Hybridization-sensitive fluorescent probe for long-term monitoring of intracellular RNA

Bioconjugate Chemistry

Volumn 20, Issue 6, 2009, Pages 1256-1261

  Kubota, Takeshi ^a   Ikeda, Shuji ^a   Yanagisawa, Hiroyuki ^a   Yuki, Mizue ^a   Okamoto, Akimitsu ^a  

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE; RIBONUCLEASE H; RNA;

ARTICLE; CONTROLLED STUDY; DNA PROBE; FLUORESCENCE; HUMAN; HUMAN CELL; MOLECULAR IMAGING; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; RNA DEGRADATION; RNA HYBRIDIZATION; RNA PROBE; RNA STRUCTURE; SYNTHESIS;

EID: 67649211935     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc900120a     Document Type: Article

References (24)

1. Paillasson, S., van de Corput, M., Dirks, R. W., Tanke, H. J., Robert-Nicoud, M., and Ronot, X. (1997) In situ hybridization in living cells: Detection of RNA molecules. Exp. Cell Res. 231, 226-233. (Pubitemid 27187532)
2. Pernthaler, J., Glockner, F. O., Schonhuber, W., and Amann, R. (2001) Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol. 30, 207-226. (Pubitemid 33287422)
3. Asseline, U. (2006) Development and applications of fluorescent oligonucleotides. Curr. Org. Chem. 10, 491-518.
4. Marti, A. A., Jockusch, S., Stevens, N., Ju, J., and Turro, N. J. (2007) Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc. Chem. Res. 40, 402-409.
5. Rodriguez, A. J., Condeelis, J., Singer, R. H., and Dictenberg, J. B. (2007) Imaging mRNA movement from transcription sites to translation sites. Semin. Cell DeV. Biol. 18, 202-208. (Pubitemid 46756371)
6. Tyagi, S., and Kramer, F. R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303-308. (Pubitemid 26149073)
7. Hopkins, J. F., and Woodson, S. A. (2005) Molecular beacons as probes of RNA unfolding under native conditions. Nucleic Acids Res. 33, 5763-5770. (Pubitemid 41742596)
8. Ikeda, S., and Okamoto, A. (2008) Hybridization-sensitive on-off DNA probe: Application of the exciton coupling effect to effective fluorescence quenching. Chem. Asian J. 3, 958-968.
9. Ikeda, S., Kubota, T., Kino, K., and Okamoto, A. (2008) Sequence dependence of fluorescence emission and quenching of doubly thiazole orange-labeled DNA: Effective design of a hybridization-sensitive probe. Bioconjugate Chem. 19, 1719-1725.
10. Kubota, T., Ikeda, S., and Okamoto, A. (2009) Doubly thiazole orange-labeled DNA for live cell RNA imaging. Bull. Chem. Soc. Jpn. 82, 110-117.
11. Inoue, H., Hayase, Y., Imura, A., Iwai, S., Miura, K., and Ohtsuka, E. (1987) Synthesis and hybridization studies on two complementary nona(2′-O-methyl)ribonucleotides. Nucleic Acids Res. 15, 6131-6149.
12. Majlessi, M., Nelson, N. C., and Becker, M. M. (1998) Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Res. 26, 2224-2229. (Pubitemid 28291770)
13. Freier, S. M., and Altmann, K. H. (1997) The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res. 25, 4429-4443. (Pubitemid 27500751)
14. Lesnik, E. A., and Freier, S. M. (1998) What affects the effect of 2′-alkoxy modifications? 1. Stabilization effect of 2′-methoxy substitutions in uniformly modified DNA oligonucleotides. Biochemistry 37, 6991-6997. (Pubitemid 28228136)
15. Kasha, M. (1963) Energy transfer mechanisms and molecular exciton model for molecular aggregates. Radiat. Res. 20, 55-70.
16. Khairutdinov, R. F., and Serpone, N. (1997) Photophysics of cyanine dyes: Subnanosecond relaxation dynamics in monomers, dimers, and H- and J-aggregates in solution. J. Phys. Chem. B 101, 2602-2610. (Pubitemid 127581055)
17. Sagawa, T., Tobata, H., and Ihara, H. (2004) 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. 2-4.
18. Fürstenberg, A., Julliard, M. D., Deligeorgiev, T. G., Gadjev, N. I., Vasilev, A. A., and Vauthey, E. (2006) Ultrafast excitedstate dynamics of DNA fluorescent intercalators: New insight into the fluorescence enhancement mechanism. J. Am. Chem. Soc. 128, 7661-7669. (Pubitemid 43877538)
19. Cramer, H., and Pfleiderer, W. (2000) Nucleotides LXIV[1]: Synthesis, hybridization and enzymatic degradation studies of 2′-O-methyl- oligoribonucleotides and 2′-O-methyl/deoxy gapmers. Nucleosides Nucleotides Nucleic Acids 19, 1765-1777. (Pubitemid 32065121)
20. Ando, T. (1966) A nuclease specific for heat-denatured DNA isolated from a product of Aspergillus oryzae. Biochim. Biophys. Acta 114, 158-168.
21. Wiegand, R. C., Godson, G. N., and Radding, C. M. (1975) Specificity of S1 nuclease from Aspergillus oryzae. J. Biol. Chem. 250, 8848-8855.
22. Lehman, I. R., and Nussbaum, A. L. (1964) The deoxyribonucleases of Escherichia coli. V. On the specificity of exonuclease I (phosphodiesterase). J. Biol. Chem. 239, 2628-2636.
23. Kusher, S. R., Nagaishi, H., Templin, A., and Clark, A. J. (1971) Genetic recombination in Escherichia coli: The role of Exonuclease I. Proc. Natl. Acad. Sci. U.S.A. 68, 824-827.
24. Berkower, I., Leis, J., and Hurwitz, J. (1973) Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid·deoxyribonucleic acid hybrid structures. J. Biol. Chem. 248, 5914-5921.