Advertisement

Fluorescence in Nucleic Acid Hybridization Assays

  • Larry E. Morrison
Chapter
Part of the Topics in Fluorescence Spectroscopy book series (TIFS, volume 7)

Conclusions

Fluorescence has provided a large variety of DNA hybridization assay formats, both heterogeneous and homogeneous. Heterogeneous formats offer high sensitivity, with time-resolved lanthanide fluorescence providing detection down to 0.01 amol, or about 6000 molecules of target nucleic acid. With amplification, the detection limit drops to the tens or hundreds of molecules, or even the single molecule level. For many applications amplification would not be necessary. The variety of environment-sensitive fluorescence properties available makes fluorescence particularly valuable to homogeneous assays where measurable properties must change in response to hybridization. Homogeneous assays conserve time and labor, but suffer in sensitivity due to fundamental constraints on probe concentration. Homogeneous assay detection levels are closer to the fmol or 0.1 fmol level. Since homogeneous assay detection levels are limited by probe concentration, sensitivity would increase tremendously if sample analytes could be concentrated into microvolumes, thereby providing amol or lower detection levels. Combining hybridization assays with amplification, however, provides 10 molecule or lower detection levels to even homogeneous assays. Since target amplification methods tend to be homogeneous, combination with a homogeneous detection system provides a completely homogeneous high sensitivity assay that can be performed in sealed vessels, thereby reducing the risk of sample cross contamination. Given the wide range of assay formats already demonstrated in fluorescence approaches to hybridization assays, it should be relatively easy to tailor either a heterogeneous or homogeneous assay to any particular need.

Keywords

Molecular Beacon Hybridization Assay Amplify Polymerase Chain Reaction Product Target Nucleic Acid Target Strand 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Mullis, K. B., and Faloona, F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155, 335–350, 1987.Google Scholar
  2. 2.
    Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., and Gingeras, T. R. Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc. Natl. Acad. Sci. USA 86, 1173–1177, 1989.Google Scholar
  3. 3.
    Guatelli, J. C., Whitfield, K. M., Kwoh, D. Y., Barringer, K. J., Richman, D. D., and Gingeras, T. R. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication [published erratum appears in Proc. Natl. Acad. Sci. USA 87, 7797, 1990]. Proc. Natl. Acad. Sci. USA 87, 1874–1878, 1990.Google Scholar
  4. 4.
    Walker, G. T., Fraiser, M. S., Schram, J. L., Little, M. C., Nadeau, J. G., and Malinowski, D. P. Strand displacement amplification—An isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 20, 1691–1696, 1992.Google Scholar
  5. 5.
    Urdea, M. S., Kolberg, J., Clyne, J., Running, J. A., Besemer, D., Warner, B., and Sanchez-Pescador, R. Application of a rapid non-radioisotopic nucleic acid analysis system to the detection of sexually transmitted disease-causing organisms and their associated antimicrobial resistances. Clin. Chem. 35, 1571–1575, 1989.Google Scholar
  6. 6.
    Lomeli, H., Tyagi, S., Pritchard, C. G., Lizardi, P. M., and Kramer, F. R. Quantitative assays based on the use of replicatable hybridization probes. Clin. Chem. 35, 1826–1831, 1989.Google Scholar
  7. 7.
    Lizardi, P. M., Huang, X., Zhu, Z., Bray-Ward, P., Thomas, D. C., and Ward, D. C. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19, 225–232, 1998.CrossRefGoogle Scholar
  8. 8.
    Meinkoth, J., and Wahl, G. Hybridization of nucleic acids immobilized on solid supports. Anal. Biochem. 138, 267–284, 1984.CrossRefGoogle Scholar
  9. 9.
    Diamandis, E. P., and Christopoulos, T. K. Europium chelate labels in time-resolved fluorescence immunoassays and DNA hybridization assays. Anal. Chem. 62, 1149A–1157A, 1990.Google Scholar
  10. 10.
    Diamandis, E. P. Time-resolved fluorometry in nucleic acid hybridization and western blotting techniques. Electrophoresis 14, 866–875, 1993.CrossRefGoogle Scholar
  11. 11.
