BRET-based method for detection of specific RNA species

Bioconjugate Chemistry

Volumn 19, Issue 1, 2008, Pages 178-184

  Walls, Zachary F ^a   Gambhir, Sanjiv S ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; BINDING SITES; ENERGY TRANSFER; FORSTER RESONANCE ENERGY TRANSFER; OLIGONUCLEOTIDES;

BINDING-SITES; IN-VITRO; RESONANCE ENERGY TRANSFER; RNA DETECTION; SPACER LENGTHS; TARGET SEQUENCES;

RNA;

COMPLEMENTARY RNA; OLIGONUCLEOTIDE; RNA;

ACCURACY; ARTICLE; BINDING SITE; BIOLUMINESCENCE RESONANCE ENERGY TRANSFER; CONJUGATION; RNA ANALYSIS; RNA PROBE; RNA SEQUENCE;

EID: 38949192176     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc700278n     Document Type: Article

References (34)

1. Alwine, J. C., Kemp, D. J., and Stark, G. R. (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc. Natl. Acad. Sci. U.S.A. 74, 5350-4.
2. Wong, M. L., and Medrano, J. F. (2005) Real-time PCR for mRNA quantitation. BioTechniques 39, 75-85.
3. Prediger, E. A. (2001) Detection and quantitation of mRNAs using ribonuclease protection assays. Methods Mol. Biol. (Totowa, NJ, U. S.) 160, 495-505.
4. Nicholls, P. J., and Malcolm, A. D. (1989) Nucleic acid analysis by sandwich hybridization. J. Clin. Lab. Anal. 3, 122-35.
5. Xu, Y., Piston, D. W., and Johnson, C. H. (1999) A bioluminescence resonance energy transfer (BRET) system: application to interacting circadian clock proteins. Proc. Natl. Acad. Sci. U.S.A. 96, 151-6.
6. De, A., Loening, A. M., & Gambhir, S. S. (2007) An improved bioluminescence resonance energy transfer strategy for imaging intracellular events in single cells and living subjects, Cancer Res. 67.
7. Loening, A. M., Fenn, T. D., Wu, A. M., and Gambhir, S. S. (2006) Consensus guided mutagenesis of Renilla luciferase yields enhanced stability and light output. Protein Eng. Des. Sel. 19, 391-400.
8. Kozlov, I. A., Melnyk, P. C., Stromsborg, K. E., Chee, M. S., Barker, D. L., and Zhao, C. (2004) Efficient strategies for the conjugation of oligonucleotides to antibodies enabling highly sensitive protein detection. Biopolymers 73, 621-30.
9. Jensen, A. A., Hansen, J. L., Sheikh, S. P., and Brauner-Osborne, H. (2002) Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET). Eur. J. Biochem. 269, 5076-87.
10. Angers, S., Salahpour, A., Joly, E., Hilairet, S., Chelsky, D., Dennis, M., and Bouvier, M. (2000) Detection of beta 2-adrenergic receptor dimerization in living cells using bioluminescence resonance energy transfer (BRET). Proc. Natl. Acad. Sci. U.S.A. 97, 3684-9.
11. Arai, R., Nakagawa, H., Kitayama, A., Ueda, H., and Nagamune, T. (2002) Detection of protein-protein interaction by bioluminescence resonance energy transfer from firefly luciferase to red fluorescent protein. J. Biosci. Bioeng. 94, 362-4.
12. 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, 3260-74.
13. Lobashevsky, A. L., Jiang, X. L., and Thomas, J. M. (2002) Allele-specific in situ analysis of microchimerism by fluorescence resonance energy transfer (FRET) in nonhuman primate tissues. Hum. Immunol. 63, 108-20.
14. Dirks, R. W., Molenaar, C., and Tanke, H. J. (2003) Visualizing RNA molecules inside the nucleus of living cells. Methods (San Diego, CA, U. S.) 29, 51-7.
15. Okabe, K., Ikeda, H., Harada, Y., and Funatsu, T. (2005) Development of real time imaging of specific messenger RNA in a living cell using artificial antisense nucleic acids. Nucleic Acids Symp. Ser. 2004, 207-8.
