Oligonucleotide Probes

  • Deming Kong
Chapter
Part of the Advanced Topics in Science and Technology in China book series (ATSTC)

Abstract

The development of methods for non-invasive, real-time imaging of gene expression would provide powerful tools for biomedical research and medical diagnostics. The major challenge for molecular imaging is the development of specific and efficient probes. For this reason, oligonucleotide probes have attracted more and more attention during the recent two decades due to their high water-solubility, low toxicity, high biocompatibility, high recognition specificity and the ability to readily mutate and self-replicate. To date, a few promising oligonucleotide probes have been designed and used in the detection and/or imaging of mRNAs in living cells[1–4]. The design principles and anti-nuclease modifications of some oligonucleotide probes have been reported and the methods for delivering these probes into cells will be described in the following sections.

Keywords

Fluorescence Resonance Energy Transfer Oligonucleotide Probe Peptide Nucleic Acid Molecular Beacon Nucleic Acid Research 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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References

  1. [1]
    Santangelo, P., N. Nitin & G. Bao (2006). “Nanostructured probes for RNA detection in living cells”, Annals of Biomedical Engineering 34: 39–50.PubMedCrossRefGoogle Scholar
  2. [2]
    Dirks, R. W., C. Molenaar & H. J. Tanke (2001). “Methods for visualizing RNA processing and transport pathways in living cells”, Histochemistry and Cell Biology 115: 3–11.PubMedGoogle Scholar
  3. [3]
    Dirks, R. W., C. Molenaar & H. J. Tanke (2003). “Visualizing RNA molecules inside the nucleus of living cells”, Methods 29: 51–57.PubMedCrossRefGoogle Scholar
  4. [4]
    Paroo, Z. & D. R. Corey (2003). “Imaging gene expression using oligonucleotides and peptide nucleic acids”, Journal of Cellular Biochemistry 90: 437–442.PubMedCrossRefGoogle Scholar
  5. [5]
    Morrisong, L. E., T. C. Halder & L. M. Stols (1989). “Solution-phase detection of polynucleotide suing interacting fluorescent labels and competitive hybridization”, Analytical Biochemistry 183: 231–244.CrossRefGoogle Scholar
  6. [6]
    Sixou, S., F. C. Szoka, G. A. Green, B. Giusti, G. Zon & D. J. Chin (1994). “Intracellular oligonucleotide hybridization detected by fluorescence resonance energy transfer (FRET)”, Nucleic Acids Research 22: 662–668.PubMedCrossRefGoogle Scholar
  7. [7]
    Kong, D. M., L. Gu, H. X. Shen & H. F. Mi (2002). “Simulation of TaqMan by two single-labelled probes”, Chemistry Communications 2584–2585.Google Scholar
  8. [8]
    Kong, D. M., Y. P. Huang, X. B. Zhang, W. H. Yang, H. X. Shen & H. F. Mi (2003). “Duplex probes: A new approach for the detection of specific nucleic acids in homogenous assays”, Analytica Chimica Acta 491: 135–143.CrossRefGoogle Scholar
  9. [9]
    Li, Q., G. Luan, Q. Guo & J. Liang (2002). “A new class of homogeneous nucleic acid probes based on specific displacement hybridization”, Nucleic Acids Research 30: E5.PubMedCrossRefGoogle Scholar
  10. [10]
    Tyagi, S. & F. R. Kramer (1996). “Molecular beacons: probes that fluoresce upon hybridization”, Natire Biotechnology 14: 303–308.CrossRefGoogle Scholar
