N.E. Broude, Stem-loop oligonucleotides: A robust tool for molecular biology and biotechnology. Trends Biotechnol 20, 249–256 (2002)
Article
CAS
Google Scholar
M.E. Brun, E. Lana, I. Rivals, G. Lefranc, P. Sarda, M. Claustres, A. Mégarbané, A. De Sario, Heterochromatic genes undergo epigenetic changes and escape silencing in immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome. PLoS One 6, e19464 (2011)
Article
CAS
Google Scholar
G. Cosa, K.S. Focsaneanu, J.R.N. McLean, J.P. McNamee, J.C. Scaiano, Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution. Photochem. Photobiol. 73, 585–599 (2001)
Article
CAS
Google Scholar
V. Czikkely, H.D. Forsterling, H. Kuhn, Light absorption and structure of aggregates of dye molecules. Chem. Phys. Lett. 6, 207–210 (1970)
Article
CAS
Google Scholar
R.W. Dirks, H.J. Tanke, Advances in fluorescent tracking of nucleic acids in living cells. BioTechniques 40, 489–496 (2006)
Article
CAS
Google Scholar
X. Fang, J.J. Li, J. Perlette, W. Tan, K. Wang, Molecular beacons: Novel fluorescent probes. Anal. Chem. 72, 747A–753A (2000)
Article
CAS
Google Scholar
A. Fürstenberg, M.D. Julliard, T.G. Deligeorgiev, N.I. Gadjev, A.A. Vasilev, E. Vauthey, Ultrafast excited-state dynamics of DNA fluorescent intercalators: New insight into the fluorescence enhancement mechanism. J. Am. Chem. Soc. 128, 7661–7669 (2006)
Article
CAS
Google Scholar
K.C. Hannah, B.A. Armitage, DNA-templated assembly of helical cyanine dye aggregates: A supramolecular chain polymerization. Acc. Chem. Res. 37, 845–853 (2004)
Article
CAS
Google Scholar
W.J. Harrison, D.L. Mateer, G.J.T. Tiddy, Liquid-crystalline J-aggregates formed by aqueous ionic cyanine dyes. J. Phys. Chem. 100, 2310–2321 (1996)
Article
CAS
Google Scholar
S. Ikeda, T. Kubota, D.O. Wang, H. Yanagisawa, T. Umemoto, A. Okamoto, Design and synthesis of caged fluorescent nucleotides and application to live cell RNA imaging. ChemBioChem 12, 2871–2880 (2011a)
Article
CAS
Google Scholar
S. Ikeda, T. Kubota, M. Yuki, A. Okamoto, Exciton-controlled hybridization-sensitive fluorescent probes: Multicolor detection of nucleic acids. Angew. Chem. Int. Ed. 48, 6480–6484 (2009)
Article
CAS
Google Scholar
S. Ikeda, A. Okamoto, Hybridization-sensitive on-off DNA probe: Application of the exciton coupling effect to effective fluorescence quenching. Chem. Asian J. 3, 958–968 (2008)
Article
CAS
Google Scholar
S. Ikeda, H. Yanagisawa, A. Nakamura, D.O. Wang, M. Yuki, A. Okamoto, Hybridization-sensitive fluorescence control in the near-infrared wavelength range. Org. Biomol. Chem. 9, 4199–4204 (2011b)
Article
CAS
Google Scholar
I. Jaco, A. Canela, E. Vera, M.A. Blasco, Centromere mitotic recombination in mammalian cells. J. Cell Biol. 181, 885–892 (2008)
Article
CAS
Google Scholar
M. Jeanpierre, C. Turleau, A. Aurias, M. Prieur, F. Ledeist, A. Fischer, E. Viegas-Pequignot, An embryonic-like methylation pattern of classical satellite DNA is observed in ICFsyndrome. Hum. Mol. Genet. 2, 731–735 (1993)
Article
CAS
Google Scholar
Y.L. Jiang, M. Rigolet, D. Bourc'his, F. Nigon, I. Bokesoy, J.P. Fryns, M. Hultén, P. Jonveaux, P. Maraschio, A. Mégarbané, A. Moncla, E. Viegas–Péquignot, DNMT3B mutations and DNA methylation defect define two types of ICF syndrome. Hum. Mutat. 25, 56–63 (2005)
