Molecular dynamics of DNA strand breaks induced by tritium transmutation

• Project/Area Number: 15K13614
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Physical chemistry
• Research Institution: Tohoku University
• Principal Investigator: Kono Hirohiko 東北大学, 理学研究科, 教授 (70178226)
• Co-Investigator(Kenkyū-buntansha): 木野 康志 東北大学, 理学研究科, 准教授 (00272005)
• Co-Investigator(Renkei-kenkyūsha): AKIYAMA Kimio 東北大学, 多元物質科学研究所, 准教授 (10167851) ; SEKINE Tsutomu 東北大学, 高度教養教育・学生支援機構, 教授 (20154651) ; KANNO Manabu 東北大学, 大学院理学研究科, 助教 (30598090)
• Project Period (FY): 2015-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 密度汎関数強束縛法 / 反応動力学 / 原子分割エネルギー / DNA鎖切断 / 塩基脱離 / ヒドロキシルラジカル / 水素引き抜き / トリチウム壊変 / 電子移動 / 分子分割エネルギー / DFTB法

Outline of Final Research Achievements

We simulated DNA strand breaks induced through β decays of tritium atoms contained in a DNA by using the density-functional based tight-binding method for electronic structure　calculations. The results of simulations were analyzed from the aspect of energy and charge transfer to examine the　mechanisms of elementary processes in DNA strand breaks. Charge rearrangement occurs after β decays of tritium, which results in a neutral radical species. We found that after a β decay of a tritium atom bound to the 3' or 5'-carbon in a sugar, a P-O bond of an adjacent phosphate group breaks. This reaction is mediated through energy and charge transfer between the neighboring sugar and phosphate and terminates with a single strand break; a double strand break, difficult to repair, never takes place as long as two tritium atoms happen to be absorbed to two sugars bridged by the same base pair.

