A structure scientific study about interaction of polyamine and left-handed DNA.

• Project/Area Number: 15590051
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical pharmacy
• Research Institution: Osaka University of Pharmaceutical Sciences
• Principal Investigator: OHISHI Hirofumi Osaka University of Pharmaceutical Sciences, Associate Professor, 薬学部, 講師 (00211095)
• Project Period (FY): 2003 – 2005
• Project Status: Completed (Fiscal Year 2005)
• Budget Amount: ¥3,100,000 (Direct Cost: ¥3,100,000); Fiscal Year 2005: ¥900,000 (Direct Cost: ¥900,000); Fiscal Year 2004: ¥900,000 (Direct Cost: ¥900,000); Fiscal Year 2003: ¥1,300,000 (Direct Cost: ¥1,300,000)
• Keywords: X-ray crystallography / Z-DNA / B-Z junction / B-Z transfer / minor groove / groove binder / B-Z combination crystal / minor groove cavity / DNA / ポリアミン / モノアミン / コンフォメーション / 左巻きDNA / Z-型DNA / B-Z転移 / ポリアミンナノワイアー / 相互作用 / 結晶構造解析 / 三重螺旋 / 転写 / 高塩濃度 / スーパコイル

Research Abstract

I understood that N1-(2-(2-aminoethylamino)ethyl)ethane-1,2-diamine PA (222) and N1-(2-(2-(2-aminoethylamino)ethylamino)ethyl)ethane-1,2-diamine PA (2222) were easy to be connected in a minor groove of Z-DNA very much and stabilized Z-DNA as a minor groove binder very much. Furthermore, I crystallize at 4 degrees Celsius, 10 degrees Celsius, 20 degrees Celsius by the high salt density with these 11 kinds of polyamine and d(CG)3 as a complex and give the salt density at 20 degrees Celsius very much and crystallize. I examine a role for Z-DNA of polyamine, stabilization action in detail by examining these. I perform crystallization of a long chain of Z-DNA which it has been said to that the above-mentioned crystallization vs. eight bases is difficult till now if I understand stabilization mechanism. I think to clarify structure of DNA such as mixture type d(CGCGCGCGCGAATTCGCGCGCGCG)2, d(CGCGCGCGAATTCGCGCGCG)2 and d(CGCGCGAATTCGCGCG)2 of B type DNA and Z type DNA to clarify B-Z transfer m echanism, Z-B transfer mechanism. As for the structure of DNA of B-Z mixture type, crystallization is tried all over the world till now, but there is not a report besides an example of our crystallization. I think about letting we bury a cavity of the big minor groove that it is it in an element of destabilization with this polyamine with the polyamine which is a minor groove binder as DNA and a complex of these long chains and stabilize structure of the whole DNA. Therefore we succeed in X-ray crystallographic analysis of left-handed DNA of a long chain. As for the structure of DNA of B-Z mixture type, crystallization is tried all over the world till now, but there is not a report besides an example of our crystallization. The groove binder polyamine which it is crawled, and I discovered is connected in a minor groove of just Z-DNA and I bury a big minor groove and stabilize structure of the whole DNA. I apply this and perform crystallization of DNA of a long chain, crystallization of B-Z-B junction structure. I think that I bring big development in structured study of DNA if I have already succeeded in crystallization of the DNA which is the longest in the world with this method now, and structure or B-Z-B junction structure of DNA of a long chain are clarified in sequence

