Lariat Formation Based on a G-Quadruplex Scaffold. (2008)
  • Author(s): Xu, Y., Sato, H., Sannohe, Y., Shinohara, K., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. 130 Pages: 16470-16471
• [Journal Article] Gquadruplex Structures of Human Telomere DNA examined by Single Molecule FRET and BrG-Substitution. (2008)
  • Author(s): Okamoto, K., Sannohe,Y., Mashimo,T., Sugiyama,H., Terazima, M.
  • Journal Title: Bioorg.Med.Chem. 16 Pages: 6873-6879
• [Journal Article] Requirement of β-Alanine Components in Sequence-Specific DNA Alkylation by Pyrrole-Imidazole Conjugates with Seven-Base Pair Recognition. (2008)
  • Author(s): Bando, T., Minoshima, M., Kashiwazaki, G., Shinohara, K., Sasaki, S., Fujimoto, J., Ohtsuki, A., Murakami, M., Nakazono, S., Sugiyama, H.
  • Journal Title: Bioorg.Med.Chem. 16 Pages: 2286-2291
• [Journal Article] Sequence-Specific Alkylation by Y-Shaped and Tandem Hairpin Pyrrole-Imidazole Polyamides. (2008)
  • Author(s): Sasaki, S., Bando, T., Minoshima, M., Shinohara, K., Sugiyama, H.
  • Journal Title: Chem.Eur.J. 18 Pages: 864-870
• [Journal Article] Terazima, M. G-Quadruplex Structures of Human Telomere DNA Examined by Single Molecule FRET and BrG-Substitution (2008)
  • Author(s): Okamoto, K., Sannohe, Y., Mashimo, T., Sugiyama, H.
  • Journal Title: Bioorg. Med. Chem 16 Pages: 6873-6879
  • Peer Reviewed
• [Journal Article] Stable Lariat Formation Based on a G-quadruplex Scaffold (2008)
  • Author(s): Sugiyama H.
  • Journal Title: J. Am. Chem. Soc. 130 Pages: 16470-16471
  • Peer Reviewed
• [Journal Article] G-Quadruplex Structures of Human Telomere DNA examined by Single Molecule FRET and BrG-Substitution (2008)
  • Author(s): Sugiyama, H., Terazima, M.
  • Journal Title: Bioorganic & Medicinal Chemistry 16 Pages: 6873-6879
  • Peer Reviewed
• [Journal Article] Photoreaction of Iodouracil in DNA duplex ; C-I bond is Cleaved via Two Different Pathways "Homolysis and (2008)
  • Author(s): Sugiyama H.
  • Journal Title: Tetrahedron Letters 49 Pages: 428-431
  • Peer Reviewed
• [Journal Article] Photoreaction at 5'-(G/C)-3' Sequence in Duplex DNA : Efficient Generation of Uracil-5 yl Radical by ChargeTransfer. (2007)
  • Author(s): Watanabe, T., Tashiro, R., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. 129 Pages: 8163-8168
• [Journal Article] DNA Alkylation by Pyrrole-Imidazole seco-CBI Conjugates with an Indole Linker : Sequence-Specific DNA Alkylation with Ten-Base-Pair Recognition throug Hetelodimer Formation. (2007)
  • Author(s): Minoshima, M., Bando, T., Sasaki, S., Shinohara, K., Shimizu, T., Fujimoto, J., Sugiyama, H.
  • Journal Title: J.Am.Chem.Soc. 129 Pages: 5384-5390
• [Journal Article] Meeting Review : First International Meeting on Quadruplex DNA (2007)
  • Author(s): Wilson, W. D., Sugiyama, H.
  • Journal Title: ACS Chem. Biol. 2 Pages: 589-594
  • Peer Reviewed
• [Journal Article] Katahira, M. Structure of a Human Telomeric DNA Sequence Stabilized by 8-Bromoguanosines, as Determined by NMR in a K^+ Solution (2007)
  • Author(s): Matsugami, A., Xu, Y., Noguchi, Y., Sugiyama, H.
  • Journal Title: FEBS Journal 274 Pages: 3545-3556
  • Peer Reviewed
• [Journal Article] Photoreaction at 5'-(G/C) AA^<Br>UT-3' Sequence in Duplex DNA : Efficient Generation of Uracil-5-yl Radical by Charge Transfer (2007)
  • Author(s): Watanabe, T., Tashiro, R., Sugiyama, H.
  • Journal Title: J. Am. Chem. Soc. 129 Pages: 8163-8168
  • Peer Reviewed
• [Journal Article] Chemical Biology that Controls DNA Structure and Function : Lessions in Organic Chemistry from Nature (2007)
  • Author(s): Sugiyama, H.
  • Journal Title: Bull. Chem. Soc. Japan. 80 Pages: 823-841
  • Peer Reviewed
• [Journal Article] I-Motif and Quadruplex-based Device that can Perform Particular Actions to Influence Biological Processes (2007)
  • Author(s): Xu, Y., Hirao, Y., Nishimura, Y., Sugiyama, H.
