Exciton-controlled imaging for effective spatiotemporal analysis of nucleic acid functions

• Project/Area Number: 20350083
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Chemistry related to living body
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: OKAMOTO Akimitsu The Institute of Physical and Chemical Research, 岡本独立主幹研究ユニット, ユニットリーダー(独立主幹研究員) (60314233)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000); Fiscal Year 2010: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2009: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000); Fiscal Year 2008: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
• Keywords: 励起子相互作用 / 蛍光イメージング / 蛍光色素 / DNA / 核酸 / 蛍光 / 色素 / イメージング

Research Abstract

A series of near-infrared fluorescent probes was designed based on the concept of emission control caused by interdye excitonic interaction. The fluorescent probes showed very weak emission in the unhybridized state, whereas they emitted near-infrared fluorescence after hybridization with the complementary nucleic acid. The hybridization-dependent switching of fluorescence emission made it possible to monitor mRNA in a human cell in the range of near-infrared wavelengths.

Research Products

• [Journal Article] ECHO-LNA Conjugates : Hybridization-sensitive Fluorescence and its Application to Fluorescent Detection of Various RNA Strands (2010)
  • Author(s): Sugizaki K.; Okamoto A.
  • Journal Title: Bioconjugate Chem. 21(12) Pages: 2276-2281
  • Peer Reviewed
• [Journal Article] Sets of RNA Repeated Tags and Hybridization-Sensitive Fluorescent Probes for Distinct Images of RNA in a Living Cell (2010)
  • Author(s): Kubota T.; Ikeda S.; Yanagisawa H.Yuki M.; Okamoto A
  • Journal Title: PLoS ONE 5(9)
  • Peer Reviewed
• [Journal Article] Excitonic interaction : Another photophysical process for fluorescence-controlled nucleic acid sensing (2010)
  • Author(s): Okamoto A
  • Journal Title: Chem.Rec. 10(3) Pages: 188-196
  • Peer Reviewed
• [Journal Article] A Probe Containing Two Base-discriminating Fluorescent (BDF) Nucleosides for SNP Typing (2010)
  • Author(s): Yoshida Y.; Niwa K.; Yamada K.; Tokeshi M.; Baba Y.; Saito Y.Okamoto A.; Saito I
  • Journal Title: Chem. Lett. 39(2) Pages: 116-117
  • NAID: 10027177147
  • Peer Reviewed
• [Journal Article] Exciton-Primer Mediated SNP Detection in SmartAmp2 Reactions (2010)
  • Author(s): Lezhava A.; Ishidao T.; Ishizu Y.; Naito K.; Hanami T.; Katayama A.; Kogo Y.; Soma T.; Ikeda S.; Murakami K.; Nogawa C.; Itch M.; Mitani Y.; Harbers M.; Okamoto A.; Hayashizaki Y
  • Journal Title: Hum.Mutat. 31(2) Pages: 208-217
  • Peer Reviewed
• [Journal Article] Hybridization-sensitive fluorescent DNA probe with self-avoidance ability (2010)
  • Author(s): Ikeda S.; Kubota T.; Yuki M.; Yanagisawa H.; Tsuruma S.; Okamoto A
  • Journal Title: Org.Biomol.Chem. 8(3) Pages: 546-551
  • Peer Reviewed
• [Journal Article] Hybridization-sensitive fluorescent DNA probe with self-avoidance ability (2010)
  • Author(s): Ikeda, S.
  • Journal Title: Org.Biomol.Chem. Volume: 8(3) Pages: 546-551
  • Peer Reviewed
• [Journal Article] Exciton-Primer Mediated SNP Detection in SmartAmp2 Reactions (2010)
  • Author(s): Lezhava, A.
  • Journal Title: Hum.Mutat. Volume: 31(2) Pages: 208-217
  • Peer Reviewed
• [Journal Article] A Probe Containing Two Base-discriminating Fluorescent (BDF) Nucleosides for SNP Typing (2010)
  • Author(s): Yoshida, Y.
