Novel fluorescent molecular beacon DNA probes for biomolecular recognition

Biomedical Photonics: Handbook

Volumn , Issue , 2003, Pages 57-1-57-23

  Wang, Kemin ^a,b   Li, Jun ^a   Fang, Xiaohong ^b   Schuster, Sheldon ^b   Vicens, Marie ^b   Kelley, Shannon ^b   Lou, Hua ^b   Li, Jianwei Jeffery ^b   Beck, Terry ^c   Hogrefe, Richard ^c   Tan, Weihong ^b  

^a HUNAN UNIVERSITY   (China)

^b UNIVERSITY OF FLORIDA   (United States)

^c TriLink BioTechnologies Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85056308584     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (64)

1. Haugland, R.P., Handbook of Fluorescent Probes and Research Chemicals, Molecular Probes, Eugene, OR, 1994.
2. Tyagi, S. and Kramer, F.R., Molecular beacons: probes that fluoresce upon hybridization, Nat. Biotech., 14, 303, 1996.
3. Lakowicz, J.R., Principles of Fluorescence Spectroscopy, 2nd ed., Kluwer Academic/Plenum Publishers, New York, 1999.
4. Tyagi, S., Bratu, D.P., and Kramer, F.R., Multicolor molecular beacons for allele discrimination, Nat. Biotechnol., 16, 49, 1996.
5. Meinkoth, J. and Wahl, G., Hybridization of nucleic acids immobilized on solid supports, Anal. Biochem., 138(2), 267, 1984.
6. Fang, X. and Tan, W., Imaging single fluorescent molecules at the interface of an optical fiber probe by evanescent wave excitation, Anal. Chem., 71(15), 3101, 1999.
7. Kostrikis, L.G., Tyagi, S., Mhlanga, M.M., Ho, D.D., and Kramer, F.R., Molecular beacons-spectral genotyping of human alleles, Science, 279, 1228, 1998.
8. Bonnet, G., Tyagi, S., Libchaber, A., and Kramer, F.R., Thermodynamic basis of the enhanced specificity of structured DNA probes, Proc. Natl. Acad. Sci. U.S.A., 96(11), 6171, 1999.
9. Matsuo, T., In situ visualization of mRNA for basic fibroblast growth factor in living cells, Biochim. Biophys. Acta, 1379, 178, 1998.
10. Tapp, I., Malmberg, L., Rennel, E., Wik, M., and Syvanen, A.C., Homogeneous scoring of singlenucleotide polymorphisms: comparison of the 5′-nuclease TaqMan assay and molecular beacon probes, Biotechniques, 28(4), 732, 2000.
11. Helps, C., Reeves, N., Tasker, S., and Harbour, D., Use of real-time quantitative PCR to detect Chlamydophila felis infection, J. Clin. Microbiol., 39(7), 2675, 2001.
12. Yuan, C.C., Peterson, R.J., Wang, C.D., Goodsaid, F., and Waters, D.J., 5′ Nuclease assays for the loci CCR5-+/Δ32, CCR 2-V64I, and SDF 1-G801A related to pathogenesis of AIDS, Clin. Chem., 46(1), 24, 2000.
13. Lewin, S.R., Vesanen, M., Kostrikis, L., Hurley, A., Duran, M., Zhang, L., Ho, D.D., and Markowitz, M., Use of real-time PCR and molecular beacons to detect virus replication in human immunodeficiency virus type 1-infected individuals on prolonged effective antiretroviral therapy, J. Virol., 73(7), 6099, 1999.
14. Zhang, L.Q., Lewin, S.R., Markowitz, M., Lin, H.H., Skulsky, E., Karanicolas, R., He, Y., Jin, X., Tuttleton, S., Vesanen, M., Spiegel, H., Kost, R., van Lunzen, J., Stellbrink, H.J., Wolinsky, S., Borkowsky, W., Palumbo, P., Kostrikis, L.G., and Ho, D.D., Measuring recent thymic emigrants in blood of normal and HIV-1-infected individuals before and after effective therapy, J. Exp. Med., 190(5), 725, 1999.
15. Vet, J.A.M., Majithia, A.R., Marras, S.A.E., Dube, S., Poiesz, B.J., and Kramer, F.R., Multiplex detection of four pathogenic retroviruses using molecular beacons, Proc. Natl. Acad. Sci. U.S.A., 96(11), 6394, 1999.
16. Giesendorf, B.A.J, Vet, J.A.M., Tyagi, S., et al., Molecular beacons: a new approach for semiautomated mutation analysis, Clin. Chem., 44(3), 482, 1998.
17. Chen, W. and Martinez, G., Molecular beacons: a real-time polymerase chain reaction assay for detecting salmonella, Anal. Biochem., 280(1), 166, 2000.
18. Schofield, P., Pell, A.N, and Krause, D.O., Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria, Appl. Environ. Microbiol., 63(3), 1143, 1997.
19. Rhee, J.T., Piatek, A.S., Small, P.M, Harris, L.M., Chaparro, S.V., Kramer, F.R., and Alland, D., Molecular epidemiologic evaluation of transmissibility and virulence of Mycobacterium tuberculosis, J. Clin. Microbiol., 37(6), 1764, 1999.
