• Journal of Innovative Optical Health Sciences
  • Vol. 2, Issue 4, 315 (2009)
ANTONY K. CHEN and ANDREW TSOURKAS*
Author Affiliations
  • Department of Bioengineering, University of Pennsylvania Philadelphia, PA 19104, USA
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    DOI: Cite this Article
    ANTONY K. CHEN, ANDREW TSOURKAS. IMAGING RNA IN LIVING CELLS WITH MOLECULAR BEACONS: CURRENT PERSPECTIVES AND CHALLENGES[J]. Journal of Innovative Optical Health Sciences, 2009, 2(4): 315 Copy Citation Text show less
    References

    [1] D. A. Hume, “Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression,” Blood 96, 2323–2328 (2000).

    [2] T. B. Kepler, T. C. Elston, “Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations,” Biophys. J. 81, 3116–3136 (2001).

    [3] I. L. Ross, C. M. Browne, D. A. Hume, “Transcription of individual genes in eukaryotic cells occurs randomly and infrequently,” Immunol. Cell. Biol. 72, 177–185 (1994).

    [4] P. S. Swain, M. B. Elowitz, E. D. Siggia, “Intrinsic and extrinsic contributions to stochasticity in gene expression,” Proc. Natl. Acad. Sci. U. S. A. 99, 12795–12800 (2002).

    [5] M. Mitsuhashi, S. Tomozawa, K. Endo, A. Shinagawa, “Quantification of mRNA in whole blood by assessing recovery of RNA and efficiency of cDNA synthesis,” Clin. Chem. 52, 634–642 (2006).

    [6] J. Lu, A. Tsourkas, “Imaging individual microRNAs in single mammalian cells in situ,” Nucleic Acids Res. 37, e100 (2009).

    [7] A. M. Femino, F. S. Fay, K. Fogarty, R. H. Singer, “Visualization of single RNA transcripts in situ,” Science 280, 585–590 (1998).

    [8] A. Raj, C. S. Peskin, D. Tranchina, D. Y. Vargas, S. Tyagi, “Stochastic mRNA synthesis in mammalian cells,” PLoS Biol. 4, e309 (2006).

    [9] A. Raj, P. van den Bogaard, S. A. Rifkin, A. van Oudenaarden, S. Tyagi, “Imaging individual mRNA molecules using multiple singly labeled probes,” Nat. Methods 5, 877–879 (2008).

    [10] G. Bao, W. J. Rhee, A. Tsourkas, “Fluorescent probes for live-cell RNA detection,” Annu. Rev. Biomed. Eng. (2009).

    [11] S. Tyagi, F. R. Kramer, “Molecular beacons: Probes that fluoresce upon hybridization,” Nat. Biotechnol. 14, 303–308 (1996).

    [12] D. P. Bratu, B. J. Cha, M. M. Mhlanga, F. R. Kramer, S. Tyagi, “Visualizing the distribution and transport of mRNAs in living cells,” Proc. Natl. Acad. Sci. U. S. A. 100, 13308–13313 (2003).

    [13] A. K. Chen, M. A. Behlke, A. Tsourkas, “Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells,” Nucleic Acids Res. 35, e105 (2007).

    [14] A. K. Chen, M. A. Behlke, A. Tsourkas, “Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA,” Nucleic Acids Res. 36, e69 (2008).

    [15] T. J. Drake, C. D. Medley, A. Sen, R. J. Rogers, W. Tan, “Stochasticity of manganese superoxide dismutase mRNA expression in breast carcinoma cells by molecular beacon imaging,” Chembiochem 6, 2041– 2047 (2005).

    [16] C. D. Medley, T. J. Drake, J. M. Tomasini, R. J. Rogers, W. Tan, “Simultaneous monitoring of the expression of multiple genes inside of single breast carcinoma cells,” Anal Chem. 77, 4713–4718 (2005).

    [17] M. M. Mhlanga, D. Y. Vargas, C. W. Fung, F. R. Kramer, S. Tyagi, “tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells,” Nucleic Acids Res. 33, 1902–1912 (2005).

    [18] N. Nitin, G. Bao, “NLS peptide conjugated molecular beacons for visualizing nuclear RNA in living cells,” Bioconjug. Chem. 19, 2205–2211 (2008).

    [19] N. Nitin, P. J. Santangelo, G. Kim, S. Nie, G. Bao, “Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells,” Nucleic Acids Res. 32, e58 (2004).

    [20] X. H. Peng, Z. H. Cao, J. T. Xia, G. W. Carlson, M. M. Lewis, W. C. Wood, L. Yang, “Real-time detection of gene expression in cancer cells using molecular beacon imaging: New strategies for cancer research,” Cancer Res. 65, 1909–1917 (2005).