    Dickson, E. F., Pollak, A., and Diamandis, E. P. Time-resolved detection of lanthanide luminescence for ultrasensitive bioanalytical assays. J Photochem. Photobiol. B 27, 3–19, 1995.Google Scholar
  12. 12.
    Syvanen, A. C., Tchen, P., Ranki, M., and Soderlund, H. Time-resolved fluorometry: A sensitive method to quantify DNA-hybrids. Nucleic Acids Res. 14, 1017–1028, 1986.Google Scholar
  13. 13.
    Dahlen, P. Detection of biotinylated DNA probes by using Eu-labeled streptavidin and time-resolved fluorometry. Anal. Biochem. 164, 78–83, 1987.CrossRefGoogle Scholar
  14. 14.
    Oser, A., Roth, W. K., and Valet, G. Sensitive non-radioactive dot-blot hybridization using DNA probes labelled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence. Nucleic Adds Res. 16, 1181–1196, 1988.Google Scholar
  15. 15.
    Oser, A., and Valet, G. Improved detection by time-resolved fluorometry of specific DNA immobilized in microtiter wells with europium/metal-chelator labelled DNA probes. Nucleic Acids Res. 16, 8178, 1988.Google Scholar
  16. 16.
    Lovgren, T., Heinonen, P., Lehtinen, P., Hakala, H., Heinola, J., Harju, R., Takalo, H., Mukkala, V. M., Schmid, R., Lonnberg, H., Pettersson, K., and litia, A. Sensitive bioaffinity assays with individual microparticles and time-resolved fluorometry. Clin. Chem. 43, 1937–1943, 1997.Google Scholar
  17. 17.
    Hakala, H., Heinonen, P., Iitia, A., and Lonnberg, H. Detection of oligonucleotide hybridization on a single microparticle by time-resolved fluorometry: Hybridization assays on polymer particles obtained by direct solid phase assembly of the oligonucleotide probes. Bioconjug. Chem. 8, 378–384, 1997.Google Scholar
  18. 18.
    Piunno, P. A., Krull, U. J., Hudson, R. H., Damha, M. J., and Cohen, H. Fiber-optic DNA sensor for fluorometric nucleic acid determination. Anal. Chem. 67, 2635–2643, 1995.CrossRefGoogle Scholar
  19. 19.
    Abel, A. P., Weller, M. G., Duveneck, G. L., Ehrat, M., and Widmer, H. M. Fiber-optic evanescent wave biosensor for the detection of oligonucleotides. Anal. Chem. 68, 2905–2912, 1996.CrossRefGoogle Scholar
  20. 20.
    Vener, T. I., Turchinsky, M. F., Knorre, V. D., Lukin Yu, V., Shcherbo, S. N., Zubov, V. P., and Sverdlov, E. D. A novel approach to nonradioactive hybridization assay of nucleic acids using stained latex particles. Anal. Biochem. 198, 308–311, 1991.CrossRefGoogle Scholar
  21. 21.
    Christopoulos, T. K., Diamandis, E. P., and Wilson, G. Quantification of nucleic acids on nitrocellulose membranes with time-resolved fluorometry. Nucleic Acids Res. 19, 6015–6019, 1991.Google Scholar
  22. 22.
    Mansfield, E. S., Worley, J. M., McKenzie, S. E., Surrey, S., Rappaport, E., and Fortina, P. Nucleic acid detection using non-radioactive labelling methods. Mol. Cell. Probes 9, 145–156, 1995.CrossRefGoogle Scholar
  23. 23.
    Evangelista, R. A., Pollak, A., and Templeton, E. F. Enzyme-amplified lanthanide luminescence for enzyme detection in bioanalytical assays. Anal. Biochem. 197, 213–224, 1991.CrossRefGoogle Scholar
  24. 24.
    Templeton, E. F., Wong, H. E., Evangelista, R. A., Granger, T., and Pollak, A. Time-resolved fluorescence detection of enzyme-amplified lanthanide luminescence for nucleic acid hybridization assays. Clin. Chem. 37, 1506–1512, 1991.Google Scholar
  25. 25.