  11. [11]
    Abravaya, K., J. Huff, R. Marshall, B. Merchant, C. Mullen, G. Schneider & J. Robinson (2003). “Molecular beacons as diagnostic tools: Technology and applications”, Clinical Chemistry Laboratory Medicine 41: 468–474.PubMedCrossRefGoogle Scholar
  12. [12]
    Broude, N. E. (2002). “Stem-loop oligonucleotides: A robust tool for molecular biology and biotechnology”, Trends in Biotechnology 20: 249–256.PubMedCrossRefGoogle Scholar
  13. [13]
    Fang, X., J. J. Li, J. Perlette, W. Tan & K. Wang (2000). “Molecular beacons: Novel fluorescent probes”, Analytical Chemistry 72: 747a–753a.PubMedCrossRefGoogle Scholar
  14. [14]
    Marras, S. A. E. (2006). “Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes”, Methods in Molecular Biology 335: 3–16.PubMedGoogle Scholar
  15. [15]
    Tan, W., K. Wang & T. J. Drake (2004). “Molecular beacons”, Current Opinion in Chemistry Biology 8: 547–553.CrossRefGoogle Scholar
  16. [16]
    Wang, K., Z. Tang, C. J. Yang, Y. Kim, X. Fang, W. Li, Y. Wu, C. D. Medley, Z. Cao, J. Li, P. Colon, H. Lin & W. Tan (2008). “Molecular engineering of DNA: Molecular beacons”, Angewandte Chemie International Edition English 47: 2–17.CrossRefGoogle Scholar
  17. [17]
    Tan, W., X. Fang, J. Li & X. Liu (2000). “Molecular beacons: A novel DNA probe for nucleic acid and protein studies”, Chemistry European Journal 6: 1107–1111.CrossRefGoogle Scholar
  18. [18]
    Kim, Y., D. Sohn & W. Tan (2008). “Molecular beacons in biomedical detection and clinical diagnosis”, International Journal of Clinical Experimental Pathology 1: 105–116.PubMedGoogle Scholar
  19. [19]
    Marras, S. A. E., S. Tyagi & F. R. Kramer (2006). “Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes”, Clinical Chimica Acta 363: 48–60.CrossRefGoogle Scholar
  20. [20]
    Li, Y., X. Zhou & D. Ye (2008). “Molecular beacons: An optimal multifunctional biological probe”, Biochemistry Biophysics Research Communications 373: 457–468.CrossRefGoogle Scholar
  21. [21]
    Tanke, H. J., R. W. Dirks & T. Raap (2005). “FISH and immunocytochemistry: Towards visualizing single target molecules in living cells”, Current Opinion in Biotechnology 16: 49–54.PubMedCrossRefGoogle Scholar
  22. [22]
    Bratu, D. P. (2006). “Molecular beacons: Fluorescent probes for detection of endogenous mRNAs in living cells”, Methods in Molecular Biology 319: 1–14.PubMedCrossRefGoogle Scholar
  23. [23]
    Fang, X, Y. Mi, J. J. Li, T. Beck, S. Schuster & W. Tan (2002). “Molecular beacons: Fluorogenic probes for living cell study”, Cell Biochemistry and Biophysics 37: 71–81.PubMedCrossRefGoogle Scholar
  24. [24]
    Täpp, I., L. Malmberg, E. Rennel, M. Wik & A. C. Syvanen (2000). “Homogeneous scoring of single-nucleotide polymorphisms: Comparison of the 5′-nuclease TaqMan assay and molecular beacon probes”, Biotechniques 28: 732–738.PubMedGoogle Scholar
  25. [25]
    Bonnet, G., S. Tyagi, A. Libchaber & F. R. Kramer (1999). “Thermodynamic basis of the enhanced specificity of structured DNA probes”, Proceedings of National Academy Of Sciences 96: 6171–6176.CrossRefGoogle Scholar
  26. [26]
    Marras, S. A. E., F. R. Kramer & S. Tyagi (1999). “Multiplex detection of single-nucleotide variations using molecular beacons”, Genetic Analysis 14: 151–156.PubMedCrossRefGoogle Scholar
