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Molecular beacons

Fluorogenic probes for living cell study

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Abstract

Molecular beacons are a new class of fluorescent probes that can report the presence of specific nucleic acids with high sensitivity and excellent specificity. In addition to their current wide applications in monitoring the progress of polymerase chain reactions, their unique properties make them promising probes for the detection and visualization of target biomolecules in living cells. This article is focused on our recent research in exploring the potential of using molecular beacon for living-cell studies in three important areas: the monitoring of mRNA in living cells, the development of ultrasmall DNA/RNA biosensors, and the novel approach of combining molecular beacon's signal transduction mechanism with aptamer's specificity for real-time protein detection. These applications demonstrate molecular beacon's unique properties in bioanalysis and bioassay development.

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References

  1. Rizzuto, R. and Fasolato, C. (1999) Imaging Living Cells, Springer-Verlag, Berlin.

    Google Scholar 

  2. Gadella, T. W. J., van der Krogt, G. N. M., and Bisselling, T. (1999) GFP-based FRET microscopy in living plant cells. Trends Plant Sci. 4, 287–291.

    Article  PubMed  Google Scholar 

  3. Tsien, R. Y. (1994) Fluorescence imaging creates a window on the cell. C&EN July 18, 34–44.

    Google Scholar 

  4. Wang, X. and Herman, B., eds. (1996) Imaging Spectroscopy and Microscopy. Wiley, New York, pp. 407–475.

    Google Scholar 

  5. Tyagi, S. and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303–308; Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49–53.

    Article  PubMed  CAS  Google Scholar 

  6. Fang, X., Li, J. J., Perlette, J., Wang, K., and Tan, W. (2000) Molecular beacons: novel fluorescent DNA probes for biomolecular recognition. Anal. Chem. 72 (23), 747A-753A; Tan, W., Fang, X., Li, J., and Liu, X. (2000) Molecular beacons: a novel DNA probe for nucleic acid and protein studies. Chem-Eur. J. 6, 1107–1111.

    Article  PubMed  CAS  Google Scholar 

  7. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy, 2nd ed. Kluwer Academic/Plenum, New York; Morrison, L. E. (1999) Homogenous detection of specific DNA sequences by fluorescence quenching and energy transfer. J. Fluoresc. 9(3), 187–196

    Google Scholar 

  8. Fang, X. and Tan, W. (1999) Imaging single fluorescent molecules at the interface of an optical fiber probe by evanescent wave excitation. Anal. Chem. 71 (15), 3101–3105; Grunwell, J. R., Glass, J. L., Lacoste, T. D., Deniz, A. A., Chemla, D. S., and Schulz, P. G. (2001) Monitoring the conformational fluoctuations of DNA hairpins using single-pair fluorescence resonance energy transfer. J. Am. Chem. Soc. 123(18), 4295–4303; Ying, L. M., Wallace, M. I., and Klenerman, D. (2001) Two-state model of conformational fluctuation in a DNA hairpin-loop. Chem. Phys. Lett. 334(1–3), 145–150; Yao, G., Fang, X., and Tan, W. Study of the hybridization between molecular beacon and its complementary DNA at single molecular level. Anal. Chem., submitted.

    Article  CAS  Google Scholar 

  9. Bonnet, G., Tyagi, S., Libchaber, A., and Kramer, F. R. (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. PNAS 96 (11), 6171–6176.

    Article  PubMed  CAS  Google Scholar 

  10. Kostrikis, L. G., Tyagi, S., Mhlanga, M. M., Ho, D. D., and Kramer, F. R. (1998) Molecular beacons—spectral genotyping of human alleles. Science 279, 1228–1229.

    Article  PubMed  CAS  Google Scholar 

  11. Giesendorf, B. A. J., Vet, J. A. M., Tyagi, S., et al. (1998) Molecular beacons: a new approach for semiautomated mutation analysis. Clin. Chem. 44(3), 482–486.

    PubMed  CAS  Google Scholar 

  12. Vet, J. A. M., Majithia, A. R., Marras, S. A. E., et al. (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc. Natl. Acad. Sci. USA 96(11), 6394–6399.

    Article  PubMed  CAS  Google Scholar 

  13. de Baar, M. P., Timmermans, E. C., Bakker, M., de Rooij, E., van Gemen, B., and Goudsmit, J. (2001) One-tube real-time isothermal amplification assay to identify and distinguish human immunodeficiency virus type 1 subtypes A, B, and C and circulating recombinant forms AE and AG. J. Clin. Microbiol. 39(5), 1895–1902; Saha, B. K., Tian, B. H., and Bucy, R. P. (2001) Quantitation of HIV-1 by real-time PCR with a unique fluorogenic probe, J. Virol. Methods 93(1–2), 33–42.

    Article  PubMed  Google Scholar 

  14. Helps, C., Reeves, N., Tasker, S., and Harbour, D. (2001) Use of real-time quantitative PCR to detect Chlamydophila felis infection. J. Clin. Microbiol. 39(7), 2675–2676; Yates, S., Penning, M., Goudsmit, J., Frantzen, I., van de Weijer, B., van Strijp, D., and van Gemen, B. (2001) Quantitative detection of hepatitis B virus DNA by real-time nucleic acid sequence-based amplification with molecular beacon detection. J. Clin. Microbiol. 39(10), 3656–3665.

    Article  PubMed  CAS  Google Scholar 

  15. Dirks, R. W., Molenaar, C., and Tanke, H. J. (2001) Methods for visualizing RNA processing and transport pathway: in living cells. Histochem. Cell Biol. 15, 3–11.

    Google Scholar 

  16. Matsuo, T. (1998) In situ visualization of messenger RNA for basic fibroblast growth factor in living cells. BBA. Gen. Subjects 1379(2), 178–184.

    Article  CAS  Google Scholar 

  17. Sokol, D. L., Zhang, X. L., Lu, P. Z., and Gewitz, A. M. (1998) Real time detection of DNA RNA hybridization in living cells. Proc. Natl. Acad. Sci. USA 95, 11,538–11,543.

    Article  CAS  Google Scholar 

  18. Molenaar, C., Marras, S. A., Slats, J. C. M., Truffert, J. C., Lemaitre, M., Raap, A. K., et al. (2001), Linear 2′ O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res. 29(17), U26-U34.

    Article  Google Scholar 

  19. Perlette, J. and Tan, W. (2001) Real time detection of molecular beacon/mRNA hybridization in single living cell. Anal. Chem. 73.

  20. Fang, X., Liu, X., Schuster, S., and Tan, W. (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. J. Am. Chem. Soc. 121, 2921–2922.

    Article  CAS  Google Scholar 

  21. Ortiz, E., Estrada, G., and Lizardi, PM. (1998) PNA molecular beacons for rapid detection of PCR amplicons. Mol. Cell. Probes 12(4), 219–226; Brown, L. J., Cummins, J., Hamilton, A., and Brown, T. (2001) Molecular beacons attached to

    Article  PubMed  CAS  Google Scholar 

  22. Liu, X. and Tan, W. (1999) A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons. Anal. Chem. 71, 5054–5059; Liu, X., Farmerie, W., Schuster, S., and Tan, W. (2000) Molecular beacons for DNA biosensors with micrometer to submicrometer dimensions. Bioanal. Chem. 283, 56–63.

    Article  PubMed  CAS  Google Scholar 

  23. Steemers, F. J., Ferguson, J. A., and Walt, D. R. (2000) Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat. Biotechnol. 18(1) 91–94.

    Article  PubMed  CAS  Google Scholar 

  24. Fang, X., Schuster, S., Liu, X., and Tan, W. (2000) Molecular beacon biosensors. SPIE 3926, 2–8; Santra, S., Tapec, R., Theodoropoulou, N., Dobson, J., Hebard, A., and Tan, W. (2001) Synthesis and characterization of silica coated iron oxide nanoparticles in microemulsion: the effect of non-ionic surfactants. Langmuir 17(10), 2900–2906; Santra, S., Wang, K. M., Tapec, R., and Tan, W. (2001) Development of novel dye-doped silica nanoparticles for biomarker application. J. Biomed. Opt. 6(2), 160–166.