  • Journal Title: Chem.Lett. Volume: 39(2) Pages: 116-117
  • Peer Reviewed
• [Journal Article] Excitonic interaction : Another photophysical process for fluorescence-controlled nucleic acid sensing (2010)
  • Author(s): Okamoto, A.
  • Journal Title: Chem.Rec. Volume: 10(3) Pages: 188-196
  • Peer Reviewed
• [Journal Article] Sets of RNA Repeated Tags and Hybridization-Sensitive Fluorescent Probes for Distinct Images of RNA in a Living Cell (2010)
  • Author(s): Kubota, T.
  • Journal Title: PLoS ONE Volume: 5(9)
  • Peer Reviewed
• [Journal Article] Hybridization-sensitive Fluorescence and its Application to Fluorescent Detection of Various RNA Strands (2010)
  • Author(s): Sugizaki, K.
  • Journal Title: Bioconjugate Chem. Volume: 21(12) Pages: 2276-2281
  • Peer Reviewed
• [Journal Article] Hybridization-sensitive fluorescent DNA probe with self-avoidance ability (2010)
  • Author(s): Ikeda, S.
  • Journal Title: Org.Biomol.Chem. 8(3) Pages: 546-551
  • Peer Reviewed
• [Journal Article] Doubly thiazole orange-labeled cytidine for functional expansion of a hybridization-sensitive probe (2009)
  • Author(s): Ikeda S.; Yuki M.; Yanagisawa H.; Okamoto A
  • Journal Title: Tetrahedron Lett. 50(51) Pages: 7191-7195
  • Peer Reviewed
• [Journal Article] Exciton-Controlled Hybridization- Sensitive Fluorescent Probes : Multicolor Detection of Nucleic Acids (2009)
  • Author(s): Ikeda S.; Kubota T.; Yuki M.; Okamoto A
  • Journal Title: Angew.Chem., Int.Ed. 48(35) Pages: 6480-6484
  • Peer Reviewed
• [Journal Article] Hybridization-Sensitive Fluorescent Probe for Long-Time Monitoring of Intracellular RNA (2009)
  • Author(s): Kubota T.; Ikeda S.; Yanagisawa H.; Yuki M.; Okamoto A
  • Journal Title: Bioconjuga to Chem. 20(6) Pages: 1256-1261
  • Peer Reviewed
• [Journal Article] Photoresponsive Tandem Zinc Finger Peptide (2009)
  • Author(s): Nomura A.; Okamoto A
  • Journal Title: Chem.Commun. Pages: 1906-1908
  • Peer Reviewed
• [Journal Article] Osmium Complexation of Mismatched DNA : Effect of the Bases Adjacent to Mismatched 5-Methylcytosine (2009)
  • Author(s): Nomura A.; Tainaka K.; Okamoto A
  • Journal Title: Bioconjugate Chem. 20(3) Pages: 603-607
  • Peer Reviewed
• [Journal Article] Doubly Thiazole Orange-Labeled DNA for Live Cell RNA Imaging (2009)
  • Author(s): Kubota T.; Ikeda S.; Okamoto A
  • Journal Title: Bull.Chem.Soc.Jpn. 82(1) Pages: 110-117
  • NAID: 10023987643
  • Peer Reviewed
• [Journal Article] Chemical approach toward efficient DNA methylation analysis (2009)
  • Author(s): Okamoto A
  • Journal Title: Org.Biomol.Chem. 7(1) Pages: 21-26
  • Peer Reviewed
• [Journal Article] Chemical approach toward efficient DNA methylation analysis (2009)
  • Author(s): Okamoto, A.
  • Journal Title: Org.Biomol.Chem. 7(1) Pages: 21-26
  • Peer Reviewed
• [Journal Article] Exciton-Controlled Hybridization-Sensitive Fluorescent Probes : Multicolor Detection of Nucleic Acids (2009)
  • Author(s): Ikeda, S.