  27. [27]
    Sokol, D. L., X. Zhang, P. Lu & A. M. Gewirtz (1998). “Real time detection of DNA. RNA hybridization in living cells”, Proceedings of National Academy of Sciences 95: 11538–11543.CrossRefGoogle Scholar
  28. [28]
    Bratu, D. P., B. J. Cha, M. M. Mhlanga, F. R. Kramer & S. Tyagi (2003). “Visualizing the distribution and transport of mRNAs in living cells”, Proceedings of National Academy of Sciences 100: 13308–13313.CrossRefGoogle Scholar
  29. [29]
    Perlette, J. & W. Tan (2001). “Real-time monitoring of intracellular mRNA hybridization inside single living cells”, Analytical Chemistry 73: 5544–5550.PubMedCrossRefGoogle Scholar
  30. [30]
    Matsuo, T. (1998). “In situ visualization of messenger RNA for basic fibroblast growth factor in living cells”, Biochimica et Biophysica Acta 1379: 178–184.PubMedCrossRefGoogle Scholar
  31. [31]
    Rhee, W. J., P. J. Santangelo, H. Jo & G. Bao (2008). “Target accessibility and signal specificity in live-cell detection of bmp-4 mRNA using molecular beacons”, Nucleic Acids Research 36: E30.PubMedCrossRefGoogle Scholar
  32. [32]
    Rhee, W. J. & G. Bao (2009). “Simultaneous detection of mRNA and protein stem cell markers in live cells”, BMC Biotechnology 9:30.PubMedCrossRefGoogle Scholar
  33. [33]
    Rodriguez, A. J., J. Condeelis, R. H. Singer & J. B. Dictenberg (2007). “Imaging mRNA movement from transcription sites to translation sites”, Seminars in Cell & Developmental Biology 18: 202–208.CrossRefGoogle Scholar
  34. [34]
    Santangelo, P. J., N. Nitin & G. Bao (2005). “Direct visualization of mRNA colocalization with mitochondria in living cells using molecular beacons”, Journal of Biomedical Optics 10: 44025.PubMedCrossRefGoogle Scholar
  35. [35]
    Santangelo, P. J., N. Nitin, L. Laconte, A. Woolums & G. Bao (2006). “Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus using molecular beacons”, Journal of Virology 80: 682–688.PubMedCrossRefGoogle Scholar
  36. [36]
    Tyagi, S. & O. Alsmadi (2004). “Imaging native Beta-actin mRNA in motile fibroblasts”, Biophysics Journal 78: 4153–4163.CrossRefGoogle Scholar
  37. [37]
    van den Bogaard, P. T. & S. Tyagi (2009). “Using molecular beacons to study dispersal of mRNPs from the gene locus”, Methods in Molecular Biology 464: 91–103.PubMedCrossRefGoogle Scholar
  38. [38]
    Vargas, D. Y., A. Raj, S. A. Marras, F. R. Kramer & S. Tyagi (2005). “Mechanism of mRNA transport in the nucleus”, Proceedings of National Academy of Sciences 102: 17008–17013.CrossRefGoogle Scholar
  39. [39]
    Wang, A., A. M. Salazar, M. V. Yates, A. Mulchandani & W. Chen (2005). “Visualization and detection of infectious coxsackievirus replication using a combined cell culture-molecular beacon assay”, Applied and Environental Microbiology 71: 8397–8401.CrossRefGoogle Scholar
  40. [40]
    Wu, Y., C. J. Yang, L. L. Moroz & W. Tan (2008). “Nucleic acid beacons for long-term real-time intracellular monitoring”, Analytical Chemistry 80: 3025–3028.PubMedCrossRefGoogle Scholar
  41. [41]
    Wang, W., Z. Q. Cui, H. Han, Z. P. Zhang, H. P. Wei, Y. F. Zhou, Z. Chen & X. E. Zhang (2008). “Imaging and characterizing influenza A virus mRNA transport in living cells”, Nucleic Acids Research 36: 4913–4928.PubMedCrossRefGoogle Scholar
  42. [42]