Research Products

• [Journal Article] Ultrafast Dynamics of a Nucleobase Analogue Illuminated by an Ultra-Short Intense X-ray Pulse of SACLA (2017)
  • Author(s): Kiyonobu Nagaya, Hirohiko Kono, Kiyoshi Ueda
  • Journal Title: SPring-8/SACLA Research Frontiers Volume: －
  • Peer Reviewed
• [Journal Article] DNA 鎖切断の反応動力学シミュレーションとAVS/Express を用いた三次元可視化 (2017)
  • Author(s): 菱沼 直樹，及川 啓太，岡田 朝彦，菅野 学，山崎 馨，Wilfredo Credo Chung，齋藤 敦子，河野 裕彦
  • Journal Title: 東北大学サイバーサイエンスセンター 大規模科学計算システム広報（SENAC） Volume: 50
  • NAID: 120006576641
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Ultrafast Dynamics of a Nucleobase Analogue Illuminated by a Short Intense X-ray Free Electron Laser Pulse (2016)
  • Author(s): K. Nagaya, K. Motomura, E. Kukk, H. Fukuzawa, S. Wada, T. Tachibana, Y. Ito, S. Mondal, T. Sakai, K. Matsunami, R. Koga, S. Ohmura, Y. Takahashi, M. Kanno, A. Rudenko, C. Nicolas, X.-J. Liu, Y. Zhang, J. Chen, M. Anand, Y. H. Jiang, D.-E. Kim, K. Tono, M. Yabashi, H. Kono, C. Miron, M. Yao, and K. Ueda
  • Journal Title: Phys. Rev. X Volume: 6 Issue: 2 Pages: 0210351-9
  • DOI: 10.1103/physrevx.6.021035
  • NAID: 120005774654
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Femtosecond Charge and Molecular Dynamics of I-containing organic molecules Induced by Intense X-Ray Free-Electron Laser Pulses (2016)
  • Author(s): K.Nagaya, K.Motomura, E.Kukk, Y.Takahashi, K.Yamazaki, S.Ohmura, H.Fukuzawa, S.Wada, S.Mondal, T.Tachibana, Y.Ito, R.Koga, T.Sakai, K.Matsunami, K.Nakamura, M.Kanno, A.Rudenko, C.Nicolas, X-J.Liu, C.Miron, Y.Zhang, Y.Jiang, J.Chen, M.Anand, D.E.Kim, K.Tono, M.Yabashi, M.Yao, H.Kono, K.Ueda
  • Journal Title: Faraday Discussions Volume: 194 Pages: 537-562
  • DOI: 10.1039/c6fd00085a
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] 短鎖 DNA の鎖切断シミュレーション (2017)
  • Author(s): 岡田 朝彦，及川 啓太，菱沼 直樹，菅野 学，木野 康志，秋山 公男，河野 裕彦
  • Organizer: 日本化学会第97春季年会
  • Place of Presentation: 慶應義塾大学日吉キャンパス,横浜市
• [Presentation] 12塩基対二本鎖DNAの鎖切断過程：溶媒中のカウンターカチオンの効果 (2016)
  • Author(s): 及川 啓太，菱沼 直樹，菅野 学，木野 康志，秋山 公男，河野 裕彦
  • Organizer: 第19回理論化学討論会
  • Place of Presentation: 早稲田大学，東京
  • Year and Date: 2016-05-23
• [Presentation] DNA鎖切断の化学反応動力学シミュレーション (2016)
  • Author(s): 菱沼 直樹, 石母田 和樹, 及川 啓太, 菅野 学, 木野 康志, 秋山 公男, 河野 裕彦
  • Organizer: 第19回理論化学討論会
  • Place of Presentation: 早稲田大学，東京
  • Year and Date: 2016-05-23
• [Presentation] Reaction dynamics simulation of DNA strand breaks:Analysis based on atom resolved energy and charge (2016)
  • Author(s): Hirohiko Kono, Naoki Hishinuma, Keita Oikawa, Kazuki Ishimoda, Manabu Kanno,Yasushi Kino, Kimio Akiyama
  • Organizer: Molecules and Laser Fields
  • Place of Presentation: Orford, Canada
  • Year and Date: 2016-05-04
  • Int'l Joint Research / Invited
• [Presentation] 短鎖モデルDNAの鎖切断過程：化学反応動力学による解析 (2016)
  • Author(s): 及川啓太・菱沼直樹・菅野学・木野康志・秋山公男・河野裕彦
  • Organizer: 日本化学会第96春季年会(2016)
  • Place of Presentation: 同志社大学 京田辺キャンパス，京都
  • Year and Date: 2016-03-24
• [Presentation] Reaction dynamics simulation of DNA strand breaks:Analysis based on atom resolved energy and charge (2016)
  • Author(s): Hirohiko Kono, Naoki Hishinuma, Keita Oikawa, Kazuki Ishimoda, Manabu Kanno, Yasushi Kino, Kimio Akiyama
  • Organizer: Molecules and Laser Fields - An Honorary Andre Bandrauk Symposium
  • Place of Presentation: Orford, Canada