  • Journal Title: Angew.Chem.,Int.Ed. 48(35) Pages: 6480-6484
  • Peer Reviewed
• [Journal Article] Heterogeneity of osmium oxidation efficiency at consecutive thymines (2008)
  • Author(s): Nomura A.; Okamoto A
  • Journal Title: Org.Biomol.Chem. 6(21) Pages: 3905-3907
  • Peer Reviewed
• [Journal Article] Sequence Dependence of Fluorescence Emission and Quenching of Doubly Thiazole Orange-Labeled DNA : Effective Design of a Hybridization-Sensitive Probe (2008)
  • Author(s): Ikeda S.; Kubota T.; Kino K.; Okamoto A
  • Journal Title: Bioconjugate Chem. 19(8) Pages: 1719-1725
  • Peer Reviewed
• [Journal Article] Hybridization-Sensitive On-Off DNA Probe : Application of the Exciton Coupling Effect to Effective Fluorescence Quenching (2008)
  • Author(s): Ikeda S.; Okamoto A
  • Journal Title: Chem.Asian J. 3(6) Pages: 958-968
  • Peer Reviewed
• [Journal Article] Synthesis and characterization of the 5-methyl-2'-deoxycytidine glycol-dioxoosmium-bipyridine ternary complex in DNA (2008)
  • Author(s): Umemoto T.; Okamoto A
  • Journal Title: Org.Biomol.Chem. 6(2) Pages: 269-271
  • Peer Reviewed
• [Journal Article] Design of a pyrene-containing fluorescence probe for labeling of RNA poly(A) tracts (2008)
  • Author(s): Tanaka K.; Okamoto A
  • Journal Title: Bioorg.Med.Chem. 16(1) Pages: 400-404
  • Peer Reviewed
• [Journal Article] Hybridization-Sensitive On-Off DNA Probe : Application of the Exciton Coupling Effect to Effective Fluorescence Quenching (2008)
  • Author(s): Ikeda, S.
  • Journal Title: Chem. Asian J. 3(6) Pages: 958-968
  • Peer Reviewed
• [Journal Article] Sequence Dependence of Fluorescence Emission and Quenching of Doubly Thiazole Orange-Labeled DNA : Effective Design of a Hybridization-Sensitive Probe (2008)
  • Author(s): Ikeda, S.
  • Journal Title: Bioconjugate Chem 19(8) Pages: 1719-1725
  • Peer Reviewed
• [Journal Article] Chemical approach toward efficient DNA methylation analysis (2008)
  • Author(s): Okamoto, A.
  • Journal Title: Org. Biomol. Chem. 7(1) Pages: 21-26
  • Peer Reviewed
• [Presentation] Fluorescent Nucleotides for Efficient Nucleic Acid Sensing (2010)
  • Author(s): Okamoto, A.