    Chiu, N. H., Christopoulos, T. K., and Peltier, J. Sandwich-type deoxyribonucleic acid hybridization assays based on enzyme amplified time-resolved fluorometry. Analyst 123, 1315–1319, 1998.CrossRefGoogle Scholar
  26. 26.
    Ioannou, P. C., and Christopoulos, T. K. Two-round enzymatic amplification combined with time-resolved fluorometry of Tb3+ chelates for enhanced sensitivity in DNA hybridization assays. Anal. Chem. 70, 698–702, 1998.CrossRefGoogle Scholar
  27. 27.
    Dahlen, P. O., Iitia, A. J., Skagius, G., Frostell, A., Nunn, M. F., and Kwiatkowski, M. Detection of human immunodeficiency virus type 1 by using the polymerase chain reaction and a time-resolved fluorescence-based hybridization assay. J. Clin. Microbiol. 29, 798–804, 1991.Google Scholar
  28. 28.
    Eggertsen, G., Eriksson, M., Wiklund, O., Iitia, A., Olofsson, S. O., Angelin, B., and Berglund, L. Time-resolved fluorometry in the genetic diagnosis of familial defective apolipoprotein B-100. J. Lipid Res. 35, 1505–1508, 1994.Google Scholar
  29. 29.
    Sjoroos, M, Ilonen, J., Reijonen, H., and Lovgren, T. Time-resolved fluorometry based sandwich hybridisation assay for HLA-DQA1 typing. Dis. Markers 14, 9–19, 1998.Google Scholar
  30. 30.
    Huoponen, K., Juvonen, V., Iitia, A., Dahlen, P., Siitari, H., Aula, P., Nikoskelainen, E., and Savontaus, M. L. Time-resolved fluorometry in the diagnosis of Leber hereditary optic neuro-retinopathy. Hum. Mutat. 3, 29–36, 1994.CrossRefGoogle Scholar
  31. 31.
    Chan, A., Diamandis, E. P., and Krajden, M. Quantification of polymerase chain reaction products in agarose gels with a fluorescent europium chelate as label and time-resolved fluorescence spectroscopy. Anal. Chem. 65, 158–163, 1993.Google Scholar
  32. 32.
    Maher, M., Dowdall, D., Glennon, M., Walshe, S., Cormican, M., Wiesner, P., Gannon, F., and Smith, T. The sensitive detection of fluorescently labelled PCR products using an automated detection system. Mol. Cell. Probes 9, 265–276, 1995.CrossRefGoogle Scholar
  33. 33.
    Lopez, E., Chypre, C., Alpha, B., and Mathis, G. Europium(III) trisbipyridine cryptate label for time-resolved fluorescence detection of polymerase chain reaction products fixed on a solid support. Clin. Chem. 39, 196–201, 1993.Google Scholar
  34. 34.
    Chehab, F. F., and Kan, Y. W. Detection of specific DNA sequences by fluorescence amplification: A color complementation assay. Proc. Natl. Acad. Sci. USA 86, 9178–9182, 1989.Google Scholar
  35. 35.
    Sjoroos, M., Iitia, A., Ilonen, J., Reijonen, H., and Lovgren, T. Triple-label hybridization assay for type-1 diabetes-related HLA alleles. Biotechniques 18, 870–877, 1995.Google Scholar
  36. 36.
    Heinonen, P., Iitia, A., Torresani, T., and Lovgren, T. Simple triple-label detection of seven cystic fibrosis mutations by time-resolved fluorometry. Clin. Chem. 43, 1142–1150, 1997.Google Scholar
  37. 37.
    Samiotaki, M., Kwiatkowski, M., Ylitalo, N., and Landegren, U. Seven-color time-resolved fluorescence hybridization analysis of human papilloma virus types. Anal. Biochem. 253, 156–161, 1997.CrossRefGoogle Scholar
  38. 38.