Research Products

• [Journal Article] Intermolecular association model of antifungal polyene macrolide via concerted =C-H… O interactions : X-ray crystal structure analysis and ab initio molecular-orbital calculations of chainin. (2006)
  • Author(s): In, Yasuko, Ohishi, Hirofumi, Miyagawa, Hiroo, Kitamura, Kunihiro, Igarashi, Yasuhiro, Ishida, Toshimasa.
  • Journal Title: Bulletin of the Chemical Society of Japan 79 Pages: 126-133
  • NAID: 10017170346
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Synthesis and properties of 2'-0,4'-C-methylene-oxy-methylene bridged nucleic acid. (2006)
  • Author(s): Hari, Yoshiyuki, Obika, Satoshi, Ohnishi, Ryo, Eguchi, Ken, Osaki, Tomohisa, Ohishi, Hirofumi, Imanishi, Takeshi
  • Journal Title: Bioorganic & Medicinal Chemistry 14 Pages: 1029-1038
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Antineoplastic Agents. 551. Isolation and Structures of Bauhiniastatins 1-4 from Bauhinia purpurea. (2006)
  • Author(s): Pettit, George R., Numata, Atsushi, Iwamoto, Chika, Usami, Yoshihide, Yamada, Takeshi, Ohishi, Hirofumi, Cragg, Gordon M
  • Journal Title: Journal of Natural Products 69 Pages: 323-327
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] 計算機科学を用いたDNAの創薬化学 (2006)
  • Author(s): 大石宏文
  • Journal Title: 生産と技術 印刷中
  • NAID: 40007273215
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Synthesis and properties of 2'-O,4'-C-methylene-oxy-methylene bridged nucleic acid. (2006)
  • Author(s): Hari, Yoshiyuki, Obika, Satoshi, Ohnishi, Ryo, Eguchi, Ken, Osaki, Tomohisa, Ohishi, Hirofumi, Imanishi, Takeshi
  • Journal Title: Bioorganic & Medicinal Chemistry 14 Pages: 1029-1038
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] 計算機科学を用いたDNAの創薬化学 (2006)
  • Author(s): 大石宏文
  • Journal Title: 生産と技術 (印刷中)
  • NAID: 40007273215
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Intermolecular association model of antifungal polyene macrolide via concerted =C-H... O interaction : X-ray crystal structure analysis and ab initio molecular-orbital calculations of chainin. (2006)
  • Author(s): In, Yasuko, Ohishi, Hirofumi, Miyagawa, Hiroo, Kitamura, Kunihiro, Igarashi, Yasuhiro, Ishida, Toshimasa.
  • Journal Title: Bulletin of the Chemical Society of Japan 79 Pages: 126-133
  • NAID: 10017170346
• [Journal Article] Synthesis and properties of 2'-O,4'-C-methylene-oxy-methylene bridged nucleic acid. (2006)
  • Author(s): Hari, Yoshiyuki, Obika, Satoshi, Ohnishi, Ryo, Eguchi, Ken, Osaki, Tomohisa, Ohishi, Hirofumi, Imanishi, Takeshi.
  • Journal Title: Bioorganic & Medicinal Chemistry 14 Pages: 1029-1038
• [Journal Article] Antineoplastic Agents. 551. Isolation and Structures of Bauhiniastatins 1-4 from Bauhinia purpurea. (2006)
  • Author(s): Pettit, George R., Numata, Atsushi, Iwamoto, Chika, Usami, Yoshihide, Yamada, Takeshi, Ohishi, Hirofumi, Cragg, Gordon M.
  • Journal Title: Journal of Natural Products 69 Pages: 323-327
• [Journal Article] The development of crystallization and X-ray crystallographyh method of long stem DNA (2005)
  • Author(s): Hirofumi Ohishi, Koji Tsukamoto, Mamiko Odoko, Kazimierz Grzeskowiak, Naoyoshi Maezaki, Nobuo Okabe, Tetsuaki Tanaka, Toshimasa Ishida
  • Journal Title: Nucleic Acids Research Supplement Pages: 67-68
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Stabilization of the left-handed Z-DNA with monoamines and polyamines (2005)
  • Author(s): Koji Tsukamoto, Mamiko Odoko, Hirofumi Ohishi, Yoichi Hiyama, Naoyoshi Maezaki, Nobuo Okabe, Tetsuaki Tanaka, Toshimasa Ishida
  • Journal Title: Nucleic Acids Research Supplement Pages: 251-252
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The development of crystallization and X-ray crystallography method of long stem DNA (2005)
  • Author(s): Hirofumi Ohishi, Koji Tsukamoto, Mamiko Odoko, Kazimierz Rzeskowiak, Naoyoshi Maezaki, Nobuo Okabe, Tetsuaki Tanaka, Toshimasa Ishida
  • Journal Title: Nucleic Acids Research Supplement Pages: 67-68
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Asymmetric Intramolecular Michael Addition of α-Sulfinyl Vinylic Carbanion to Enoates. (2004)
  • Author(s): Maezaki, Naoyoshi, Sawamoto, Hiroaki, Yuyama, Sachiko, Yoshigami, Ryoko, Suzuki, Tomoko, Izumi, Mayuko, Ohishi, Hirofumi, Tanaka, Tetsuaki.
  • Journal Title: Journal of Organic Chemistry 69 Pages: 6335-6340
• [Journal Article] Berberine/γ-cyclodextrin inclusion structure studied by 1H-NMR spectroscopy and molecular-dynamics calculations. (2004)
  • Author(s): Kamigauchi, Miyoko, Kanbara, Narumi, Sugiura, Makiko, Iwasa, Kinuko, Ohishi, Hirofumi, Ishida, Toshimasa.
  • Journal Title: Helvetica Chimica Acta 87 Pages: 264-271
• [Journal Article] The X-ray crystallographic study of the conformation of Z-DNA which bound to polyamine for the minor groove at room temperature and low temperature (2004)
  • Author(s): Hirofumi Ohishi, Toshimasa Ishida, Kenji Suzuki, Kazimierz Grzeskowiak, Mamiko Odoko, Nobuo Okabe
  • Journal Title: Nucleic Acids Research S2 Pages: 256-257
• [Publications] Kamigauchi, Miyoko: "Berberine/γ-cyclodextrin inclusion structure studied by 1H -NMR spectroscopy and molecular-dynamics calculations."Helvetica Chimica Acta. 87(1). 264-271 (2004)
• [Publications] Maezaki, Naoyoshi: "Synthesis of chiral vinylic sulfoxides by Pd -catalyzed asymmet ric sulfinylzincation"Tetrahedron. 59(50). 9895-9906 (2003)
• [Publications] In, Yasuko: "Concerted Interaction between conjugate d double bond CHs and multiplo OHs in polyene macrollde antiblotic chainin : weak : C-H・・・O interactions responsible for Intrinsic molecular assembly"Chemical Communications. 14. 1692-1693 (2003)
• [Publications] Harusawa, Shinya: "Synthesis of (±)-trans- or cis-(5-aminomethyltetrahydrofuranyl)imidazole by Mitsunobu cyclization : Synthetic studies toward novel histamine H3 or H4 -ligands"Chemical & Pharmaceutical Bulletin. 51(3). 325-329 (2003)
• [Publications] Kamigauchi, Miyoko: "Difference between enzymatic and chemical N -methylations of protoberberine -type alkaloid, dependent on the stereoisomer of (-)-N-methyl-7,8,13,13a-tetrahydroberberinium salt"Bulletin of the Chemical Society of Japan. 76(3). 587-593 (2003)