  • Organizer: 11th International Chemistry Conference and Exhibition in Africa (11 ICCA)
  • Place of Presentation: Luxor, Egypt(Invited)
  • Year and Date: 2010-11-20
• [Presentation] Photochemical design for live cell RNA imaging (2010)
  • Author(s): Akimitsu Okamoto
  • Organizer: International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2010)
  • Place of Presentation: Honolulu, USA(Invited)
• [Presentation] DNA-osmium complex : Pinpoint detection of methylated cytosines (2010)
  • Author(s): Akimitsu Okamoto
  • Organizer: International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2010)
  • Place of Presentation: Honolulu, USA(Invited)
• [Presentation] Artificial Zinc Finger Peptide for Recognition of Methylated DNA Duplex (2010)
  • Author(s): Akiko Nomura, Akimitsu Okamoto
  • Organizer: The 5th Asian Biological Inorganic Chemistry Conference
  • Place of Presentation: Kaohsiung, Taiwan
• [Presentation] Fluorescent Nucleotides for Efficient Nucleic Acid Sensin (2010)
  • Author(s): Akimitsu Okamoto
  • Organizer: 11th International Chemistry Conference and Exhibition in Africa (11 ICCA)
  • Place of Presentation: Luxor, Egypt(Invited)
• [Presentation] A short talk on ICON and ECHO probes (2010)
  • Author(s): Akimitsu Okamoto
  • Organizer: Asian 3 Roundtable on Nucleic Acids (A3RONA 2010 JAPAN)
  • Place of Presentation: Osaka, Japan(Invited)
• [Presentation] Application of artificial DNA probes in genome-scale DNA methylation analysis and evaluation of nucleic acid functions (2010)
  • Author(s): Akimitsu Okamoto
  • Organizer: BIG-CAS Seminar
  • Place of Presentation: Beijing, China(Invited)
• [Presentation] Hybridization-Sensitive Fluorescent Nucleic Acids for Live Cell RNA Imaging (2010)
  • Author(s): Akimitsu Okamoto
  • Organizer: 2nd Workshop on Fluorescence Chemosensor and Bio-imaging
  • Place of Presentation: Dalian, China(Invited)
• [Presentation] Exciton-controlled Hybridization-sensitive Fluorescent Oligonucleotides (2010)
  • Author(s): Takeshi Kubota, Shuji Ikeda, Hiroyuki Yanagisawa, Mizue Yuki, Kaori Sugizaki, Akimitsu Okamoto
  • Organizer: 29th International Round Table on Nucleosides, Nucleotides and Nucleic Acids (IRT 2010)
  • Place of Presentation: Lyon, France
• [Presentation] Thiazole Orange Dimer on a Nucleotide : Application to Live Cell RNA Imaging (2010)
  • Author(s): Akimitsu Okamoto, Shuji Ikeda, Takeshi Kubota
  • Organizer: 23th IUPAC Symposium on Photochemistry
  • Place of Presentation: Ferrara, Italy
• [Presentation] Hybridization-Sensitive Fluorescent Nucleic Acids for Effective RNA Imaging (2010)
  • Author(s): Shuji Ikeda, Takeshi Kubota, Akimitsu Okamoto
  • Organizer: Challenges in Organic Chemistry and Chemical Biology (ISACS1)
  • Place of Presentation: San Francisco, USA
• [Presentation] Addition of Osmium to DNA Pyrimidine Bases (2009)
  • Author(s): 岡本晃充
  • Organizer: 14th International Conference on Biological Inorganic Chemistry(ICBIC 14)
  • Place of Presentation: Nagoya Congress Center, Nagoya
  • Year and Date: 2009-07-28
• [Presentation] ICON Probe : Osmium Complexation for Pinpoint Detection of Methylated Cytosines (2009)
  • Author(s): Akimitsu Okamoto
  • Organizer: BIT Life Sciences' 2nd Annual Congress and Expo of Molecular Diagnostics (CEMD-2009)
  • Place of Presentation: Beijing, China(Invited)
• [Presentation] Photochemical Probe Design for Multicolor RNA Imaging in Living Cells (2009)
  • Author(s): Takeshi Kubota, Shuji Ikeda, Akimitsu Okamoto
  • Organizer: 11th International Kyoto Conference on New Aspects of Organic Chemistry (IKCOC-11)
  • Place of Presentation: Kyoto, Japan
• [Presentation] Exciton-controlled fluorescence : Application to hybridization-sensitive fluorescent DNA probe (2009)
  • Author(s): Akimitsu Okamoto, Shuji Ikeda, Takeshi Kubota, Mizue Yuki, Hiroyuki Yanagisawa
