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Research on molecular structure and repair of complex DNA damage

Research Project

Project/Area Number 22310038
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Risk sciences of radiation/Chemicals
Research InstitutionJapan Atomic Energy Agency

Principal Investigator

SHIKAZONO Naoya  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 量子ビーム応用研究センター, 研究主幹 (10354961)

Co-Investigator(Kenkyū-buntansha) AKAMATSU Ken  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 量子ビーム応用研究センター, 研究副主幹 (70360401)
HIGUCHI Mariko  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 原子力基礎工学研究センター, 任期付研究員 (90370460)
MURAKAMI Hiroshi  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 量子ビーム応用研究センター, 研究職 (50291092)
Co-Investigator(Renkei-kenkyūsha) YOKOYA Akinari  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 先端基礎研究センター, 研究主席 (10354987)
FUJII Kentaro  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 先端基礎研究センター, 研究副主幹 (00360404)
URUSHIBARA Ayumi  独立行政法人日本原子力研究開発機構, 原子力科学研究部門 先端基礎研究センター, 任期付研究員 (80391275)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2014: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2013: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2012: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2011: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2010: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Keywords複雑損傷 / 分子構造 / 分子動力学 / 蛍光共鳴エネルギー移動 / 突然変異 / 難修復性 / FRET / DNA分子構造 / 分子動力学計算 / テラヘルツ分光 / 生物影響
Outline of Final Research Achievements

It is proposed that ionizing radiation induces complex damage, which is a type of damage that multiple DNA lesions are localized within 1-2 helical turns of DNA. To detect complex damage, we developed a new method based on fluorescence resonance energy transfer, and assessed the structure of the complex damage comprised of abasic sites. We also analyzed the binding potential of repair enzymes with molecular dynamics simulations as well as the mutagenic potentiail of various types of complex damage, in order to understand the underlying mechanism(s) of the retardation of repair of the complex damage.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (48 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (14 results) (of which Peer Reviewed: 14 results,  Open Access: 1 results,  Acknowledgement Compliant: 2 results) Presentation (32 results) (of which Invited: 1 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Chemical repair activity of free radical scavenger, edaravone: Reduction reactions with dGMP hydroxyl radical adducts and suppression of base lesions and AP sites on irradiated plasmid DNA.2015

    • Author(s)
      Hata K, Urushibara A, Yamashita S, Lin M, Muroya Y, Shikazono N, Yokoya A, Fu H, Katsumura Y
    • Journal Title

      Journal of Radiation Research

      Volume: 56 Issue: 1 Pages: 59-66

    • DOI

      10.1093/jrr/rru079

    • NAID

      120006502225

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Localization estimation of ionizing radiation-induced abasic sites in DNA in the solid state using fluorescence resonance energy transfer.2015

    • Author(s)
      Akamatsu K, Shikazono N, Saito T
    • Journal Title

      Radiation Research

      Volume: 183 Issue: 1 Pages: 105-113

    • DOI

      10.1667/rr13780.1

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Terahertz dynamics of water before and after water shedding from reverse micelles.2015

    • Author(s)
      Murakami H
    • Journal Title

      Journal of Molecular Liquids

      Volume: 未定 Pages: 37-43

    • DOI

      10.1016/j.molliq.2015.03.015

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Towards Laser Driven Hadron Cancer Radiotherapy: A Review of Progress.2014

    • Author(s)
      Ledingham KWD, Bolton PR, Shikazono N, Ma CM
    • Journal Title

      Applied Sciences

      Volume: 4 Issue: 3 Pages: 402-443

    • DOI

      10.3390/app4030402

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Significance of DNA Polymerase I in in vivo processing of clustered DNA damage2013

    • Author(s)
      Shikazono, N., Akamatsu, K., Takahashi, M., Noguchi, M., Urushibara, A., O’Neill, P. and Yokoya, A.
    • Journal Title

      Mutatation Research

      Volume: 749 Issue: 1-2 Pages: 9-15

    • DOI

      10.1016/j.mrfmmm.2013.07.010

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chemical repair of base lesions, AP-sites, and strand breaks on plasmid DNA in dilute aqueous solution by ascorbic acid2013

    • Author(s)
      Hata K, Urushibara A, Yamashita S, Shikazono N, Yokoya A, Katsumura Y
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 434 Issue: 2 Pages: 341-345