    Tsourkas, A., M. A. Behlke & G. Bao (2002). “Structure-function relationship of shared-stem and conventional molecular beacons”, Nucleic Acids Research 30: 4208–4215.PubMedCrossRefGoogle Scholar
  43. [43]
    Kong, D. M., L. Gu, H. X. Shen & H. F. Mi (2002). “A modified molecular beacon combining the properties of TaqMan probe”, Chemistry Communication 854–855.Google Scholar
  44. [44]
    Tyagi, S., D. P. Bratu & F. R. Kramer (1998). “Multicolor molecular beacons for allele discrimination”, Nature Biotechnology 16: 49–53.PubMedCrossRefGoogle Scholar
  45. [45]
    Kostrikis, L. G., S. Tyagi, M. M. Mhlanga, D. D. Ho & F. R. Kramer (1998). “Spectral genotyping of human alleles”, Science 279: 1228–1229.PubMedCrossRefGoogle Scholar
  46. [46]
    Peng, X. H., Z. H. Cao, J. T. Xia, G. W. Carlson, M. M. Lewis, W. C. Wood & L. Yang (2005). “Real-time detection of gene expression in cancer cells using molecular beacon imaging: New strategies for cancer research”, Cancer Research 65: 1909–1917.PubMedCrossRefGoogle Scholar
  47. [47]
    Nesterova, I. V., S. S. Erdem, S. Pakhomov, R. P. Hammer & S. A. Soper (2009). “Phthalocyanine dimerization-based molecular beacons using near-IR fluorescence”, Journal of the American Chemical Society 131: 2432–2433.PubMedCrossRefGoogle Scholar
  48. [48]
    Cardullo, R. A., S. Agrawal, C. Flores, P. C. Zamecnik & D. E. Wolf (1988). “Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer”, Proceedings of National Academy of Sciences 85: 8790–8794.CrossRefGoogle Scholar
  49. [49]
    Mergny, J. L., A. S. Boutorine, T. Garestier, F. Belloc, M. Rougee, N. V. Bulychev, A. A. Koshkin, J. Bourson, A. V. Lebedev, B. Valeur, N. T. Thung & C. Helene (1994). “Fluorescence energy transfer as a probe for nucleic acid structures and sequences”, Nucleic Acid Research 22: 920–928.CrossRefGoogle Scholar
  50. [50]
    Didenko, V. V. (2001). “DNA probes using fluorescence resonance energy transfer (FERT): Designs and applications”, Biotechniques 31: 1106–1116, 1118, 1120–1121.PubMedGoogle Scholar
  51. [51]
    Tsuji, A., Y. Sato, M. Hirano. T. Suga, H. Koshimoto, T. Taguchi & S. Ohsuka (2001). “Development of a time-resolved fluorometric method for observing hybridization in living cells using fluorescence resonance energy transfer”, Biophysical Journal 81: 501–515.PubMedCrossRefGoogle Scholar
  52. [52]
    Tsourkas, A., M. A. Behlke, Y. Xu & G. Bao (2003). “Spectroscopic features of dual fluorescence/luminescence resonance energy-transfer molecular beacons”, Analytical Chemistry 75: 3697–3703.PubMedCrossRefGoogle Scholar
  53. [53]
    Tsourkas, A., M. A. Behlke, S. D. Rose & G. Bao (2003). “Hybridization kinetics and thermodynamics of molecular beacons”, Nucleic Acids Research 31: 1319–1330.PubMedCrossRefGoogle Scholar
  54. [54]
    Santangelo, P. J., B. Nix, A. Tsourkas & G. Bao (2004). “Dual FRET molecular beacons for mRNA detection in living cells”, Nucleic Acids Research 32: E57.PubMedCrossRefGoogle Scholar
  55. [55]
    Svanvik, N., G. Westman, D. Wang & M. Kubista (2000). “Light-up probes: Thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution”, Analytical Biochemistry 281: 26–35.PubMedCrossRefGoogle Scholar
  56. [56]
    Svanvik, N., J. Nygren, G. Westman & M. Kubista (2001). “Free-probe fluorescence of light-up probes”, Journal of the American Chemitry Society 123: 803–809.CrossRefGoogle Scholar