  • Organizer: The 6th International symposium on Nucleic Acid Chemistry (61SNAC2009)
  • Place of Presentation: Takayama, Japan
• [Presentation] Doubly Dye-Labeled Nucleotide : Toward Efficient RNA Imaging (2009)
  • Author(s): Akimitsu Okamoto
  • Organizer: The 13th Asian Chemical Congress
  • Place of Presentation: Shanghai, China(Invited)
• [Presentation] Exciton-controlled probes for live cell RNA imaging (2009)
  • Author(s): Akimitsu Okamoto
  • Organizer: 42nd IUPAC Congress
  • Place of Presentation: Glasgow, UK(Invited)
• [Presentation] Addition of Osmium to DNA Pyrimidine Bases (2009)
  • Author(s): Akimitsu Okamoto
  • Organizer: 14th International Conference on Biological Inorganic Chemistry
  • Place of Presentation: Nagoya, Japan(Invited)
• [Presentation] Excitonic Interaction : New Photochemical Control for Nucleic Acid Imaging (2009)
  • Author(s): Akimitsu Okamoto
  • Organizer: The Fifth iCeMS International Symposium
  • Place of Presentation: Kyoto, Japan(Invited)
• [Presentation] Doubly Dye-Labeled Nucleotide: Synthesis, Photochemistry, and Application to RNA Imaging (2009)
  • Author(s): Akimitsu Okamoto, Shuji Ikeda, Mizue Yuki, Takeshi Kubota
  • Organizer: Tenth Tetrahedron Symposium
  • Place of Presentation: Paris, France
• [Presentation] DNA-Osmium Complex for DNA Methylation Analysis (2008)
  • Author(s): 岡本晃充
  • Organizer: 31st National Medicinal Chemistry Symposium
  • Place of Presentation: University of Pittsburgh
  • Year and Date: 2008-06-18
• [Presentation] Control of DNA binding by a zinc finger peptide having and azobenzene photo-switch (2008)
  • Author(s): Akiko Nomura, Akimitsu Okamoto
  • Organizer: 4th Asian Biological Inorganic Chemistry Conference
  • Place of Presentation: Jeju, Korea
• [Presentation] Reactivity of Thymine Doublet in Single Strand DNA with Osmium Reagent (2008)
  • Author(s): Akiko Nomura, Akimitsu Okamoto
  • Organizer: joint Symposium of 18th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids and 35th International Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Kyoto, Japan
• [Presentation] Intracellular mRNA imaging with a hybridization sensitive fluorescent nucleotide (2008)
  • Author(s): Takeshi Kubota, Shuji Ikeda, Akimitsu Okamoto
  • Organizer: joint Symposium of 18th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids and 35th International Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Kyoto, Japan
• [Presentation] Design of a fluorescent probe for DNA/RNA imaging (2008)
  • Author(s): Akimitsu Okamoto, Takeshi Kubota, Shuji Ikeda
  • Organizer: joint Symposium of 18th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids and 35th International Symposium on Nucleic Acids Chemistry
  • Place of Presentation: Kyoto, Japan
• [Presentation] Doubly Thiazole Orange-Labeled Nucleotide Application to Hybridization-Sensitive DNA Probe (2008)
  • Author(s): Takeshi Kubota, Shuji Ikeda, Akimitsu Okamoto
  • Organizer: 2008 Korea-Japan Symposium on Frontier Photoscience (KJFP 2008)
  • Place of Presentation: Jeju, Korea(Invited)
• [Presentation] DNA-Osmium Complex for DNA Methylation Analysis (2008)
  • Author(s): Akimitsu Okamoto
  • Organizer: 31st National Medicinal Chemistry Symposium, American Chemical Society
  • Place of Presentation: Pittsburgh, USA(Invited)
• [Presentation] Synthesis of bipyridine-adenine conjugates for DNA methylation analysis (2008)
  • Author(s): Kazuki Tainaka, Akimitsu Okamoto
  • Organizer: 14th Symposium on Chemistry of Nucleic Acid Components
  • Place of Presentation: Cesky Krumlov, Czech
• [Book] 実験医学増刊 生命現象の動的理解を目指すライブイメージング「第3章-5生細胞内mRNAの検出」 (2008)
  • Author(s): 岡本晃充
  • Total Pages: 7
  • Publisher: 羊土社
• [Remarks]
  • URL: http://www.riken.jp/lab-www/okamotoiru/indexj.htm