    • DOI

      10.1016/j.bbrc.2013.03.075

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nanometer-scale water droplet free from the constraint of reverse micelles at low temperatures2013

    • Author(s)
      Murakami H, Sada T, Yamada M, Harada M
    • Journal Title

      Physical Review E

      Volume: 88 Issue: 5 Pages: 52304-52304

    • DOI

      10.1103/physreve.88.052304

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The mutagenic potential of 8-oxoG/single strand break-containing clusters depends on their relative positions2012

    • Author(s)
      Miho Noguchi
    • Journal Title

      Mutation Research

      Volume: 732 Issue: 1-2 Pages: 34-42

    • DOI

      10.1016/j.mrfmmm.2011.12.009

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Yield of single- and double-strand breaks and nucleobase lesions in fully hydrated plasmid DNA films irradiated with high-LET charged particles2012

    • Author(s)
      Ushigome Takeshi
    • Journal Title

      Radiation Research

      Volume: (In press) Issue: 5 Pages: 914-627

    • DOI

      10.1667/rr2701.1

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A methodology for estimating localization of apurinic/apyrimidinic sites in DNA using fluorescence resonance energy transfer.2012

    • Author(s)
      Akamatsu, K.
    • Journal Title

      Analytical Biochemistry

      Volume: 433 Issue: 2 Pages: 171-180

    • DOI

      10.1016/j.ab.2012.10.004

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A possible overestimation of the effect of acetylation on lysine residues in KQ mutant analysis2012

    • Author(s)
      Hirofumi Fujimoto, Mariko Higuchi, Manabu Koike, Hirotaka Ode, Miroslav Pinak, Juraj Kotulic Bunta, Toshiyuki Nemoto, Takashi Sakudoh, Naoko Honda, Hideaki Maekawa, Kimiaki Saito, Kozo Tsuchida
    • Journal Title

      J. Comput. Chem

      Volume: 33 Issue: 3 Pages: 239-246

    • DOI

      10.1002/jcc.21956

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Terahertz absorption spectroscopy of protein-containing reverse micellar solution2012

    • Author(s)
      Murakami H, Toyota Y, Nishi T, Nashima S
    • Journal Title

      Chemical Physics Letters

      Volume: 519-520 Pages: 105-109

    • DOI

      10.1016/j.cplett.2011.11.029

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A model for analysis of the yield and the level of clustering of radiation-induced DNA-strand breaks in hydrated plasmids2011

    • Author(s)
      Shikazono N, Yokoya A, Urushibara A., Noguchi M, Fujii K
    • Journal Title

      Radiation Protection Dosimetry

      Volume: 143 Pages: 181-185

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enhanced resolution of molecular recognition to distinguish structure similar molecules by different conformational responses of a protein upon ligand binding2011

    • Author(s)
      Higuchi M, Fujii J, Yonetani Y, Kitao A, Go N
    • Journal Title

      Journal of Structural Biology

      Volume: 173 Pages: 20-28

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Water and biomolecules confined in nanometer-scale reverse micelles studied using spectroscopic techniques in wide frequency and temperature ranges2015

    • Author(s)
      Murakami, H
    • Organizer
      Energy, Materials,Nanotechnology Meeting on Droplets
    • Place of Presentation
      プーケット(タイ)
    • Year and Date
      2015-05-08 – 2015-05-11
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] クラスターDNA損傷による変異誘発におけるDNAポリメラーゼの関与2014

    • Author(s)
      鹿園直哉、赤松憲
    • Organizer
      第57回日本放射線影響学会
    • Place of Presentation
      かごしま県民交流センター(鹿児島県鹿児島市)
    • Year and Date
      2014-10-01 – 2014-10-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] FRETを用いた放射線DNA損傷の局在性評価2014

    • Author(s)
      赤松憲、鹿園直哉
    • Organizer
      第57回日本放射線影響学会
    • Place of Presentation
      かごしま県民交流センター(鹿児島県鹿児島市)
    • Year and Date
      2014-10-01 – 2014-10-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] Slowing-down of Terahertz water motions and water shedding from reverse micelles2014

    • Author(s)
      Murakami, H
    • Organizer
      Open Questions on the Origin of Life 2014
    • Place of Presentation
      International Institute for Advanced Studies(Kizugawashi, Kyoto)
    • Year and Date
      2014-09-06 – 2014-09-08
    • Related Report
      2014 Annual Research Report
  • [Presentation] Terahertz dynamics of water confined in reverse micelles2014