  57. [57]
    Privat, E., T. Melvin, U. Asseline & P. Vigny (2001). “Oligonucleotideconjugated thiazole orange probe as ‘light-up’ probes for messenger ribonucleic acid molecules in living cells”, Photochemistry and Photobiology 4: 532–541.CrossRefGoogle Scholar
  58. [58]
    Dirks, R. W., C. Molenaar & H. J. Tanke (2001). “Methods for visualizing RNA processing and transport pathways in living cells”, Histochemistry and Cell Biology 115: 3–11.PubMedGoogle Scholar
  59. [59]
    Molenaar, C., S. A. Marras, J. C. Slats, J. C. Truffert, M. Lemaitre, A. K. Raap, R. W. Dirks & H. J. Tanke (2001). “Linear − O-methyl RNA probes for the visualization of RNA in living cells”, Nucleic Acids Research 29: E89.PubMedCrossRefGoogle Scholar
  60. [60]
    Li, J. J., R. Geyer & W. Tan (2000). “Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA”, Nucleic Acids Research 28: E52.PubMedCrossRefGoogle Scholar
  61. [61]
    Fisher, T. L., T. Terhorst, X. Cao & R. W. Wagner (1993). “Intracellular disposition and metabolism of fluorescently-labeled unmodified and modified oligonucleotides microinjected into mammalian cells”, Nucleic Acids Research 21: 3857–3865.PubMedCrossRefGoogle Scholar
  62. [62]
    Leonetti, J. P., N. Mechti, G. Degols, C. Gagnor & B. Lebleu (1991). “Intracellular distribution of microinjected antisense oligonucleotides”, Proceedings of National Academy of Sciences 88: 2702–2706.CrossRefGoogle Scholar
  63. [63]
    Uchiyama, H., K. Hirano, M. Kashiwasaka-Jibu & K. Taira (1996). “Detection of undegraded oligonucleotides in vivo by fluorescence resonance energy transfer. Nuclease activities in living sea urchin eggs”, Journal of Biology and Chemistry 271: 380–384.CrossRefGoogle Scholar
  64. [64]
    Cummins, L. L., S. R. Owens, L. M. Risen, E. A. Lesnik, S. M. Freier, D. McGee, C. J. Guinosso & P. D. Cook (1995). “Characterization of fully 2′-modified oligoribonucleotide hetero-and homoduplex hybridization and nuclease sensitivity”, Nucleic Acids Research 23: 2019–2024.PubMedCrossRefGoogle Scholar
  65. [65]
    Tsourkas, A., M. A. Behlke & G. Bao (2002). “Hybridization of 2′-O-methyl and 2′-deoxy molecular beacons to RNA and DNA targets”, Nucleic Acids Research 30: 5168–5174.PubMedCrossRefGoogle Scholar
  66. [66]
    Egholm, M., O. Buchardt, L. Christensen, C. Behrens, S. M. Freier, D. A. Driver, R. H. Berg, S. K. Kim, B. Norden & P. E. Nielsen (1993). “PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules”, Nature 365: 566–568.PubMedCrossRefGoogle Scholar
  67. [67]
    Ratilainen, T., A. Holmén, E. Tuite, G. Haaima, L. Christensen, P. E. Nielsen & B. Nordén (1998). “Hybridization of peptide nucleic acid”, Biochemistry 37: 12331–12342.PubMedCrossRefGoogle Scholar
  68. [68]
    Uhlmann, E., A. Peyman, G. Breipohl & D. W. Will (1998). “PNA: Synthetic polyamide nucleic acids with unusual binding properties”, Angewandte Chemie International Edition 37: 2796–2823.CrossRefGoogle Scholar
  69. [69]
    Demidov, V. V., V. N. Potaman, M. D. Frank-Kamenetskii, M. Egholm, O. Buchardt, S. H. Sönnichsen & P. E. Nielsen (1994). “Stability of peptide nucleic acids in human serum and cellular extracts”, Biochemical Pharmacology 48: 1310–1313.PubMedCrossRefGoogle Scholar
