Reduction-triggered fluorescent amplification probe for the detection of endogenous RNAs in living human cells

Bioconjugate Chemistry

Volumn 20, Issue 5, 2009, Pages 1026-1036

  Furukawa, Kazuhiro ^a,b   Abe, Hiroshi ^a   Hibino, Kayo ^a   Sako, Yasushi ^a   Tsuneda, Satoshi ^b   Ito, Yoshihiro ^a  

^a RIKEN   (Japan)

^b WASEDA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AZIDOMETHYL FLUORESCEIN; BETA ACTIN; FLUORESCEIN DERIVATIVE; MESSENGER RNA; OLIGONUCLEOTIDE; RNA 28S; STREPTOLYSIN O; UNCLASSIFIED DRUG; AZIDE; COUMARIN; COUMARIN DERIVATIVE; DNA; FLUORESCEIN; FLUORESCENT DYE; RNA;

ARTICLE; CATALYSIS; CELL STRAIN HL 60; FLOW CYTOMETRY; FLUORESCENCE; FLUORESCENCE MICROSCOPY; HUMAN; HUMAN CELL; RNA PROBE; RNA PROCESSING; RNA TRANSCRIPTION; SIGNAL DETECTION; STAUDINGER REACTION; SYNTHESIS; TURNOVER TIME; CELL SURVIVAL; CHEMISTRY; DRUG DESIGN; HL 60 CELL LINE; KINETICS; METABOLISM; MOLECULAR IMAGING; OXIDATION REDUCTION REACTION; PROCEDURES; SPECTROFLUOROMETRY;

EUKARYOTA;

AZIDES; CELL SURVIVAL; COUMARINS; DNA; DRUG DESIGN; FLOW CYTOMETRY; FLUORESCEIN; FLUORESCENT DYES; HL-60 CELLS; HUMANS; KINETICS; MICROSCOPY, FLUORESCENCE; MOLECULAR IMAGING; OXIDATION-REDUCTION; RNA; RNA, MESSENGER; RNA, RIBOSOMAL, 28S; SPECTROMETRY, FLUORESCENCE;

EID: 66149188263     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc900040t     Document Type: Article

References (67)