  • Journal Title: Bioorg. Med. Chem. 15 Pages: 1275-1279
  • Peer Reviewed
• [Journal Article] Photochemical Determination of Different DNA Structures (2007)
  • Author(s): Xu, Y., Tashiro, R., Sugiyama, H.
  • Journal Title: Nature Protocols 2 Pages: 78-87
  • Peer Reviewed
• [Journal Article] Photochemical Determination of Different DNA Structures (2007)
  • Author(s): Sugiyama, H; Xu, Y.
  • Journal Title: Nature Protocols 2 Pages: 78-87
  • Peer Reviewed
• [Journal Article] DNA Alkylation by Pyrroie-Imidazoie seco-CBI Conjugates with an Indole Linker: Sequence-Specific DNA Alkylation with Ten-Base-Pair Recognition throug Hetelodimer Formation (2007)
  • Author(s): Sugiyama H.; Bando, T.
  • Journal Title: J. Am. Chem. Soc. 129 Pages: 5384-5390
  • Peer Reviewed
• [Journal Article] Chemical Biology that Controls DNA structure and Function: Lessons in Organic Chemistry from Nature (2007)
  • Author(s): Sugiyama H.
  • Journal Title: Bull. Chem. Soc. Japan 80 Pages: 823-841
  • NAID: 130004152308
  • Peer Reviewed
• [Presentation] Chemical Biology that Controls DNA Structure and Function (2011)
  • Author(s): 杉山弘
  • Organizer: Fukui Institute for Fundamental Chemistry Kyoto University
  • Place of Presentation: Kyoto
• [Presentation] Photoreactivity of 5-Halopyrimidines in Nucleic Acids (2010)
  • Author(s): Sugiyama, H.
  • Organizer: Radiation Researchi Society 56^<th> Annual Meting
  • Place of Presentation: Maui, Hawaii
  • Year and Date: 2010-09-26
• [Presentation] PI Polyamide as a Artificial Genetic Switch (2010)
  • Author(s): 杉山弘
  • Organizer: 2010 International Chemical Congress of Pacific Basin Societies (PACIFICHEM)
  • Place of Presentation: Hawaii, USA
• [Presentation] Recognition of Specific DNA Sequences by Pyrrole-Imidazole Polyamides (2010)
  • Author(s): T.Bando
  • Organizer: 2010 International Chemical Congress of Pacific Basin Societies (PACIFICHEM)
  • Place of Presentation: Hawaii, USA
• [Presentation] Chemical Biology that Controls DNA Structure and Function (2010)
  • Author(s): 杉山弘
  • Organizer: Asian 3 Roundtable on Nucleic Acids
  • Place of Presentation: Osaka
• [Presentation] DNAナノ構造を利用した四重鎖構造形成の直接的観測 (2010)
  • Author(s): 三戸祐太, 遠藤政幸, 勝田陽介, 日高久美, 杉山弘
  • Organizer: 第4回バイオ関連化学シンポジウム
  • Place of Presentation: 大阪
• [Presentation] ピレン連結DNA中におけるブロモウラシルの光反応の解析 (2010)
  • Author(s): 田代竜, 大朏彰道, 杉山弘
  • Organizer: 第32回日本光医学.発光生物学会
  • Place of Presentation: 東京
• [Presentation] DNAの構造と機能をコントロールするケミカルバイオロジー (2010)
  • Author(s): 杉山弘
  • Organizer: ミニシンポジウム「生命科学の未来について」
  • Place of Presentation: 東京
• [Presentation] 遺伝子発現を制御するPIポリアミド (2009)
  • Author(s): 杉山弘
  • Organizer: 「生体調節のケミカルバイオロジー」シンポジウム
  • Place of Presentation: 前橋市
  • Year and Date: 2009-03-27
• [Presentation] Chemical Biology that controls DNA Structure and Function (2009)
  • Author(s): 杉山弘
  • Organizer: Hecht Symposium
  • Place of Presentation: Virginia,USA
• [Presentation] 光で核酸の構造と物性を観る (2009)
  • Author(s): 杉山弘
  • Organizer: 弟31回日本光医学光生物学会
  • Place of Presentation: 大阪
• [Presentation] PIポリアミドコンジュゲートによる配列特異的DNAアルキル化反応 (2009)
  • Author(s): 板東俊和, 蓑島維文, 篠原・憲一, 杉山弘
  • Organizer: 第12回がん分子標的治療学会学術集会
  • Place of Presentation: 徳島
• [Presentation] DNAの構造と機能をあやつるケミカルバイオロジー (2009)
  • Author(s): 杉山弘
  • Organizer: シンポジウム「革新的量子化学の展望」
  • Place of Presentation: 京都市
• [Presentation] 遺伝子発現を制御するPIポリアミド (2009)
  • Author(s): 杉山弘
  • Organizer: 「生体調節のケミカルバイオロジー」シンポジウム
  • Place of Presentation: 前橋
• [Presentation] 光で核酸の構造と物性を観る (2009)
  • Author(s): 杉山弘
  • Organizer: 弟31回日本光医学光生物学会 特別講演
  • Place of Presentation: 大阪「梅田スカイビル」
• [Presentation] ゲノム情報をあやつる有機化学 (2008)
  • Author(s): 杉山弘
  • Organizer: SORSTジョイントシンポジウム(8)
  • Place of Presentation: コクヨホール(品川)
  • Year and Date: 2008-01-30
• [Presentation] ゲノム情報をあやつる有機化学 (2008)
  • Author(s): 杉山弘
  • Organizer: SORTジョイントシンポジウム「有機合成力」-・そのダイナミズム
  • Place of Presentation: 東京
  • Year and Date: 2008-01-11
• [Presentation] 機能性ピロール-イミダゾールポリアミドによる特異的DNA塩基配列の検出 (2008)
  • Author(s): 板東俊和
  • Organizer: 第18回アンチセンスシンポジウム
  • Place of Presentation: 岐阜
• [Presentation] Chemical biology that controls DNA structure and function (2008)
  • Author(s): 杉山弘
  • Organizer: Nucleic Acid Topics Telluride
  • Place of Presentation: USA
• [Presentation] Photochemistry of 5-halouracil-containing DNA (2007)
  • Author(s): 杉山弘
  • Organizer: 12th Congress of the European Society for Photobiology
  • Place of Presentation: Bath, U.K.