    • Author(s)
      Murakami, H
    • Organizer
      20th International Symposium on Surfactants in Solution
    • Place of Presentation
      University of Coimbra(Portugal)
    • Year and Date
      2014-06-22 – 2014-06-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Construction of plasmid containing clustered DNA damage to analyze its in vivo repair2013

    • Author(s)
      Takahashi M, Shikazono N
    • Organizer
      Heavy ion in therapy and space radiation symposium 2013
    • Place of Presentation
      京葉銀行文化プラザ(千葉県千葉市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] DNA脱塩基部位の局在性評価法の開発と放射線照射DNAへの適用2013

    • Author(s)
      赤松憲、鹿園直哉
    • Organizer
      第51回日本生物物理学会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] DNA鎖に生じた損傷の分布様式を調べるための実験と理論2013

    • Author(s)
      赤松憲、鹿園直哉
    • Organizer
      第23回日本数理生物学会
    • Place of Presentation
      静岡大学浜松キャンパス(静岡県静岡市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 逆ミセル拘束水のテラヘルツダイナミクスの温度変化の異常性2013

    • Author(s)
      村上洋
    • Organizer
      日本物理学会 2013年秋期大会
    • Place of Presentation
      徳島大学常三島キャンパス(徳島県徳島市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Terahertz spectroscopy of nanometer water droplet in a wide temperature range2013

    • Author(s)
      Murakami H
    • Organizer
      7th International Discussion Meeting on Relaxation in Complex Systems
    • Place of Presentation
      Universitat Politecnica de Catalunya(Spain Barcelona)
    • Related Report
      2013 Annual Research Report
  • [Presentation] The repair of a clustered damage site is influenced by the surrounding DNA lesions2011

    • Author(s)
      高橋桃子、鹿園直哉
    • Organizer
      第34回日本分子生物学会
    • Place of Presentation
      横浜(日本)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] Inhibition of binding of Fpg to multiple damaged DNA2011

    • Author(s)
      樋口真理子、M.Pinak
    • Organizer
      第34回日本分子生物学会
    • Place of Presentation
      横浜(日本)
    • Year and Date
      2011-12-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] FRETを利用した放射線誘発DNA損傷の損傷位置ばらつき評価法の開発2011

    • Author(s)
      赤松憲、鹿園直哉
    • Organizer
      第54回日本放射線影響学会
    • Place of Presentation
      京都(日本)
    • Year and Date
      2011-11-18
    • Related Report
      2011 Annual Research Report
  • [Presentation] クラスターDNA損傷の修復におけるPolIの役割2011

    • Author(s)
      鹿園直哉、野口実穂、漆原あゆみ、横谷明徳
    • Organizer
      第54回日本放射線影響学会
    • Place of Presentation
      京都(日本)
    • Year and Date
      2011-11-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] 修復酵素hOgg1と二つの損傷が近くにあるDNAの結合に関する研究2011

    • Author(s)
      樋口真理子、M.Pinak
    • Organizer
      第49回日本生物物理学会
    • Place of Presentation
      姫路(日本)
    • Year and Date
      2011-09-18
    • Related Report
      2011 Annual Research Report
  • [Presentation] ナノ拘束空間中水の揺らぎの温度変化2011

    • Author(s)
      村上洋、佐田幸子、山田真紗子、原田雅史
    • Organizer
      第49回日本生物物理学会
    • Place of Presentation
      姫路(日本)
    • Year and Date
      2011-09-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] Significance of the repair synthesis in determining the biological consequences of clustered DNA damage2011

    • Author(s)
      Shikazono N, Noguchi M, Urushibara A, O'Neill P, Yokoya A
    • Organizer
      14^<th> International Congress of Radiation Research
    • Place of Presentation
      ワルシャワ(ポーランド)
    • Year and Date
      2011-08-30
    • Related Report
      2011 Annual Research Report
  • [Presentation] Ion beam-induced DNA damage and its biological effects2010

    • Author(s)
      Shikazono N
    • Organizer
      第20回日本MRS学術シンポジウム
    • Place of Presentation
      横浜(日本)
    • Year and Date
      2010-12-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] 蛍光消光現象を活用した放射線誘発DNA損傷の損傷位置ばらつき評価法の開発2010