    Article  CAS  Google Scholar 

  25. Li, J., Fang, X., Schuster, S., and Tan, W. (2000) Molecular beacons: a novel approach to detect protein-DNA interactions. Angew. Chem. 39, 1049–1052.

    Article  CAS  Google Scholar 

  26. Fang, X., Li, J., and Tan, W. (2000) Using molecular beacons to probe the interactions between lactic dehydrogenase and single strand DNA. Anal. Chem. 72(14), 3250–3258.

    Article  CAS  Google Scholar 

  27. Li, J., Geyer, R., and Tan, W. (2000) Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA. Nucleic Acids Res. 28(52), 1–5.

    Article  CAS  Google Scholar 

  28. Bar-Ziv, R. and Libchaber, A. (2001) Effects of DNA sequence and structure on binding of RecA to single-stranded DNA. Proc. Natl. Acad. Sci. USA 98(16), 9068–9073.

    Article  PubMed  CAS  Google Scholar 

  29. Yamamoto, R. and Kumar, P. K. R. (2000) Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes to Cells 5(5), 389–396.

    Article  PubMed  CAS  Google Scholar 

  30. Hamaguchi, N., Ellington, A., and Stanton, M. (2001) Aptamer beacons for the direct detection of proteins. Anal. Biochem. 294(2), 126–131.

    Article  PubMed  CAS  Google Scholar 

  31. Li, J., Perlette, J., Fang, X., Kelley, S., and Tan, W. (2000) Novel molecular beacon DNA probes for protein-nucleic acid interaction studies. SPIE 3926, 14–21; Li, J. J. Fang, X., and Tan, W. (2001) Molecular aptamer beacon: a novel molecular probe for real time protein recognition. J. Am. Chem. Soc. submitted.

    Google Scholar 

  32. Tan, W., Kopelman, R., Barker, S., and Miller, M. (1999) Ultrasmall optical sensors for cellular measurements. Anal. Chem. 71, 606A-612A.

    PubMed  CAS  Google Scholar 

  33. Cullum, B. M. and Vo-Dinh, T. (2000) The development of optical nanosensors for biological measurement. Trends Biotechnol. 18(9) 388–393.

    Article  PubMed  CAS  Google Scholar 

  34. Tan, W., Shi, Y., Smith, S., Birnbaum, D., and Kopelman, R. (1992) Submicrometer intracellular chemical optical fiber sensors. Science 258, 778–781.

    Article  PubMed  CAS  Google Scholar 

  35. Zeisel, D., Dutoit, B., Deckert, V., Roth, T., and Zenobi, R. (1997) Optical spectroscopy and laser desorption on a nanometer scale. Anal. Chem. 69, 749–754.

    Article  CAS  Google Scholar 

  36. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505–510; Ellington, A. D. and Szostak J. W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822.

    Article  PubMed  CAS  Google Scholar 

  37. Jayasena, S. D. (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45, 1628–1650.

    PubMed  CAS  Google Scholar 

  38. Zhang, P., Beck, T., and Tan, W. (2001) Design of molecular beacon DNA probe with two fluorophores. Angew. Chem. Int. Ed. 40(2), 402–405.

    Article  CAS  Google Scholar 

  39. Claesson-Welsh, L., Eriksson, A., Westermark, B., and Heldin, C.-H. (1989) cDNA cloning and expression of the human a-type platelet-derived growth-factor (PDGF) receptor establishes structural similarity to the b-type PDGF receptor. Proc. Natl. Acad. Sci. USA 86, 4917–4921.

    Article  PubMed  CAS  Google Scholar 

  40. Fang, X., Cao, Z., Terry, B., and Tan, W. (2001) Molecular aptamer for real-time oncoprotein PDGF monitoring by fluorescence anisotropy, Anal. Chem. 73; Fang, X., Vicens, M., and Tan, W. Novel molecular beacon aptamer for oncoprotein PDGF studies with cancer cells. Unpublished.

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Correspondence to Weihong Tan.

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Fang, X., Mi, Y., Li, J.J. et al. Molecular beacons. Cell Biochem Biophys 37, 71–81 (2002). https://doi.org/10.1385/CBB:37:2:071

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