    Bortolin, S., Christopoulos, T. K., and Verhaegen, M. Quantitative polymerase chain reaction using a recombinant DNA internal standard and time-resolved fluorometry. Anal. Chem. 68, 834–840, 1996.CrossRefGoogle Scholar
  39. 39.
    Mansfield, E. S. Diagnosis of Down syndrome and other aneuploidies using quantitative polymerase chain reaction and small tandem repeat polymorphisms. Hum. Mol. Genet. 2, 43–50, 1993.Google Scholar
  40. 40.
    Adinolfi, M., Pertl, B., and Sherlock, J. Rapid detection of aneuploidies by microsatellite and the quantitative fluorescent polymerase chain reaction. Prenat. Diagn. 17, 1299–1311, 1997.Google Scholar
  41. 41.
    Verma, L., Macdonald, F., Leedham, P., McConachie, M., Dhanjal, S., and Hulten, M. Rapid and simple prenatal DNA diagnosis of Down’s syndrome. Lancet 352, 9–12, 1998.CrossRefGoogle Scholar
  42. 42.
    Vlieger, A. M., Medenblik, A. M., van Gijlswijk, R. P., Tanke, H. J., van der Ploeg, M., Gratama, J. W., and Raap, A. K. Quantitation of polymerase chain reaction products by hybridization-based assays with fluorescent, colorimetric, or chemiluminescent detection. Anal. Biochem. 205, 1–7, 1992.CrossRefGoogle Scholar
  43. 43.
    Livak, K. J., Hobbs, F. W., and Zagursky, R. J. Detection of single base differences using biotinylated nucleotides with very long linker arms. Nucleic Acids Res. 20, 4831–4837, 1992.Google Scholar
  44. 44.
    Del Tito, B. J., Jr., Poff, H. E., 3rd, Novotny, M. A., Cartledge, D. M., Walker, R. I., 2nd, Earl, C. D., and Bailey, A. L. Automated fluorescent analysis procedure for enzymatic mutation detection. Clin. Chem. 44, 731–739, 1998.Google Scholar
  45. 45.
    Landegren, U., Kaiser, R., Sanders, J., and Hood, L. A ligase-mediated gene detection technique. Science 241, 1077–1080, 1988.Google Scholar
  46. 46.
    Grossman, P. D., Bloch, W., Brinson, E., Chang, C. C., Eggerding, F. A., Fung, S., lovannisci, D. M., Woo, S., Winn-Deen, E. S., and lovannisci, D. A. High-density multiplex detection of nucleic acid sequences: Oligonucleotide ligation assay and sequence-coded separation [published erratum appears in Nucleic Acids Res. 26, 5539, 1998]. Nucleic Acids Res. 22, 4527–4534, 1994.Google Scholar
  47. 47.
    Eggerding, F. A. A one-step coupled amplification and oligonucleotide ligation procedure for multiplex genetic typing. PCR Methods Applic. 4, 337–345, 1995.Google Scholar
  48. 48.
    Eggerding, F. A., Iovannisci, D.M., Brinson, E., Grossman, P., and Winn-Deen, E.S. Fluorescence-based oligonucleotide ligation assay for analysis of cystic fibrosis transmembrane conductance regulator gene mutations. Hum. Mutat. 5, 153–165, 1995.CrossRefGoogle Scholar
  49. 49.
    Samiotaki, M., Kwiatkowski, M., Parik, J., and Landegren, U. Dual-color detection of DNA sequence variants by ligase-mediated analysis. Genomics 20, 238–242, 1994.CrossRefGoogle Scholar
  50. 50.
    Kwiatkowski, M., Samiotaki, M., Lamminmaki, U., Mukkala, V. M., and Landegren, U. Solid-phase synthesis of chelate-labelled oligonucleotides: Application in triple-color ligase-mediated gene analysis. Nucleic Acids Res. 22, 2604–2611, 1994.Google Scholar
  51. 51.
    Bortolin, S., and Christopoulos, T. K. Detection of BCR-ABL transcripts from the Philadelphia translocation by hybridization in microtiter wells and time-resolved immunofluorometry. Clin. Chem. 41, 693–699, 1995.Google Scholar
  52. 52.