• [Presentation] DNAを分子標的とした薬剤の設計 (2007)
  • Author(s): 杉山弘
  • Organizer: 日本薬学会北陸支部平成19年度特別講演会
  • Place of Presentation: 金沢
• [Presentation] Chiral wedge molecule inhibits telomerase activity (2007)
  • Author(s): 杉山弘
  • Organizer: First International Meeting on Quadruples DNA
  • Place of Presentation: Louisville,KY,USA
• [Presentation] DNAの多様な構造とその反応性 (2007)
  • Author(s): 杉山弘
  • Organizer: 分子系の構造と電子状態-「生物物質科学」研究会
  • Place of Presentation: 東京
• [Presentation] Chemical biology that controls DNA structure and function (2007)
  • Author(s): Sugiyama, H.
  • Organizer: The 5th Internationa Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Tokyo
• [Presentation] Photochemistry of 5-halouracil-containing DNA (2007)
  • Author(s): Sugiyama, H.
  • Organizer: 12th Congress of the European Society for PhotobiologyBath
  • Place of Presentation: U. K.
• [Presentation] Chemistry that Controls DNA Structure and Function (2007)
  • Author(s): Sugiyama, H.
  • Organizer: East China University of Science and Technology
  • Place of Presentation: Shanghai, China
• [Presentation] Chiral wedge molecule inhibits telomerase activity (2007)
  • Author(s): Sugiyama, H.
  • Organizer: First International Meeting on Quadruples DNA
  • Place of Presentation: Louisville, KY, USA
• [Book] 基礎ケミカルバイオロジー(化学同人) (2011)
  • Author(s): 杉山弘, 板東俊和
  • Total Pages: 195
• [Book] 基礎ケミカルバイオロジー (2011)
  • Author(s): 杉山弘、板東俊和
  • Total Pages: 195
  • Publisher: 化学同人
• [Book] ウィーバー分子生物学 第4版(化学同人) (2008)
  • Author(s): R.F.Weaver著, 杉山弘・井上丹・森井孝 監訳
  • Total Pages: 1022
• [Book] ウィーバー分子生物学 第4版 (2008)
  • Author(s): R. F. Weaver, 著, 杉山弘・井上丹・森井孝, 監訳
  • Total Pages: 1022
  • Publisher: 化学同人
• [Book] ウィーバー分子生物学第4版 (2008)
  • Author(s): R. F. Weaver著, 杉山弘監訳
  • Total Pages: 1022
  • Publisher: 化学同人
• [Remarks] ホームページ等
  • URL: http://kuchem.kyoto-u.ac.jp/chembio/
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/chembio/publication/
• [Remarks] 研究業績・論文リスト参照
  • URL: http://kuchem.kyoto-u.ac.jp/chembio/
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/chembio/publication/all.html#2009
• [Remarks] 論文リスト:
  • URL: http://kuchem.kyoto-u.ac.jp/chembio/Chemicalpage/publication2008.htm
• [Remarks] 論文リスト
  • URL: http://kuchem.kyoto-u.ac.jp/chembio/Chemicalpage/publication2007.htm
• [Patent(Industrial Property Rights)] 標的遺伝子特異的ヒストン修飾制御剤 (2008)
  • Inventor(s): 永瀬浩喜, 杉山弘
  • Industrial Property Rights Holder: 学校法人日本大学
  • Industrial Property Number: 2008-172795
  • Filing Date: 2008-07-01
• [Patent(Industrial Property Rights)] インターストランドクロスリンク剤の合成方法 (2008)
  • Inventor(s): 杉山弘
  • Industrial Property Rights Holder: 科学技術振興機構
  • Acquisition Date: 2008-01-11