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Nuclear Bodies and Noncoding RNAs pp 69–87Cite as

Visualization of Nucleic Acids with Synthetic Exciton-Controlled Fluorescent Oligonucleotide Probes

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1262))

Abstract

Engineered probes to adapt new photochemical properties upon recognition of target nucleic acids offer powerful tools to DNA and RNA visualization technologies. Herein, we describe a rapid and effective visualization method of nucleic acids in both fixed and living cells with hybridization-sensitive fluorescent oligonucleotide probes. These probes are efficiently quenched in an aqueous environment due to the homodimeric, excitonic interactions between fluorophores but become highly fluorescent upon hybridization to DNA or RNA with complementary sequences. The fast hybridization kinetics and quick fluorescence activation of the new probes allow applications to simplify the conventional fluorescent in situ hybridization protocols and reduce the amount of time to process the samples. Furthermore, hybridization-sensitive fluorescence emission of the probes allows monitoring dynamic behaviors of RNA in living cells.

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Author information

Authors and Affiliations

  1. Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, 606-8501, Japan

    Dan Ohtan Wang

  2. Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, 153-8904, Japan

    Akimitsu Okamoto

Authors
  1. Dan Ohtan Wang
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  2. Akimitsu Okamoto
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Corresponding author

Correspondence to Dan Ohtan Wang .

Editor information

Editors and Affiliations

  1. RNA Biology Laboratory, RIKEN, Saitama, Japan

    Shinichi Nakagawa

  2. Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan

    Tetsuro Hirose

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Wang, D.O., Okamoto, A. (2015). Visualization of Nucleic Acids with Synthetic Exciton-Controlled Fluorescent Oligonucleotide Probes. In: Nakagawa, S., Hirose, T. (eds) Nuclear Bodies and Noncoding RNAs. Methods in Molecular Biology, vol 1262. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2253-6_5

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  • DOI: https://doi.org/10.1007/978-1-4939-2253-6_5

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2252-9

  • Online ISBN: 978-1-4939-2253-6

  • eBook Packages: Springer Protocols

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