20. De Ronde, A., van Dooren, M., van der Hoek, L., Bouwhuis, D., De Rooij, E., van Gemen, B., De Boer, R., and Goudsmit, J., Establishment of new transmissible and drug-sensitive human immunodeficiency virus type 1 wild types due to transmission of nucleoside analogue-resistant virus, J. Virol., 75(2), 595, 2001.
21. Martinson, J.J., Hong, L., Karanicolas, R., Moore, J.P., and Kostrikis, L.G., Global distribution of the CCR2-64I/CCR5-59653T HIV-1 disease-protective haplotype, AIDS, 14(5), 483, 2000.
22. De Baar, M.P., Timmer, E.C., Bakker, M., De Rooij, E., van Gemen, B., and Goudsmit, J., Onetube 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, 2001.
23. De Baar, M.P., van Dooren, M.W., De Rooij, E., Bakker, M., van Gemen, B., Goudsmit, J., and De Ronde, A., Single rapid real-time monitored isothermal RNA amplification assay for quantification of human immunodeficiency virus type 1 isolates from groups M, N, and O, J. Clin. Microbiol., 39(4), 1378, 2001.
24. McKillip, J.L. and Drake, M., Molecular beacon polymerase chain reaction detection of Escherichia coli O157:H7 in milk, J. Food Prot., 63(7), 855, 2000.
25. Li, Q.G., Liang, J.X., Luan, G.Y., Zhang, Y., and Wang, K., Molecular beacon-based homogeneous fluorescence PCR assay for the diagnosis of infectious diseases, Anal. Sci., 16(2), 245, 2000.
26. Fortin, N.Y., Mulchandani, A., and Chen, W., Use of real-time polymerase chain reaction and molecular beacons for the detection of Escherichia coli O157: H7, Anal. Biochem., 289(2), 281, 2001.
27. Chen, W., Martinez, G., and Mulchandani, A., Molecular beacons: a real-time polymerase chain reaction assay for detecting salmonella similar species such as Escherichia coli and Citrobacter freundii in real time PCR assays, Anal. Biochem., 280(1), 166, 2000.
28. Fang, X.H., Mi, Y.M., Li, J.J., Terry, B., and Tan, W.H., Real-time imaging of mRNA in single living cells using molecular beacons, Molecular Beacons: “Lights up” Probes for Living Cell Study, Cell Biochem. Biophys., 37, 4, 2002.
29. Dirks, R.W., Molenaar, C., and Tanke, H.J., Methods for visualizing RNA processing and transport pathway in living cells, Histochem. Cell. Biol., 15, 3, 2001.
30. Matsuo, T., In situ visualization of messenger RNA for basic fibroblast growth factor in living cells, Bba-gen Subjects, 1379(2), 178, 1998.
31. Sokol, D.L., Zhang, X.L., Lu, P.Z., and Gewitz, A.M., Real time detection of DNA RNA hybridization in living cells, Proc. Natl. Acad. Sci. U.S.A., 95, 11538, 1998.
32. Tsuji, A., Koshimoto, H., Sato, Y., Hirano, M., Sei-Iida, Y., Kondo, S., and Ishibashi, K., Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope, Biophys. J., 78(6), 3260, 2000.
33. Li, J., Fang, X., Schuster, S., and Tan, W., Molecular beacons: a novel approach to detect protein- DNA interactions, Angew. Chem. Int. Ed., 39, 1049, 2000.
34. Fang, X., Li, J., and Tan, W., Using molecular beacons to probe the interactions between lactic dehydrogenase and single strand DNA, Anal. Chem., 72(14), 3250, 2000.
35. Li, J., Geyer, R., and Tan, W., Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA, Nucleic Acids Res., 28(e52), 1, 2000.
36. Tung, C.H., Mahmood, U., Bredow, S., and Weissleder, R., In vivo imaging of proteolytic enzyme activity using a novel molecular reporter, Cancer Res., 60(17), 4953, 2000.
37. Biggins, J.B., Prudent, J.R., Marshall, D.J., Ruppen, M., and Thorson, J.S., A continuous assay for DNA cleavage: the application of “break lights” to enediynes, iron-dependent agents, and nucleases, Proc. Natl. Acad. Sci. U.S.A., 97(25), 13537, 2000.
38. Strouse, R.J., Hakki, F.Z., Wang, S.C., DeFusco, A.W., Garrett, J.L., and Schenerman, M.A., Using molecular beacons to quantify low levels of type I endonuclease activity, Biopharm. Appl. Technol. Biopharm. Dev., 13(4), 40, 2000.
39. Li, J.J., Fang, X., and Tan, W., Molecular aptamer beacon: a novel molecular probe for real time protein recognition, Biochem. Biophys. Res. Commun., 292(1), 31, 2002.