Article
CAS
Google Scholar
P.A. Jones, P.W. Laird, Cancer-epigenetics comes of age. Nature Genet 21, 163–167 (1999)
Article
CAS
Google Scholar
P.L. Jones, A.P. Wolffe, Relationships between chromatin organization and DNA methylation in determining gene expression. Semin. Cancer Biol. 9, 339–347 (1999)
Article
CAS
Google Scholar
M. Kasha, Energy transfer mechanisms and the molecular exciton model for molecular aggregates. Radiat. Res. 20, 55–70 (1963)
Article
CAS
Google Scholar
M. Kasha, H.R. Rawls, M.A. El-Bayoumi, The exciton model in molecular spectroscopy. Pure Appl. Chem. 11, 371–392 (1965)
Article
CAS
Google Scholar
R.F. Khairutdinov, N. Serpone, Photophysics of cyanine dyes: Subnanosecond relaxation dynamics in monomers, dimers, and H- and J-aggregates in solution. J. Phys. Chem. B 101, 2602–2610 (1997)
Article
CAS
Google Scholar
T. Kubota, S. Ikeda, A. Okamoto, Doubly thiazole orange-labeled DNA for live cell RNA imaging. Bull. Chem. Soc. Jpn. 82, 110–117 (2009a)
Article
CAS
Google Scholar
T. Kubota, S. Ikeda, H. Yanagisawa, M. Yuki, A. Okamoto, Hybridization-sensitive fluorescent probe for long-term monitoring of intracellular RNA. Bioconjug. Chem. 20, 1256–1261 (2009b)
Article
CAS
Google Scholar
G.S. Levinson, W.T. Simpson, W. Curtis, Electronic spectra of pyridocyanine dyes with assignments of transitions. J. Am. Chem. Soc. 79, 4314–4320 (1957)
Article
CAS
Google Scholar
J.M. Levsky, R.H. Singer, Fluorescence in situ hybridization: Past, present and future. J. Cell Sci. 116, 2833–2838 (2003)
Article
CAS
Google Scholar
E. Li, Chromatin modification and epigenetic reprogramming in mammalian development. Nat. Rev. Genet. 3, 662–673 (2002)
Article
CAS
Google Scholar
Y. Li, Y. Miyanari, K. Shirane, H. Nitta, T. Kubota, H. Ohashi, A. Okamoto, H. Sasaki, Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes. Nucleic Acids Res. 41, e186 (2013)
Article
CAS
Google Scholar
E.G. McRae, M. Kasha, Enhancement of phosphorescence ability upon aggregation of dye molecules. J. Chem. Phys. 28, 721–722 (1958)
Article
CAS
Google Scholar
J. Nath, K.L. Johnson, A review of fluorescence in situ hybridization (FISH): Current status and future prospects. Biotech. Histochem. 75, 54–78 (2000)
Article
CAS
Google Scholar
A. Okamoto, ECHO probes: A concept of fluorescence control for practical nucleic acid sensing. Chem. Soc. Rev. 40, 5815–5828 (2011)
Article
CAS
Google Scholar
A. Okamoto, DNA-osmium complexes: Recent developments for operative chemical analysis of DNA epigenetic modification. ChemMedChem 9, 1958–1965 (2014)
Article
CAS
Google Scholar
A. Okamoto, K. Sugizaki, M. Yuki, H. Yanagisawa, S. Ikeda, T. Sueoka, G. Hayashi, D.O. Wang, A nucleic acid probe labeled with desmethyl thiazole orange: A new type of hybridization-sensitive fluorescent oligonucleotide for live-cell RNA imaging. Org. Biomol. Chem. 11, 362–371 (2013)
Article
CAS
Google Scholar
A. Okamoto, K. Tanabe, T. Inasaki, I. Saito, Phototriggered drug release from functionalized oligonucleotides by a molecular Beacon strategy. Angew. Chem. Int. Ed. 42, 2502–2504 (2003)
Article
CAS
Google Scholar