    Galvan, B., Christopoulos, T. K., and Diamandis, E. P. Detection of prostate-specific antigen mRNA by reverse transcription polymerase chain reaction and time-resolved fluorometry. Clin. Chem. 41, 1705–1709, 1995.Google Scholar
  53. 53.
    Wu, D. Y., and Wallace, R. B. The ligation amplification reaction (LAR)—Amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 4, 560–569, 1989.CrossRefGoogle Scholar
  54. 54.
    Abravaya, K., Carrino, J. J., Muldoon, S., and Lee, H. H. Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res. 23, 675–682, 1995.Google Scholar
  55. 55.
    Bush, C. E., Vanden Brink, K. M., Sherman, D. G., Peterson, W. R., Beninsig, L. A., and Godsey, J. H. Detection of Escherichia coli rRNA using target amplification and time-resolved fluorescence detection. Mol. Cell. Probes 5, 467–472, 1991.Google Scholar
  56. 56.
    Forster, T. Transfer mechanisms of electronic excitation. Disc. Faraday Soc. 27, 7–17, 1959.CrossRefGoogle Scholar
  57. 57.
    Morrison, L. E. in Nonisotopic Probing, Blotting, and Sequencing, Kricka, L. J., ed. San Diego, CA: Academic Press, 1995, pp. 429–471.Google Scholar
  58. 58.
    Morrison, L. Homogeneous detection of specific DNA sequences by fluorescence quenching and energy transfer. J. Fluores. 9, 187–196, 1999.CrossRefGoogle Scholar
  59. 59.
    Heller, M. J., Morrison, L. E., Prevatt, W. D., and Akin, C. Light-emitting polynucleotide hybridization diagnostic method. European patent application 070 685, 1983.Google Scholar
  60. 60.
    Heller, M. J., and Morrison, L. E. in Rapid Detection and Identification of Infectious Agents, Kingsbury, D. T, and Falkow, S., eds. Orlando, FL: Academic Press, 1985, pp. 245–256.Google Scholar
  61. 61.
    Cardullo, R. A., Agrawal, S., Flores, C., Zamecnik, P. C., and Wolf, D. E. Deleclion of nucleic acid hybridization by nonradialive fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 85, 8790–8794, 1988.Google Scholar
  62. 62.
    Mergny, J. L., Garestier, T., Rougee, M., Lebedev, A. V, Chassignol, M., Thuong, N. T., and Helene, C. Fluorescence energy transfer between two triple helix-forming oligonucleotides bound to duplex DNA. Biochemistry 33, 15321–15328, 1994.CrossRefGoogle Scholar
  63. 63.
    Morrison, L. E. Competitive homogeneous assay. European patent application 232 967, 1987; United States patent 5,928,862, 1999.Google Scholar
  64. 64.
    Morrison, L. E., Halder, T. C., and Stols, L. M. Solution-phase detection of polynucleotides using interacting fluorescent labels and competitive hybridization. Anal. Biochem. 183, 231–244, 1989.CrossRefGoogle Scholar
  65. 65.
    Heller, M. J., and Jablonski, E. J. Fluorescent Stokes shift probes for polynucleotide hybridization assays. European patent application 229 943, 1987.Google Scholar
  66. 66.
    Bannwarth, W., and Muller, F. Energy transfer from a lumazine (=pteridine-2,4(lH,3H)-dione) chromophore to bathophenanthroline-ruthenium(II) ucomplexes during hybridization processes of DNA. Helv. Chim. Acta 74, 2000–2008, 1991.CrossRefGoogle Scholar
  67. 67.
    Tyagi, S., and Kramer, F. R. Molecular beacons: Probes that fluoresce upon hybridization. Nature Biotechnol. 14, 303–308, 1996.Google Scholar
  68. 68.
    Tyagi, S., Bratu, D. P., and Kramer, F. R. Multicolor molecular beacons for allele discrimination. Nature Biotechnol 16, 49–53, 1998.CrossRefGoogle Scholar
  69. 69.