    [21] J. Perlette, W. Tan, “Real-time monitoring of intracellular mRNA hybridization inside single living cells,” Anal. Chem. 73, 5544–5550 (2001).

    [22] W. J. Rhee, G. Bao, “Simultaneous detection of mRNA and protein stem cell markers in live cells,” BMC Biotechnol. 9, 30 (2009).

    [23] W. J. Rhee, P. J. Santangelo, H. Jo, G. Bao, “Target accessibility and signal specificity in live-cell detection of BMP-4 mRNA using molecular beacons,” Nucleic Acids Res. 36, e30 (2008).

    [24] A. J. Rodriguez, J. Condeelis, R. H. Singer, J. B. Dictenberg, “Imaging mRNA movement from transcription sites to translation sites,” Semin. Cell Dev. Biol. 18, 202–208 (2007).

    [25] P. Santangelo, N. Nitin, L. LaConte, A. Woolums, G. Bao, “Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus, using molecular beacons,” J. Virol. 80, 682–688 (2006).

    [26] P. J. Santangelo, B. Nix, A. Tsourkas, G. Bao, “Dual FRET molecular beacons for mRNA detection in living cells,” Nucleic Acids Res. 32, e57 (2004).

    [27] S. Tyagi, O. Alsmadi, “Imaging native beta-actin mRNA in motile fibroblasts,” Biophys. J. 87, 4153– 4162 (2004).

    [28] W.Wang, Z. Q. Cui, H. Han, Z. P. Zhang,H. P. Wei, Y. F. Zhou, Z. Chen, X. E. Zhang, “Imaging and characterizing influenza A virus mRNA transport in living cells,” Nucleic Acids Res. 36, 4913–4928 (2008).

    [29] Y. Wu, C. J. Yang, L. L. Moroz, W. Tan, “Nucleic acid beacons for long-term real-time intracellular monitoring,” Anal. Chem. 80, 3025–3028 (2008).

    [30] H. Y. Yeh, M. V. Yates, A. Mulchandani, W. Chen, “Visualizing the dynamics of viral replication in living cells via Tat peptide delivery of nucleaseresistant molecular beacons,” Proc. Natl. Acad. Sci. U. S. A. 105, 17522–17525 (2008).

    [31] S. Tyagi, O. Alsmadi, “Imaging native [beta]-actin mRNA in motile fibroblasts,” Biophys. J. (2004).

    [32] D. Y. Vargas, A. Raj, S. A. Marras, F. R. Kramer, S. Tyagi, “Mechanism of mRNA transport in the nucleus,” Proc. Natl. Acad. Sci. U. S. A. 102, 17008–17013 (2005).

    [33] A. K. Chen, Z. Cheng, M. A. Behlke, A. Tsourkas, “Assessing the sensitivity of commercially available fluorophores to the intracellular environment,” Anal. Chem. 80, 7437–7444 (2008).

    [34] J. H. Kim, D. Morikis, M. Ozkan, “Adaptation of inorganic quantum dots for stable molecular beacons,” Sens. Actuators B-Chem. 102, 315–319 (2004).

    [35] W. C. Chan, D. J. Maxwell, X. Gao, R. E. Bailey, M. Han, S. Nie, “Luminescent quantum dots for multiplexed biological detection and imaging,” Curr. Opin. Biotechnol. 13, 40–46 (2002).

    [36] S. A. Marras, F. R. Kramer, S. Tyagi, “Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes,” Nucleic Acids Res. 30, e122 (2002).

    [37] B. Dubertret, M. Calame, A. J. Libchaber, “Singlemismatch detection using gold-quenched fluorescent oligonucleotides,” Nat. Biotechnol. 19, 365–370 (2001).

    [38] C. J. Yang, H. Lin, W. Tan, “Molecular assembly of superquenchers in signaling molecular interactions,” J. Am. Chem. Soc. 127, 12772–12773 (2005).

    [39] F. Hide, B. J. Schwartz, M. A. Diaz-Garcia, A. J. Heeger, “Conjugated polymers as solid-state laser materials,” Synth. Met. 91, 35–40 (1997).

    [40] S. A. Kushon, K. D. Ley, K. Bradford, R. M. Jones, D. McBranch, D. Whitten, “Detection of DNA hybridization via fluorescent polymer superquenching,” Langmuir 18, 7245–7249 (2002).

    [41] L. D. Lu, R. M. Jones, D. McBranch, D. Whitten, “Surface-enhanced superquenching of cyanine dyes as J-aggregates on Laponite clay nanoparticles,” Langmuir 18, 7706–7713 (2002).

    [42] L.Chen, D.W. McBranch,H. L.Wang, R. Helgeson, F. Wudl, D. G. Whitten, “Highly sensitive biological and chemical sensors based on reversible fluorescence quenching in a conjugated polymer,” Proc. Natl. Acad. Sci. U. S. A. 96, 12287–12292 (1999).