40. Osborne, S.E., Matsumura, I., and Ellington, A.D., Aptamers as therapeutic and diagnostic reagents: problems and prospects, Curr. Opinion Chem. Biol., 1, 5, 1997.
41. Jayasena, S.D., Aptamers: an emerging class of molecules that rival antibodies in diagnostics, Clin. Chem., 45, 1628, 1999.
42. Zhang, P., Beck, T., and Tan, W., Design of molecular beacon DNA probe with two fluorophores, Angew. Chem. Int. Ed., 40(2), 402, 2000.
43. Hamaguchi, N., Ellington, A., and Stanton, M., Aptamer beacons for the direct detection of proteins, Anal. Biochem., 294(2), 126, 2001.
44. Yamamoto, R. and Kumar, P.K.R., Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1, Genes Cells, 5(5), 389, 2000.
45. Fang, X., Vicens, M., Cao, Z., and Tan, W., Signaling oncoprotein by molecular beacon aptamer fluorescent probe, J. Am. Chem. Soc., submitted.
46. Fang, X., Liu, X., Schuster, S., and Tan, W., Designing a novel molecular beacon for surfaceimmobilized DNA hybridization studies, J. Am. Chem. Soc., 121, 2921, 1999.
47. Liu, X., Farmerie, W., Schuster, S., and Tan, W., Molecular beacons for DNA biosensors with micrometer to submicrometer dimensions, Anal. Biochem., 283, 56, 2000.
48. Liu, X. and Tan, W., A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons, Anal. Chem., 71, 5054, 1999.
49. Fang, X., Liu, X., and Tan, W., Single and multiple molecular beacon probes for DNA by hybridization studies on a silica glass surface, Proc. SPIE, 3602, 149, 1999.
50. Ortiz, E., Estrada, G., and Lizardi, P.M., PNA molecular beacons for rapid detection of PCR amplicons, Mol. Cell. Probes, 12(4), 219, 1998.
51. Tan, W., Shi, Y., Smith, S., Birnbaum, D., and Kopelman, R., Submicrometer intracellular chemical optical fiber sensors, Science, 258, 778, 1992.
52. Zeisel, D., Dutoit, B., Deckert, V., Roth, T., and Zenobi, R., Optical spectroscopy and laser desorption on a nanometer scale, Anal. Chem., 69, 749, 1997.
53. Perlette, J. and Tan, W., Real time detection of molecular beacon mRNA hybridization in single living cell, Anal. Chem., 73, 5631, 2001.
54. Tan, W.H., Optical measurements on the nanometer scale, Trends Anal. Chem., 17, 501, 1998.
55. Tan, W.H., Kopelman, R., Barker, S.L., and Miller, M.T., Ultrasmall optical sensors for cellular measurements, Anal. Chem., 71, 606A, 1999.
56. Zhang, P., Beck, T., and Tan, W., Design of molecular beacon DNA probe with two fluorophores, Angew. Chem. Int. Ed., 40, 402, 2001.
57. Steemers, F.J, Ferguson, J.A., and Walt, D.R., Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays, Nat. Biotechnol., 18(1), 91, 2000.
58. Li, J., Tan, W., Wang, K., Xiao, D., Yang, X., He, X., and Tang, Z., Ultrasensitive optical DNA biosensor based on surface immobilization of molecular beacon by a bridge structure, Anal. Sci., 17(10), 1149, 2001.
59. Li, J., Tan, W., Wang, K., Yang, X., Tang, Z., and He, X., Optical DNA biosensor based on molecular beacon immobilized on sol-gel membrane, SPIE Int. Conf. Sensing Unit Sensor Technol., Wuhan, China, 2001.
60. Li, J., Tan, W., Wang, K., He, X., Yang, X., and Tang, Z., Cellular application of optical fiber DNA biosensor based on biotinylated molecular beacon by sol-gel immobilization, Anal. Chem., submitted.
61. Santra, S., Tapec, R., Theodoropoulou, N., Dobson, J., Hebard, A., and Tan, W., Synthesis and characterization of silica coated iron oxide nanoparticles in microemulsion: the effect of non-ionic surfactants, Langmuir, 17(10), 2900, 2001.
62. Santra, S., Wang, K.M., Tapec, R., and Tan, W., Development of novel dye-doped silica nanoparticles for biomarker application, J. Biomed. Opt., 6(2), 160, 2001.
63. Benoit, V., Steel, A., Torres, M., Lu, Y.Y., Yang, H.J., and Cooper, J., Evaluation of three-dimensional microchannel glass biochips for multiplexed nucleic acid fluorescence hybridization assays, Anal. Chem., 73(11), 2412, 2001.
64. Zhang, P. and Tan, W., Direct observation of single-molecule generation at a solid-liquid interface, Chem. Eur. J., 6, 1087, 2000.