    Bonnet, G., Tyagi, S., Libchaber, A., and Kramer, F. R. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA 96, 6171–6176, 1999.Google Scholar
  70. 70.
    Morrison, L. E. Time-resolved detection of energy transfer: Theory and application to immunoassays. Anal. Biochem. 174, 101–120, 1988.CrossRefGoogle Scholar
  71. 71.
    Mathis, G. Rare earth cryptates and homogeneous fluoroimmunoassays with human sera. Clin. Chem. 39, 1953–1959, 1993.Google Scholar
  72. 72.
    Ebata, K., Masuko, M., Ohtani, H., and Kashiwasake-Jibu, M. Nucleic acid hybridization accompanied with excimer formation from two pyrene-labeled probes. Photochem. Photobiol. 62, 836–839, 1995.Google Scholar
  73. 73.
    Paris, P. L., Langenhan, J. M., and Kool, E. T. Probing DNA sequences in solution with a monomer-excimer fluorescence color change. Nucleic Acids Rex. 26, 3789–3793, 1998.Google Scholar
  74. 74.
    Oser, A., and Valet, G. Nonradioactive assay of DNA hybridization by DNA-template-mediated formation of a ternary TbIII complex in pure liquid phase. Chem. Int. Ed. Engl. 29, 1167–1169,1990.Google Scholar
  75. 75.
    Castro, A., and Williams, J. G. Single-molecule detection of specific nucleic acid sequences in unamplified genomic DNA. Anal. Chem. 69, 3915–3920, 1997.CrossRefGoogle Scholar
  76. 76.
    Kierzek, R., Li, Y., Turner, D. H., and Bevilacqua, P. C. 5′-Amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation. J. Am. Chem. Soc. 115, 4985–4992, 1993.CrossRefGoogle Scholar
  77. 77.
    Yguerabide, J., Talavera, E., Alvarez, J. M., and Afkir, M. Pyrene-labeled DNA probes for homogeneous detection of complementary DNA sequences: Poly(C) model system. Anal. Biochem. 241, 238–247, 1996.CrossRefGoogle Scholar
  78. 78.
    Lee, S. P., Porter, D., Chirikjian, J. G., Knutson, J. R., and Han, M. K. A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease. Anal. Biochem. 220, 377–383, 1994.CrossRefGoogle Scholar
  79. 79.
    Talavera, E., Alvarez-Pez, J., Ballesteros, L., and Bermejo, R. Fluorescein-labeled DNA probes for homogeneous hybridization assays: Application to DNA E. coli renaturation. Appl. Spectrosc. 51, 401–406, 1997.CrossRefGoogle Scholar
  80. 80.
    Ishiguro, T., Saitoh, J., Yawata, H., Otsuka, M., Inoue, T., and Sugiura, Y. Fluorescence detection of specific sequence of nucleic acids by oxazole yellow-linked oligonucleotides. Homogeneous quantitative monitoring of in vitro transcription. Nucleic Acids Res. 24, 4992–4997, 1996.CrossRefGoogle Scholar
  81. 81.
    Perrin, M. F. Polarisation de la lumiere de fluorescence. Vie moyenne des molecules dans ľetat excite. J. Phys. Radium 7, 390–401, 1926.Google Scholar
  82. 82.
    Weber, G. in Fluorescence and Phosphorescence Analysis, Hercules, D. M., ed., New York: Interscience, 1966, pp. 217–240.Google Scholar
  83. 83.
    Kumke, M. U., Li, G., McGown, L. B., Walker, G. T., and Linn, C. P. Hybridization of fluorescein-labeled DNA oligomers detected by fluorescence anisotropy with protein binding enhancement. Anal. Chem. 67, 3945–3951, 1995.CrossRefGoogle Scholar
  84. 84.
    Tsuruoka, M., Yano, K., Ikebukuro, K., Nakayama, H., Masuda, Y., and Karube, I. Optimization of the rate of DNA hybridization and rapid detection of methicillin resistant Staphylococcus aureus DNA using fluorescence polarization. J. Biotechnol. 48, 201–208, 1996.CrossRefGoogle Scholar
  85. 85.