    [43] G. Bonnet, S. Tyagi, A. Libchaber, F. R. Kramer, “Thermodynamic basis of the enhanced specificity of structured DNA probes,” Proc. Natl. Acad. Sci. U. S. A. 96, 6171–6176 (1999).

    [44] A. Tsourkas, M. A. Behlke, G. Bao, “Structurefunction relationships of shared-stem and conventional molecular beacons,” Nucleic Acids Res. 30, 4208–4215 (2002).

    [45] A. Tsourkas, M. A. Behlke, S. D. Rose, G. Bao, “Hybridization kinetics and thermodynamics of molecular beacons,” Nucleic Acids Res. 31, 1319– 1330 (2003).

    [46] R. M. van Dam, S. R. Quake, “Gene expression analysis with universal n-mer arrays,” Genome Res. 12, 145–152 (2002).

    [47] L. K. Gifford, D. Jordan, V. Pattanayak, K. Vernovsky, B. T. Do, A. M. Gewirtz, P. Lu, “Stemless self-quenching reporter molecules identify target sequences in mRNA,” Anal. Biochem. 347, 77–88 (2005).

    [48] J. J. Li, X. Fang, S.M. Schuster,W. Tan, “Molecular beacons: A novel approach to detect protein—DNA interactions. This work was partially supported by a U.S. NSF Career Award (CHE-9733650) and by a U.S. Office of Naval Research Young Investigator Award (N00014-98-1-0621),”Angew. Chem. Int. Ed. Engl. 39, 1049-1052 (2000).

    [49] J. J. Li, R. Geyer, W. Tan, “Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA,” Nucleic Acids Res. 28, E52 (2000).

    [50] A. K. Chen, M. A. Behlke, A. Tsourkas, “Subcellular trafficking and functionality of 2’-O-methyl and 2‘-O-methyl-phosphorothioate molecular beacons,” Nucleic Acids Res. In press (2009).

    [51] A. Tsourkas, M. A. Behlke, G. Bao, “Hybridization of 2‘-O-methyl and 2‘-deoxy molecular beacons to RNA and DNA targets,” Nucleic Acids Res. 30, 5168–5174 (2002).

    [52] C.Molenaar, S. A.Marras, J. C. Slats, J. C. Truffert, M. Lemaitre, A. K. Raap, R. W. Dirks, H. J. Tanke, “Linear 2’ O-methyl RNA probes for the visualization of RNA in living cells,” Nucleic Acids Res. 29, E89–89 (2001).

    [53] L. Wang, C. J. Yang, C. D. Medley, S. A. Benner, W. Tan, “Locked nucleic acid molecular beacons,” J. Am. Chem. Soc. 127, 15664–15665 (2005).

    [54] C. J. Yang, L. Wang, Y. Wu, Y. Kim, C. D. Medley, H. Lin, W. Tan, “Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons,” Nucleic Acids Res. 35, 4030– 4041 (2007).

    [55] Y. Kim, C. J. Yang, W. Tan, “Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem,” Nucleic Acids Res. 35, 7279–7287 (2007).

    [56] L. Good, P. E. Nielsen, “Progress in developing PNA as a gene-targeted drug,” Antisense Nucleic Acid Drug Dev. 7, 431–437 (1997).

    [57] I. Leiros, J. Timmins, D. R. Hall, S. McSweeney, “Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans,” EMBO J. 24, 906–918 (2005).

    [58] M. Egholm, P. E. Nielsen, O. Buchardt, R. H. Berg, “Recognition of guanine and adenine in DNA by cytosine and thymine containing peptide nucleicacids (PNA),” J. Am. Chem. Soc. 114, 9677–9678 (1992).

    [59] K. L. Dueholm, M. Egholm, C. Behrens, L. Christensen, H. F. Hansen, T.Vulpius, K.H. Petersen, R. H. Berg, P. E. Nielsen, O. Buchardt, “Synthesis of peptide nucleic-acid monomers containing the 4 natural nucleobases — thymine, cytosine, adenine, and guanine and their oligomerization,” J. Org. Chem. 59, 5767–5773 (1994).

    [60] M. L. Graber, D. C. DiLillo, B. L. Friedman, E. Pastoriza-Munoz, “Characteristics of fluoroprobes for measuring intracellular pH,” Anal. Biochem. 156, 202-212 (1986).

    ANTONY K. CHEN, ANDREW TSOURKAS. IMAGING RNA IN LIVING CELLS WITH MOLECULAR BEACONS: CURRENT PERSPECTIVES AND CHALLENGES[J]. Journal of Innovative Optical Health Sciences, 2009, 2(4): 315
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