1. Shav-Tal, Y., Darzacq, X., and Singer, R. H. (2006) Gene expression within a dynamic nuclear landscape. EMBO J. 25, 3469-3479. (Pubitemid 44264858)
2. Dirks, R. W., and Tanke, H. J. (2006) Advances in fluorescent tracking of nucleic acids in living cells. Biotechniques 40, 489-496. (Pubitemid 46534930)
3. Behrens, S., Fuchs, B. M., Mueller, F., and Amann, R. (2003) Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit? Appl. Environ. Microbiol. 69, 4935-4941. (Pubitemid 36992959)
4. Dirks, R. W., Molenaar, C., and Tanke, H. J. (2001) Methods for visualizing RNA processing and transport pathways in living cells. Histochem. Cell Biol. 115, 3-11. (Pubitemid 32202048)
5. Czaplinski, K., and Singer, R. H. (2006) Pathways for mRNA localization in the cytoplasm. Trends Biochem. Sci. 31, 687-693.
6. Shav-Tal, Y., Darzacq, X., Shenoy, S. M., Fusco, D., Janicki, S. M., Spector, D. L., and Singer, R. H. (2004) Dynamics of single mRNPs in nuclei of living cells. Science 304, 1797-1800. (Pubitemid 38787895)
7. Levsky, J. M., and Singer, R. H. (2003) Fluorescence in situ hybridization: past, present and future. J. Cell Sci. 116, 2833-2838. (Pubitemid 36926972)
8. Isaacs, F. J., Dwyer, D. J., Ding, C. M., Pervouchine, D. D., Cantor, C. R., and Collins, J. J. (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841-847. (Pubitemid 38886602)
9. Hasegawa, S., Jackson, W. C., Tsien, R. Y., and Rao, J. (2003) Imaging Tetrahymena ribozyme splicing activity in single live mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 100, 14892-14896. (Pubitemid 37517987)
10. 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)
11. Lewin, B. (1997) Gene VI ed., Oxford university press, Inc., New York.
12. Giles, R. V., and Tidd, D. M. (1992) Increased specificity for antisense oligodeoxynucleotide targeting of RNA cleavage by RNaseH using chimeric methylphosphonodiester phosphodiester structures. Nucleic Acids Res. 20, 763-770.
13. Tu, G. C., Cao, Q. N., Zhou, F., and Israel, Y. (1998) Tetranucleotide GGGA motif in primary RNA transcripts: Novel target site for antisense design. J. Biol. Chem. 273, 25125-25131. (Pubitemid 28443271)
14. Sohail, M., and Southern, E. M. (2000) Selecting optimal antisense reagents. Adv. Drug Delivery Rev. 44, 23-34.
15. Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49-58. (Pubitemid 28035948)
16. Tyagi, S., and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303-308. (Pubitemid 26149073)
17. Piatek, A. S., Tyagi, S., Pol, A. C., Telenti, A., Miller, L. P., Kramer, F. R., and Alland, D. (1998) Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 16, 359-363. (Pubitemid 28164656)
18. Tyagi, S., Marras, S. A., and Kramer, F. R. (2000) Wavelength-shifting molecular beacons. Nat. Biotechnol. 18, 1191-1196.
19. Bratu, D. P., Cha, B. J., Mhlanga, M. M., Kramer, F. R., and Tyagi, S. (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl. Acad. Sci. U.S.A. 100, 13308-13313. (Pubitemid 37444738)
20. Vargas, D. Y., Raj, A., Marras, S. A. E., Kramer, F. R., and Tyagi, S. (2005) Mechanism of mRNA transport in the nucleus. Proc. Natl. Acad. Sci. U.S.A. 102, 17008-17013. (Pubitemid 41692674)
21. Sando, S., and Kool, E. T. (2002) Imaging of RNA in bacteria with self-ligating quenched probes. J. Am. Chem. Soc. 124, 9686-9687.
22. Silverman, A. P., and Kool, E. T. (2006) Detecting RNA and DNA with templated chemical reactions. Chem. Rev. 106, 3775-3789. (Pubitemid 44565984)
23. Abe, H., and Kool, E. T. (2006) Flow cytometric detection of specific RNAs in native human cells with quenched autoligating FRET probes. Proc. Natl. Acad. Sci. U.S.A. 103, 263-268. (Pubitemid 43122389)
24. Silverman, A. P., and Kool, E. T. (2007) Oligonucleotide probes for RNA-targeted fluorescence in situ hybridization. Adv. Clin. Chem. 43, 79-115.
25. Sando, S., and Kool, E. T. (2002) Quencher as leaving group: efficient detection of DNA-joining reactions. J. Am. Chem. Soc. 124, 2096-2097. (Pubitemid 34267080)
26. Abe, H., and Kool, E. T. (2004) Destabilizing universal linkers for signal amplification in self-ligating probes for RNA. J. Am. Chem. Soc. 126, 13980-13986. (Pubitemid 39447073)
27. Sando, S., Abe, H., and Kool, E. T. (2004) Quenched autoligating DNAs: multicolor identification of nucleic acids at single nucleotide resolution. J. Am. Chem. Soc. 126, 1081-1087. (Pubitemid 38140738)
28. Fang, X. H., Li, J. J., and Tan, W. H. (2000) Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Anal. Chem. 72, 3280-3285. (Pubitemid 30482504)
29. Tsuji, A., Koshimoto, H., Sato, Y., Hirano, M., Sei-Iida, Y., Kondo, S., and Ishibashi, K. (2000) Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope. Biophys. J. 78, 3260-3274. (Pubitemid 30396954)
30. Molenaar, C., Marras, S. A., Slats, J. C. M., Truffert, J. C., Lemaitre, M., Raap, A. K., Dirks, R. W., and Tanke, H. J. (2001) Linear 2′ O-methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res. 29, e89.
31. Perlette, J., and Tan, W. (2001) Real-time monitoring of intracellular mRNA hybridization inside single living cells. Anal. Chem. 73, 5544-5550. (Pubitemid 33108566)
32. Bratu, D. P., Cha, B. J., Mhlanga, M. M., Kramer, F. R., and Tyagi, S. (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl. Acad. Sci. U.S.A. 100, 13308-13313. (Pubitemid 37444738)
33. Santangelo, P. J., Nix, B., Tsourkas, A., and Bao, G. (2004) Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res. 32, e57.
34. Nitin, N., Santangelo, P. J., Kim, G., Nie, S., and Bao, G. (2004) Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells. Nucleic Acids Res. 32, e58.
35. Matsuo, T. (1998) In situ visualization of messenger RNA for basic fibroblast growth factor in living cells. Biochim. Biophys. Acta 1379, 178-184. (Pubitemid 28252893)
36. Tyagi, S., and Alsmadi, O. (2004) Imaging native beta-Actin mRNA in motile fibroblasts. Biophys. J. 87, 4153-4162. (Pubitemid 39602919)
37. Sokol, D. L., Zhang, X., Lu, P., and Gewirtz, A. M. (1998) Real time detection of DNA.RNA hybridization in living cells. Proc. Natl. Acad. Sci. U.S.A. 95, 11538-11543. (Pubitemid 28460450)
38. Wang, W., Cui, Z. Q., Han, H., Zhang, Z. P., Wei, H. P., Zhou, Y. F., Chen, Z., and Zhang, X. E. (2008) Imaging and characterizing influenza A virus mRNA transport in living cells. Nucleic Acids Res. 36, 4913-4928.
39. Chen, A. K., Behlke, M. A., and Tsourkas, A. (2007) Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells. Nucleic Acids Res. 35, e105.
40. 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.
41. Dose, C., Ficht, S., and Seitz, O. (2006) Reducing product inhibition in DNA-template-controlled ligation reactions. Angew. Chem., Int. Ed. 45, 5369-5373. (Pubitemid 44289380)
42. Dose, C., and Seitz, O. (2008) Single nucleotide specific detection of DNA by native chemical ligation of fluorescence labeled PNA-probes. Bioorg. Med. Chem. 16, 65-77.
43. Dose, C., and Seitz, O. (2005) Convergent synthesis of peptide nucleic acids by native chemical Ligation. Org. Lett. 7, 4365-4368. (Pubitemid 41436648)
44. Ma, Z., and Taylor, J. S. (2003) PNA-based RNA-triggered drug-releasing system. Bioconjugate Chem. 14, 679-683. (Pubitemid 36597380)
45. Ma, Z., and Taylor, J. S. (2001) Nucleic acid triggered catalytic drug and probe release: a new concept for the design of chemotherapeutic and diagnostic agents. Bioorg. Med. Chem. 9, 2501-2510. (Pubitemid 32834637)
46. Ma, Z., and Taylor, J. S. (2000) Nucleic acid-triggered catalytic drug release. Proc. Natl. Acad. Sci. U.S.A. 97, 11159-11163.