  70. [70]
    Kitagawa, F., Y. Ohori, H. Ikeda, H. Fujimori, Y. Murakami & Y. Nakamura (2002). “Design of a molecular beacon PNA”, Nucleic Acids Research Supplement 143–144.Google Scholar
  71. [71]
    Xi, C., M. Balberg, S. A. Boppart & L. Raskin (2003). “Use of DNA and peptide nucleic acid molecular beacons for detection and quantification of rRNA in solution and in whole cells”, Applied and Environmental Microbiology 69: 5673–5678.PubMedCrossRefGoogle Scholar
  72. [72]
    Kuhn, H., V. V. Demidov, J. M. Coull, M. J. Fiandaca, B. D. Gildea & M. D. Frank-Kamenetskii (2002). “Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets”, Journal of the American Chemistry Society 124: 1097–1103.CrossRefGoogle Scholar
  73. [73]
    Tsuji, A., H. Koshimoto, Y. Sato, M. Hirano, Y. Sei-Iida, S. Kondo & K. Ishibashi (2000). “Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope”, Biophysical Journal 78: 3260–3274.PubMedCrossRefGoogle Scholar
  74. [74]
    Zameenik, P., J. Aghajanian, M. Zameenik, J. Goodchild & G. Witman (1994). “Electron micrographic studies of transport of oligodeoxynucleotides across eukaryotic cell membranes”, Proceedings of National Academy of Sciences 91: 3156–3160.CrossRefGoogle Scholar
  75. [75]
    Clarenc, J. P., B. Lebleu & J. P. Lonetti (1993). “Characterization of the nuclear binding sites of oligodeoxyribonucleotides and their analogs”, Journal of Biological Chemistry 268: 5600–5604.PubMedGoogle Scholar
  76. [76]
    Shah, R. & W. S. El-Deiry (2004). “Dependent activation of a molecular beacon in tumor cells following exposure to doxorubicin chemotherapy”, Cancer Biology & Therapy 3: 871–875.CrossRefGoogle Scholar
  77. [77]
    Barton, G. M. & R. Medzhitov (2002). “Retroviral delivery of small interfering RNA into primary cells”, Proceedings of National Academy of Sciences 99: 14943–14945.CrossRefGoogle Scholar
  78. [78]
    Cheung, C. Y., N. Murthy, P. S. Stayton & A. S. Hoffman (2001). “A pH-sensitive polymer that enhances cationic lipid-mediated gene transfer”, Bioconjugate Chemistry 12: 906–910.PubMedCrossRefGoogle Scholar
  79. [79]
    Nitin, N., P. J. Santangelo, G. Kim, S. Nie & G. Bao (2001). “Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells”, Nucleic Acids Research 32: E58.CrossRefGoogle Scholar
  80. [80]
    Yeh, H. Y., M. V. Yates, A. Mulchandani & W. Chen (2008). “Visualizing the dynamics of viral replication in living cells via Tat peptide delivery of nuclease-resistant molecular beacons”, Proceedings of National Academy of Sciences 105: 17522–17525.CrossRefGoogle Scholar
  81. [81]
    Nitin, N. & G. Bao (2008). “NLS peptide conjugated molecular beacons for visualizing nuclear RNA in living cells”, Bioconjugate Chemistry 19: 2205–2211.PubMedCrossRefGoogle Scholar
  82. [82]
    Mhlanga, M. M., D. Y. Vargas, C. W. Fung, F. R. Kramer & S. Tyagi (2005). “tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells”, Nucleic Acids Research 33: 1902–1912.PubMedCrossRefGoogle Scholar

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© Zhejiang University Press, Hangzhou and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Deming Kong
    • 1
  1. 1.Research Center for Analytical Sciences, College of ChemistryNankai UniversityTianjin

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