I. Oomoto, A. Suzuki-Hirano, H. Umeshima, Y.W. Han, H. Yanagisawa, P. Carlton, Y. Harada, M. Kengaku, A. Okamoto, T. Shimogori, D.O. Wang, ECHO-liveFISH: In vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues. Nucleic Acid Res. 43, e126 (2015)
Article
CAS
Google Scholar
A.S. Piatek, S. Tyagi, A.C. Pol, A. Telenti, L.P. Miller, F.R. Kramer, D. Alland, Molecular beacon sequence analysis for detecting drug resistance in mycobacterium tuberculosis. Nat. Biotechnol. 16, 359–363 (1998)
Article
CAS
Google Scholar
K.D. Robertson, DNA methylation and human disease. Nat. Rev. Genet. 6, 597–610 (2005)
Article
CAS
Google Scholar
U. Rösch, S. Yao, R. Wortmann, F. Würthner, Fluorescent H-aggregates of merocyanine dyes. Angew. Chem. Int. Ed. 45, 7026–7030 (2006)
Article
CAS
Google Scholar
T. Sagawa, H. Tobata, H. Ihara, Exciton interactions in cyanine dye-hyaluronic acid (HA) complex: Reversible and biphasic molecular switching of chromophores induced by random coil-to-double-helix phase transition of HA. Chem. Commun., 2090–2091 (2004)
H. Shiura, A. Okamoto, H. Sasaki, K. Abe, Whole-mount MeFISH: A novel technique for simultaneous visualization of specific DNA methylation and protein/RNA expression. PLoS One 4, e95750 (2014)
Article
Google Scholar
A.P. Silverman, E.T. Kool, Quenched probes for highly specific detection of cellular RNAs. Trends Biotechnol. 23, 225–230 (2005)
Article
CAS
Google Scholar
L.D. Simon, K.H. Abramo, J.K. Sell, L.B. McGown, Oxazole yellow dye interactions with short DNA oligomers of homogeneous base composition and their hybrids. Biospectroscopy 4, 17–25 (1998)
Article
CAS
Google Scholar
I. Smolina, C. Lee, M. Frank-Kamenetskii, Detection of low-copy-number genomic DNA sequences in individual bacterial cells by using peptide nucleic acid-assisted rolling-circle amplification and fluorescence in situ hybridization. Appl. Environ. Microbiol. 73, 2324–2328 (2007)
Article
CAS
Google Scholar
W. Tan, K. Wang, T.J. Drake, Molecular beacons. Curr. Opin. Chem. Biol. 8, 547–553 (2004)
Article
CAS
Google Scholar
K. Tanaka, K. Tainaka, T. Umemoto, A. Nomura, A. Okamoto, An osmium-DNA interstrand complex: Application to facile DNA methylation analysis. J. Am. Chem. Soc. 129, 14511–14517 (2007)
Article
CAS
Google Scholar
S. Tyagi, D.P. Btaru, F.R. Kramer, Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49–53 (1998)
Article
CAS
Google Scholar
S. Tyagi, F.R. Kramer, Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303–308 (1996)
Article
CAS
Google Scholar
D.O. Wang, H. Matsuno, S. Ikeda, A. Nakamura, H. Yanagisawa, Y. Hayashi, A. Okamoto, A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes. RNA 18, 166–175 (2012)
Article
CAS
Google Scholar
D.O. Wang, A. Okamoto, ECHO probes: Fluorescence emission control for nucleic acid imaging. J. Photochem. Photobiol. C 13, 112–123 (2012)
Article
CAS
Google Scholar
R. Weigert, N. Porat-Shliom, P. Amornphimoltham, Imaging cell biology in live animals: Ready for prime time. J. Cell Biol. 201, 969–979 (2013)
Article
CAS
Google Scholar
W. West, S. Pearce, The dimeric state of cyanine dyes. J. Phys. Chem. 69, 1894–1903 (1965)
Article
CAS
Google Scholar
S. Zeena, K.G. Thomas, Conformational switching and exciton interactions in hemicyanine-based bichromophores. J. Am. Chem. Soc. 123, 7859–7865 (2001)
Article
CAS
Google Scholar