    • Author(s)
      赤松憲、鹿園直哉
    • Organizer
      第53回日本放射線影響学会
    • Place of Presentation
      京都(日本)
    • Year and Date
      2010-10-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Processing and biological consequences of clustered DNA damage containing a single strand break and an AP site2010

    • Author(s)
      Shikazono N, Noguchi M, Urushibara A, O'Neill P, Yokoya A
    • Organizer
      56^<th> Annual Meeting of the Radiation Research Society
    • Place of Presentation
      ハワイ(米国)
    • Year and Date
      2010-09-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] DNA鎖上に生じた損傷位置のばらつき評価法の開発とその放射線照射DNAへの適用2010

    • Author(s)
      赤松憲、鹿園直哉
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      仙台(日本)
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] クラスターDNA損傷が修復酵素hOGG1の結合に関する分子動力学シミュレーション2010

    • Author(s)
      樋口真理子, Pinak M.
    • Organizer
      第48回日本生物物理学会年会
    • Place of Presentation
      仙台(日本)
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] クラスターDNA損傷が修復酵素hOGG1の基質認識に及ぼす影響2010

    • Author(s)
      樋口真理子, Pinak M.
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌(日本)
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] Molecular dynamics simulation of cluster damaged DNA and hOGG12010

    • Author(s)
      Higuchi M, Pinak M
    • Organizer
      11th International Workshop on Radiation Damage to DNA
    • Place of Presentation
      アトランタ(米国)
    • Year and Date
      2010-05-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Significance of strand break repair in determining the mutagenic potential of clustered DNA damage.

    • Author(s)
      Shikazono, N.
    • Organizer
      The 12th International Workshop on Radiation Damage to DNA
    • Place of Presentation
      Courtyard Prague Flora, Prague, Czech Republic
    • Related Report
      2012 Annual Research Report
  • [Presentation] Development of a methodology for estimating the degree of localization of AP-sites on DNA with an application of Forster resonance energy transfer.

    • Author(s)
      Akamatsu, K.
    • Organizer
      The 12th International Workshop on Radiation Damage to DNA
    • Place of Presentation
      Courtyard Prague Flora, Prague, Czech Republic
    • Related Report
      2012 Annual Research Report
  • [Presentation] クラスターDNA損傷とその周辺のDNA損傷の突然変異の発生頻度に関する解析

    • Author(s)
      高橋桃子
    • Organizer
      日本放射線影響学会 第55回大会
    • Place of Presentation
      東北大学(宮城県仙台市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] 脱塩基部位の局在性評価法の開発と放射線照射DNAへの適用

    • Author(s)
      赤松憲
    • Organizer
      日本放射線影響学会 第55回大会
    • Place of Presentation
      東北大学(宮城県仙台市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] クラスターDNA損傷を含むプラスミドの合成法の開発

    • Author(s)
      高橋桃子
    • Organizer
      第35回 日本分子生物学会
    • Place of Presentation
      福岡国際会議場(福岡県福岡市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] ナノ拘束水のテラヘルツ分光の温度変化測定

    • Author(s)
      村上洋
    • Organizer
      日本物理学会 第68回大会
    • Place of Presentation
      広島大学(広島県東広島市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Terahertz absorption spectra of nanometer-confined water at low temperatures

    • Author(s)
      Murakami, H.
    • Organizer
      The 37th International Conference on Infrared, Millimeter and Terahertz Waves
    • Place of Presentation
      University of Wollongong, Wollongong, Australia
    • Related Report
      2012 Annual Research Report
  • [Presentation] Ku binds to complex damaged double strand break DNA

    • Author(s)
      Higuchi, M.
    • Organizer
      第12回日本蛋白質科学会
    • Place of Presentation
      名古屋国際会議場(愛知県名古屋市)
    • Related Report
      2012 Annual Research Report
  • [Book] Proteins and water confined in nanometer-scale reverse micelles studied by near infrared, terahertz, and ultrafast visible spectroscopies. In Advances in Protein Chemistry and Structural Biology vol.932013

    • Author(s)
      Murakami H
    • Total Pages
      28
    • Publisher
      Elsevier Oxford
    • Related Report
      2013 Annual Research Report
  • [Remarks] 医療・バイオ応用量子ビーム技術解析ユニット/照射細胞解析研究グループ

    • URL

      http://www.taka.jaea.go.jp/rab_div/dna/index_j.html

    • Related Report
      2012 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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