  • Int'l Joint Research / Invited
• [Presentation] Femtosecond Charge and Molecular Dynamics of I-containing organic molecules Induced by Intense X-Ray Free-Electron Laser Pulses (2016)
  • Author(s): K.Ueda, K.Nagaya, K.Motomura, E.Kukk, Y.Takahashi, K.Yamazaki, S.Ohmura, H.Fukuzawa, S.Wada, S.Mondal, T.Tachibana, Y.Ito, R.Koga, T.Sakai, K.Matsunami, K.Nakamura, M.Kanno, A.Rudenko, C.Nicolas, X.-J.Liu, C.Miron, Y.Zhang, Y.Jiang, J.Chen, M.Anand, D.E.Kim, K.Tono, M.Yabashi, M.Yao, H.Kono
  • Organizer: Ultrafast Imaging of Photochemical Dynamics: Faraday Discussion
  • Place of Presentation: Edinburgh, United Kingdom
  • Int'l Joint Research / Invited
• [Presentation] ＤＮＡの鎖切断：反応動力学と電子論 (2016)
  • Author(s): 河野 裕彦
  • Organizer: 化学反応経路探索のニューフロンティア(SRPS2016)
  • Place of Presentation: 京都教育文化センター,京都市
  • Invited
• [Presentation] Simulation of XFEL-induced Coulomb explosion: Momentum correlations and energy distributions of fragment ions of multiply charged 5-iodouracil (2016)
  • Author(s): Y. Takahashi, M. Kanno, N. Hishinuma, K. Nakamura, K. Nagaya, H. Fukuzawa, S. Ohmura, K. Ueda, H. Kono
  • Organizer: 第 32 回化学反応討論会
  • Place of Presentation: 大宮ソニックシティ,さいたま市
  • Int'l Joint Research
• [Presentation] カウンターカチオンが引き起こすDNA鎖切断：化学反応動力学シミュレーション解析 (2016)
  • Author(s): 及川 啓太，菱沼 直樹，菅野 学，木野 康志，秋山 公男，河野 裕彦
  • Organizer: 第10回分子科学討論会
  • Place of Presentation: 神戸ファッションマート,神戸市
• [Presentation] Molecular dynamics simulation of the strand break processes in model DNAs: Analysis of electron and energy transfer (2015)
  • Author(s): Hirohiko Kono, Naoki Hishinuma, Manabu Kanno, Yasushi Kino, and Kimio Akiyama
  • Organizer: The International Chemical Congress of Pacific Basin Societies 2015 (PACIFICHEM 2015)
  • Place of Presentation: Honolulu, Hawaii
  • Year and Date: 2015-12-19
  • Int'l Joint Research / Invited
• [Presentation] ナノ・バイオ分子の動力学：分子ベアリング内部 回転とＤＮＡ鎖切断 (2015)
  • Author(s): 河野裕彦
  • Organizer: 第6回 CMSI 研究会
  • Place of Presentation: 東京大学，東京
  • Year and Date: 2015-12-07
• [Presentation] 化学反応動力学によるDNA鎖切断過程の探索：電荷・振動エネルギー解析 (2015)
  • Author(s): 菱沼直樹・菅野学・木野康志・秋山公男・河野裕彦
  • Organizer: 第5回CSJ化学フェスタ2015
  • Place of Presentation: タワーホール船堀，東京
  • Year and Date: 2015-10-13
• [Presentation] Strand Breaks in Model DNAs Induced by the Charge and Energy Transfer among Nucleotides (2015)
  • Author(s): H. Kono, N. Hishinuma, and M. Kanno
  • Organizer: 6th Japan-Czeckh-Slovakia International Symposium on Theoretical Chemistry
  • Place of Presentation: Smolenice Castle, Slovakia
  • Year and Date: 2015-10-12
  • Int'l Joint Research / Invited
• [Presentation] DNA strand break caused by charge and vibrational energy transfer between nucleotides: Reaction dynamics approach (2015)
  • Author(s): N. Hishinuma, M. Kanno, Y. Kino, K. Akiyama, H. Kono
  • Organizer: 第59回放射化学討論会
  • Place of Presentation: 東北大学，仙台
  • Year and Date: 2015-09-25
• [Presentation] モデル二本鎖DNAにおける鎖切断過程の電荷・エネルギー移動解析 (2015)
  • Author(s): 菱沼直樹，菅野学，木野康志，秋山 公男，河野 裕彦
  • Organizer: 第9回分子科学討論会
  • Place of Presentation: 東京工業大学大岡山キャンパス，東京
  • Year and Date: 2015-09-16
• [Presentation] An Atom Resolved View of Chemical Reactions: Application to Nanocarbons and Model DNAs (2015)
  • Author(s): H. Kono
  • Organizer: 第31回化学反応討論会
  • Place of Presentation: 北海道大学，札幌
  • Year and Date: 2015-06-05
  • Int'l Joint Research / Invited