47. Cai, J., Li, X., Yue, X., and Taylor, J. S. (2004) Nucleic acid-triggered fluorescent probe activation by the Staudinger reaction. J. Am. Chem. Soc. 126, 16324-16325. (Pubitemid 40081921)
48. Abe, H., Wang, J., Furukawa, K., Oki, K., Uda, M., Tsuneda, S., and Ito, Y. (2008) A reduction-triggered fluorescence probe for sensing nucleic acids. Bioconjugate Chem. 19, 1219-1226.
49. Pianowski, Z. L., and Winssinger, N. (2007) Fluorescence-based detection of single nucleotide permutation in DNA via catalytically templated reaction. Chem. Commun. 37, 3820-3822. (Pubitemid 47429101)
50. Franzini, R. M., and Kool, E. T. (2008) 7-azidomethoxycoumarins as profluorophores for templated nucleic acid detection. ChemBioChem 9, 2981-2988.
51. Grossmann, T. N., and Seitz, O. (2006) DNA-catalyzed transfer of a reporter group. J. Am. Chem. Soc. 128, 15596-15597.
52. Sando, S., Sasaki, T., Kanatani, K., and Aoyama, Y. (2003) Amplified nucleic acid sensing using programmed self-cleaving DNAzyme. J. Am. Chem. Soc. 125, 15720-15721. (Pubitemid 37553670)
53. Franzini, R. M., and Kool, E. T. (2008) Organometallic activation of a fluorogen for templated nucleic acid detection. Org. Lett. 10, 2935-2938.
54. Abe, H., and Kool, E. T. (2005) Universal linkers for signal amplification in auto-ligating probes. Nucleic Acids Symp. Ser. 49, 37-38.
55. Lemieux, G. A., de Graffenried, C. L., and Bertozzi, C. R. (2003) A fluorogenic dye activated by the Staudinger ligation. J. Am. Chem. Soc. 125, 4708-4709. (Pubitemid 36505354)
56. Kojima, H., Nakatsubo, N., Kikuchi, K., Kawahara, S., Kirino, Y., Nagoshi, H., Hirata, Y., and Nagano, T. (1998) Detection and imaging of nitric oxide with novel fluorescent indicators: Diaminofluoresceins. Anal. Chem. 70, 2446-2453. (Pubitemid 128501019)
57. Maeda, H., Fukuyasu, Y., Yoshida, S., Fukuda, M., Saeki, K., Matsuno, H., Yamauchi, Y., Yoshida, K., Hirata, K., and Miyamoto, K. (2004) Fluorescent probes for hydrogen peroxide based on a non-oxidative mechanism. Angew. Chem., Int. Ed. 43, 2389-2391. (Pubitemid 39257736)
58. Miller, E. W., Tulyathan, O., Isacoff, E. Y., and Chang, C. J. (2007) Molecular imaging of hydrogen peroxide produced for cell signaling. Nat. Chem. Biol. 3, 263-267. (Pubitemid 46625830)
59. Dale, T. J., and Rebek, J., Jr. (2006) Fluorescent sensors for organophosphorus nerve agent mimics. J. Am. Chem. Soc. 128, 4500-4501.
60. Marras, S. A., Kramer, F. R., and Tyagi, S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122.
61. Loubinoux, B., Tabbache, S., Gerardin, P., and Miazimbakana, J. (1988) Protection of phenols via the azidomethylene group: Application in the synthesis of unstable phenolic compounds. Tetrahedron 44, 6055-6064.
62. Young, T., and Kiessling, L. L. (2002) A strategy for the synthesis of sulfated peptides. Angew. Chem., Int. Ed. 41, 3449-3451. (Pubitemid 35230653)
63. Sakurai, K., Snyder, T. M., and Liu, D. R. (2005) DNA-templated functional group transformations enable sequence-programmed synthesis using small-molecule reagents. J. Am. Chem. Soc. 127, 1660-1661. (Pubitemid 40229149)
64. Payne, R. J., Toscano, M. D., Bulloch, E. M., Abell, A. D., and Abell, C. (2005) Design and synthesis of aromatic inhibitors of anthranilate synthase. Org. Biomol. Chem. 3, 2271-2281.
65. Pinnisi, E. (1998) A closer look at SNPs suggests difficulties. Science 281, 1787-1789.
66. Jensen, K. K., Orum, H., Nielsen, P. E., and Norden, B. (1997) Kinetics for hybridization of peptide nucleic acids (PNA) with DNA and RNA studied with the BIAcore technique. Biochemistry 36, 5072-5077. (Pubitemid 27180989)
67. 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)