Controlling the higher-order structure of genomic DNA in relation to its genetic activity

• Project/Area Number: 25390038
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Nanobioscience
• Research Institution: Ritsumeikan University
• Principal Investigator: YOSHIKAWA Yuko 立命館大学, 総合科学技術研究機構, 教授 (80291871)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2013: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: 長鎖DNA / 単一分子観察 / 高次構造 / 二重鎖切断 / DNA損傷 / 一分子イメージング / 長鎖DNAの高次構造 / 構造機能相関 / １分子イメージング

Outline of Final Research Achievements

Through the use of single-molecule observation with fluorescence microscopy, we studied the higher-order structural change of a giant DNA molecule. Results obtained are as follows.
(1) The effects of linear, branched and cyclic polyamines on the higher-order structure of giant DNA were examined. These polyamines showed distinct activities, thus highlighting the importance of polyamine backbone structure. (2) The protective effect of ascorbic acid (AsA) against double-strand breaks in DNA was evaluated. Samples were exposed to three different irradiations: visible light, gamma-ray and ultrasound. It was found that AsA had almost no protective effect against the damage caused by ultrasound.

Research Products

• [Journal Article] Highly Concentrated Ethanol Solutions: Good Solvents for DNA as Revealed by Single-Molecule Observation (2016)
  • Author(s): Oda Y., Sadakane K., Yoshikawa Y., Imanaka T., Takiguchi K., Hayashi M., Kenmotsu T. and Yoshikawa K.
  • Journal Title: ChemPhysChem Volume: 17 Issue: 4 Pages: 471-473
  • DOI: 10.1002/cphc.201500988
  • Peer Reviewed / Open Access
• [Journal Article] Structurally Diverse Polyamines: Solid-Phase Synthesis and Interaction with DNA (2015)
  • Author(s): Naoki Umezawa1, Yuhei Horai,. Yuki Imamura, Makoto Kawakubo, Mariko Nakahira, Nobuki Kato, Akira Muramatsu, Yuko Yoshikawa, Kenichi Yoshikawa, Tsunehiko Higuchi
  • Journal Title: ChemBioChem Volume: 16 Issue: 12 Pages: 1811-1819
  • DOI: 10.1002/cbic.201500121
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Protective Effect of Ascorbic Acid against Double-strand Breaks in Giant DNA: Marked Differences among the Damage Induced by Photo-irradiation, Gamma-rays and Ultrasound (2015)
  • Author(s): Yue Ma, Naoki Ogawa, Yuko Yoshikawa, Toshiaki Mori, Tadayuki Imanaka, Yoshiaki Watanabe and Kenichi Yoshikawa
  • Journal Title: Chemical Physics Letters Volume: 638 Pages: 205-209
  • DOI: 10.1016/j.cplett.2015.08.054
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles. (2014)
  • Author(s): Okada K, Hidese R, Fukuda W, Niitsu M, Takao K, Horai Y, Umezawa N, Higuchi T, Oshima T, Yoshikawa Y, Imanaka T, Fujiwara S
  • Journal Title: J.Bacteriol. Volume: 196 Issue: 10 Pages: 1866-1876
  • DOI: 10.1128/jb.01515-14
  • Peer Reviewed
• [Journal Article] Structural change of DNA induced by nucleoid proteins: Growth phase-specific Fis and stationary phase-specific Dps (2013)
  • Author(s): Yuko T. Sato, Shun N. Watanabe, Takahiro Kenmotsu, Masatoshi Ichikawa, Yuko Yoshikawa, Jun Teramoto, Tadayuki Imanaka, Akira Ishihama and Kenichi Yoshikawa
  • Journal Title: Biophysical Journal Volume: 105 Issue: 4 Pages: 1037-1044
  • DOI: 10.1016/j.bpj.2013.07.025
  • Peer Reviewed
• [Journal Article] Chromatin compaction protects genomic DNA from radiation damage. (2013)
  • Author(s): Takata, H., Hanafusa, T., Mori, T., Shimura, M., Iida,Y., Ishikawa, K., Yoshikawa, K., Yoshikawa, Y., Maeshima, K.
  • Journal Title: PLOS ONE Volume: 8 Issue: 10 Pages: e75622-e75622
  • DOI: 10.1371/journal.pone.0075622
  • Peer Reviewed / Open Access
• [Journal Article] Effect of low-frequency ultrasound on double-strand breaks in giant DNA molecules (2013)
  • Author(s): Kenji Yoshida, Naoki Ogawa, Kagawa Yukihiro, Hiraku Tabata, Yoshiaki Watanabe, Takahiro Kenmotsu, Yuko Yoshikawa and Kenichi Yoshikawa
  • Journal Title: Applied Physics Letters Volume: 103 Issue: 6 Pages: 63705-63705
  • DOI: 10.1063/1.4818125
  • Peer Reviewed
• [Presentation] 超好熱菌由来の分岐型ポリアミンが引き起こすゲノムDNAの特異な高次構造変化 (2014)
  • Author(s): 村松 晃, 吉川 祐子, 福田 青郎, 藤原 伸介, 梅澤 直樹, 神戸 俊夫, 今中 忠行, 吉川 研一
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜(神奈川県）
  • Year and Date: 2014-11-27
• [Presentation] Chiral preference of tetravalent polyamines in DNA compaction (2013)
  • Author(s): Y. Yoshikawa1, N. Umezawa, Y. Imamura, T. Kanbe, N. Kato, K. Yoshikawa, T. Imanaka, T. Higuch
  • Organizer: The International Conference on Medical Physics
  • Place of Presentation: Brighton, UK
• [Presentation] Structural changes of DNA induced by antitumor tetrazolato-bridged dinuclear platinum(II) complexes with different alkyl chain lengths
  • Author(s): Y. Yoshikawa, A. Muramatsu, S. Komeda, W. Fukuda, T. Kanbe, K. Yoshikawa, T. Imanaka
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド(兵庫県）
• [Remarks] 立命館大学 生命科学部 生物工学科 環境バイオテクノロジー研究室ホームページ
  • URL: http://www.ritsumei.ac.jp/lifescience/skbiot/imanaka/HPindex.html