    Kinjo, M., and Rigler, R. Ultrasensitive hybridization analysis using fluorescence correlation spectroscopy. Nucleic Acids Res. 23, 1795–1799, 1995.Google Scholar
  86. 86.
    Lee, L. G., Connell, C. R., and Bloch, W. Allelic discrimination by nick-translation PCR with fluorogenic probes. Nucleic Acids Res. 21, 3761–3766, 1993.Google Scholar
  87. 87.
    Faas, S. J., Menon, R., Braun, E. R., Rudert, W. A., and Trucco, M. Sequence-specific priming and exonuclease-released fluorescence detection of HLA-DQB1 alleles. Tissue Antigens 48, 97–112, 1996.CrossRefGoogle Scholar
  88. 88.
    Gelmini, S., Orlando, C., Sestini, R., Vona, G., Pinzani, P., Ruocco, L., and Pazzagli, M. Quantitative polymerase chain reaction-based homogeneous assay with fluorogenic probes to measure c-erbB-2 oncogene amplification. Clin. Chem. 43, 752–758, 1997.Google Scholar
  89. 89.
    Ibrahim, M. S., Esposito, J. J., Jahrling, P. B., and Lofts, R. S. The potential of 5′ nuclease PCR for detecting a single-base polymorphism in Orthopoxvirus. Mol. Cell. Probes II, 143–147, 1997.Google Scholar
  90. 90.
    Swan, D. C., Tucker, R. A., Holloway, B. P., and Icenogle, J. P. A sensitive, type-specific, fluorogenic probe assay for detection of human papillomavirus DNA. J. Clin. Microbiol. 35, 886–891, 1997.Google Scholar
  91. 91.
    Bieche, I., Olivi, M., Champeme, M. H., Vidaud, D., Lidereau, R., and Vidaud, M. Novel approach to quantitative polymerase chain reaction using real-time detection: Application to the detection of gene amplification in breast cancer. Int. J. Cancer 78, 661–666, 1998.Google Scholar
  92. 92.
    Gibson, U. E., Heid, C. A., and Williams, P. M. A novel method for real time quantitative RT-PCR. Genome Res. 6, 995–1001, 1996.Google Scholar
  93. 93.
    Schofield, P., Pell, A. N., and Krause, D. 0. Molecular beacons: Trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria. Appl. Environ. Microbiol. 63, 1143–1147, 1997.Google Scholar
  94. 94.
    Piatek, A. S., Tyagi, S., Pol, A. C., Telenti, A., Miller, L. P., Kramer, F. R., and Alland, D. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis [see comments]. Nature Biotechnol. 16, 359–363, 1998.CrossRefGoogle Scholar
  95. 95.
    Vet, J. A., Majithia, A. R., Marras, S. A., Tyagi, S., Dube, S., Poiesz, B. J., and Kramer, F. R. Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc. Natl. Acad. Sci. USA 96, 6394–6399, 1999.CrossRefGoogle Scholar
  96. 96.
    Wittwer, C. T., Herrmann, M. G., Moss, A. A., and Rasmussen, R. P. Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22, 130–131, 134–138, 1997.Google Scholar
  97. 97.
    Lay, M. J., and Wittwer, C. T. Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin. Chem. 43, 2262–2267, 1997.Google Scholar
  98. 98.
    Bernard, P. S., Lay, M. J., and Wittwer, C. T. Integrated amplification and detection of the C677T point mutation in the methylenetetrahydrofolate reductase gene by fluorescence resonance energy transfer and probe melting curves. Anal. Biochem. 255, 101–107, 1998.CrossRefGoogle Scholar
  99. 99.
    Chen, X., and Kwok, P. Y. Template-directed dye-terminator incorporation (TDI) assay: A homogeneous DNA diagnostic method based on fluorescence resonance energy transfer. Nucleic Acids Res. 25, 347–353, 1997.Google Scholar
  100. 100.
    Chen, X., Zehnbauer, B., