Fluorescent hybridization probes for sensitive and selective DNA and RNA detection

Accounts of Chemical Research

Volumn 40, Issue 6, 2007, Pages 402-409

  Martí, Angel A ^a   Jockusch, Steffen ^a   Stevens, Nathan ^a   Ju, Jingyue ^b,c   Turro, Nicholas J ^a,b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b Columbia University College of Physicians and Surgeons ^*  (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FLUORESCENT DYE; PYRENE; PYRENE DERIVATIVE; RNA;

ANIMAL; APLYSIA; CELL CULTURE; CHEMISTRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBE; REVIEW;

ANIMALS; APLYSIA; CELLS, CULTURED; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; PYRENES; RNA;

EID: 34447334212     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar600013q     Document Type: Review

References (48)

1. Marras, S. A. E.; Tyagi, S.; Kramer, F. R. Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin. Chim. Acta 2006, 363, 48-60.
2. Santangelo, P.; Nitin, N.; Bao, G. Nanostructured probes for RNA detection in living cells. Ann. Biomed. Eng. 2006, 34, 39-50.
3. Silverman, A. P.; Kool, E. T. Quenched probes for highly specific detection of cellular RNAs. Trends Biotechnol. 2005, 23, 225-230.
4. Manganelli, R.; Tyagi, S.; Smith, I. Real time PCR using molecular beacons. In Mycobacterium Tuberculosis Protocols: Methods in Molecular Medicine; Parish, T., Stoker, N. G., Eds.; Humana Press, Inc.: Totowa, NJ, 2001; Vol. 54, pp 295-310.
5. Turro, N. J.; Barton, J. K.; Tomalia, D. A. Molecular recognition and chemistry in restricted reaction spaces. Photophysics and photoinduced electron transfer on the surfaces of micelles, dendrimers and DNA. Acc. Chem. Res. 1991, 24, 332-340.
6. Pyle, A. M.; Rehmann, J. P.; Meshoyrer, R.; Kumar, C. V.; Turro, N. J.; Barton, J. K. Mixed-ligand complexes of ruthenium(II): Factors governing binding to DNA. J. Am. Chem. Soc. 1989, 111, 3051-3058.
7. Suzuki, T.; Fujikura, K.; Hegashiyama, T.; Takata, K. DNA staining for fluorescence and laser confocal microscopy. J. Histochem. Cytochem. 1997, 45, 49-53.
8. Kitamura, M.; Nimura, A.; Yamana, K.; Shimidzu, T. Oligonucleotides with bis-pyrene adduct in the backbone: Synthesis and properties of intramolecular excimer forming probe. Nucleic Acids Symp. Ser. 1991, 25, 67-68.
9. Lamond, A. I.; Sproat, B. S. Antisense oligonucleotides made of 2′-O-alkyl-RNA: Their properties and applications in RNA biochemistry. FEBS Lett. 1993, 325, 123-127.
10. Ranasinghe, R. T.; Brown, T. Fluorescence based strategies for genetic analysis. Chem. Commun. 2005, 5787-5502.
11. Hu, J.-Y.; Meng, X.; Schacher, S. Target interactions regulates distribution and stability of specific mRNAs. J. Neurosci. 2002, 22, 2669-2678.
12. Martí, A. A.; Jockusch, S.; Li, Z.; Ju, J.; Turro, N. J. Molecular beacons with intrinsically florescence nucleotides. Nucleic Acids Res. 2006, 34, e50.
13. Jockusch, S.; Martí, A. A.; Turro, N. J.; Li, Z.; Li, X.; Ju, J.; Stevens, N.; Akins, D. L. Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences. Photochem. Photobiol. Sci. 2006, 5, 493-498.
14. Li, X.; Li, Z.; Martí, A. A.; Jockusch, S.; Stevens, N.; Akins, D. L.; Turro, N. J.; Ju, J. Combinatorial fluorescence energy transfer molecular beacon for probing nucleic acid sequences. Photochem. Photobiol. Sci. 2006, 5, 896-902.
15. Martí, A. A.; Li, X.; Jockusch, S.; Li, Z.; Raveendra, B.; Kalachikov, S.; Russo, J. J.; Morozova, I.; Puthanveettil, S. V.; Ju, J.; Turro, N. J. Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy. Nucleic Acids Res. 2006, 34, 3161-3168.
16. Martí, A. A.; Li, X.; Jockusch, S.; Stevens, N.; Li, Z.; Raveendra, B.; Kalachikov, S.; Morozova, I.; Russo, J. J.; Akins, D. L.; Ju, J.; Turro, N. J. Design and characterization of two-dye and three dye binary fluorescent probes for mRNA detection. Tetrahedron 2007, 63, 3591-3600.
17. Tyagi, S.; Kramer, F. R. Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 1996, 14, 303-308.
18. Frutos, A. G.; Pal, S.; Quesada, M.; Lahiri, J. Method for detection of single-base mismatches using bimolecular beacons. J. Am. Chem. Soc. 2002, 124, 2396-2397.
19. Varma-Basil, M.; El-Hajj, H.; Marras, S. A. E.; Hazbon, M. H.; Mann, J. M.; Connell, N. D.; Kramer, F. R.; Alland, D. Molecular beacons for multiplex detection of four bacterial bioterrorism agents. Clin. Chem. 2004, 50, 1060-1063.
20. Tan, W.; Wang, K.; Drake, T. J. Molecular beacons. Curr. Opin. Chem. Biol. 2004, 8, 547-553.
21. Tsourkas, A.; Bao, G. Shedding light on health and disease using molecular beacons. Briefings Funct. Genomics Proteomics 2003, 1, 372-384.
22. Santangelo, P. J.; Nix, B.; Tsourkas, A.; Bao, G. Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res. 2004, 32, e57.
23. Tanke, H. J.; Dirks, R. W.; Raap, T. FISH and immunocytochemistry: Towards visualizing single target molecules in living cells. Curr. Opin. Biotechnol. 2005, 16, 49-54.
24. Cardullo, R. A.; Agrawal, S.; Flores, C.; Zamecnik, P. C.; Wolf, D. E. Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 8790-8794.
25. Turro, N. J. Modem Molecular Photochemistry, University Science Books: Sausalito, CA, 1991.
26. Lakowicz, J. R. Principles of Fluorescence Spectroscopy, 2nd ed.; Kluwer Academic/Plenum Publishers: New York, 1999; pp 368-394.
27. Tong, A. K.; Li, Z.; Ju, J. Combinatorial fluorescence energy transfer tags: New molecular tools for genomic applications. IEEE J. Quantum Electron. 2002, 38, 110-121.
28. Mergny, J.-L.; Boutorine, A. S.; Garestier, T.; Belloc, F.; Rougée, M.; Bulychev, N. V.; Koshkin, A. A.; Bourson, J.; Lebedev, A. V.; Valeur, B.; Thuong, N. T.; Hèléne, C. Fluorescent energy transfer as a probe for nucleic acid structures and sequences. Nucleic Acids Res. 1994, 22, 920-928.
29. Sei-Iida, Y.; Koshimoto, H.; Kondo, S.; Tsuji, A. Real-time monitoring of in vitro transcriptional RNA synthesis using fluorescence resonance energy transfer. Nucleic Acids Res. 2000, 28, e59.
30. Tsuji, A.; Koshimoto, H.; Sato, Y.; Hirano, M.; Sei-Iida, Y.; Kondo, S.; Ishibashi, K. Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope. Biophys. J. 2000, 78, 3260-3274.
31. Rosmarin, D.; Pei, Z.; Blaser, M. J.; Tyagi, S. In U.S. Patent and Trademark Office; United States Department of Commerce: Alexandria, VA, 2006; pp 1-14.
32. Yang, C. J.; Martinez, K.; Lin, H.; Tan, W. Hybrid molecular probe for nucleic acid analysis in biological samples. J. Am. Chem. Soc. 2006, 128, 9986-9987.
33. Zhang, P.; Beck, T.; Tan, W. Design of a molecular beacon DNA probe with two fluorophores. Angew. Chem., Int. Ed. 2001, 40, 402-405.
34. Tong, A. K.; Jockusch, S.; Li, Z.; Zhu, H.-R.; Akins, D. L.; Turro, N. J.; Ju, J. Triple fluorescence energy transfer in covalently trichromophore-labeled DNA. J. Am. Chem. Soc. 2001, 123, 12923-12924.
35. Sapsford, K. E.; Berti, L.; Medintz, I. L. Materials for fluorescence resonance energy transfer analysis: Beyong traditional donor-acceptor combinations. Angew. Chem., Int. Ed. 2006, 45, 4562-4588.
36. Yamana, K.; Fukunaga, Y.; Ohtani, Y.; Sato, S.; Nakamura, M.; Kim, W. J.; Akaike, T.; Maruyama, A. DNA mismatch detection using a pyrene-excimer-forming probe. Chem. Commun. 2005, 2509-2511.
37. Kashida, H.; Asanuma, H.; Komiyama, M. Insertion of two pyrene moieties into oligodeoxyribonucletides for the efficient detection of deletion polymorphisms. Chem. Commun. 2006, 2768-2770.
38. Fujimoto, K.; Shimizu, H.; Inouye, M. Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons. J. Org. Chem. 2004, 69, 3271-3275.
39. Ebata, K.; Masuko, M.; Ohtani, H.; Kashiwasake-Jibu, M. Nucleic acid hybridization accompanied with excimer formation from two pyrene-labeled probes. Photochem. Photobiol. 1995, 62, 836-839.
40. Masuko, M.; Ohtani, H.; Ebata, K.; Shimadzu, A. Optimization of excimer-forming two-probe nucleic acid hybridization method with pyrene as a fluorophore. Nucleic Acids Res. 1998, 26, 5409-5416.
41. Paris, P. L.; Langenhan, J. M.; Kool, E. T. Probing DNA sequences in solution with a monomer-excimer fluorescence color change. Nucleic Acids Res. 1998, 26, 3789-3793.
42. Yang, C. J.; Jockusch, S.; Vincens, M.; Turro, N. J.; Tan, W. Light switching excimer probes for rapid protein monitoring in complex biological fluids. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17278-17283.
43. Tremblay, M. S.; Zhu, Q.; Martí, A. A.; Dyer, J.; Halim, M.; Jockusch, S.; Turro, N. J.; Sames, D. Phosphorilation state-responsive lanthanide peptide conjugates: A luminescence switch based on reversible complex reorganization. Org. Lett. 2006, 8, 2723-2726.
44. Carlsson, K.; Liljeborg, A. Confocal fluorescence microscopy using spectral and lifetime information to simultaneously record four fluorophores with high channel separation. J. Microsc. 1996, 185, 37-46.
45. Kim, J. H.; Stephens, J. P.; Morikis, D.; Ozkana, M. Hybrid inorganic-organic molecular beacons. Sens. Lett. 2004, 2, 85-90.
46. Levy, M.; Cater, S. F.; Ellington, A. D. Quantum-dot aptamer beacons for the detection of proteins. ChemBioChem 2005, 6, 2163-2166.
47. Jockusch, S.; Li, Z.; Ju, J.; Turro, N. J. Two-photon excitation induced fluorescence of a trifluorophore-labeled DNA. Photochem. Photobiol. 2005, 81, 238-241.
48. Okamoto, A.; Inasaki, T.; Saito, I. Nitroxide-labeled guanine as an ESR spin probe for structural study of DNA. Bioorg. Med. Chem. Lett. 2004, 14, 3415-3418.