16. 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.
17. Tsourkas, A., Behlke, M. A., Xu, Y., and Bao, G. (2003) Spectroscopic features of dual fluorescence/luminescence resonance energy-transfer molecular beacons. Anal. Chem. 75, 3697-703.
18. Okamura, Y., Kondo, S., Sase, I., Suga, T., Mise, K., Furusawa, I., Kawakami, S., and Watanabe, Y. (2000) Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucleic Acids Res. 28, E107.
19. Cardullo, R. A., Agrawal, S., Flores, C., Zamecnik, P. C., and Wolf, D. E. (1988) Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. U.S.A. 85, 8790-4.
20. De, A., and Gambhir, S. S. (2005) Noninvasive imaging of protein-protein interactions from live cells and living subjects using bioluminescence resonance energy transfer. FASEB J. 19, 2017-9.
21. Renz, M., and Kurz, C. (1984) A colorimetric method for DNA hybridization. Nucleic Acids Res. 12, 3435-44.
22. Salisch, H., Ryll, M., Leise, R., and Neumann, U. (2000) Use of an alkaline phosphatase-labelled probe for the detection of Mycoplasma synoviae in chickens. J. Vet. Med. 47, 27-35.
23. Jablonski, E., Moomaw, E. W., Tullis, R. H., and Ruth, J. L. (1986) Preparation of oligodeoxynucleotide-alkaline phosphatase conjugates and their use as hybridization probes. Nucleic Acids Res. 14, 6115-28.
24. Guerasimova, A., Ivanov, I., and Lehrach, H. (1999) A method of one-step enzyme labelling of short oligonucleotide probes for filter hybridisation. Nucleic Acids Res. 27, 703-5.
25. Ruth, J. L. (1996) Oligozymes. Oligonucleotide-enzyme conjugates. Mol. Biotechnol. 6, 163-78.
26. Matsuhisa, A., Kishi, Y., and Shiba, K. (1994) A simple staining method for dna and rna blotted on a membrane using a polyethyleneimine-enzyme conjugate. J. Biochem. 116, 478-81.
27. Watson, J. D., and Crick, F. H. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature (London) 171, 737-8.
28. Stryer, L. (1978) Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47, 819-46.
29. Paulmurugan, R., Umezawa, Y., and Gambhir, S. S. (2002) Noninvasive imaging of protein-protein interactions in living subjects by using reporter protein complementation and reconstitution strategies. Proc. Natl. Acad. Sci. U.S.A. 99, 15608-13.
30. Jones, S. W., Christison, R., Bundell, K., Voyce, C. J., Brockbank, S. M., Newham, P., and Lindsay, M. A. (2005) Characterisation of cell-penetrating peptide-mediated peptide delivery. Br. J. Pharmacol. 145, 1093-102.
31. Al-Taei, S., Penning, N. A., Simpson, J. C., Futaki, S., Takeuchi, T., Nakase, I., and Jones, A. T. (2006) Intracellular traffic and fate of protein transduction domains HIV-1 TAT peptide and octaarginine. Implications for their utilization as drug delivery vectors. Bioconjugate Chem. 17, 90-100.
32. Shi, N., Boado, R. J., and Pardridge, W. M. (2000) Antisense imaging of gene expression in the brain in vivo. Proc. Natl. Acad. Sci. U.S.A. 97, 14709-14.
33. Kobayashi, N., Kuramoto, T., Yamaoka, K., Hashida, M., and Takakura, Y. (2001) Hepatic uptake and gene expression mechanisms following intravenous administration of plasmid DNA by conventional and hydrodynamics-based procedures. J. Pharmacol. Exp. Ther. 297, 853-60.
34. Thrush, E., Levi, O., Ha, W., Wang, K., Smith, S. J., Jr., and Harris, J. S. (2003) Integrated bio-fluorescence sensor. J. Chromatogr. 1013, 103-10.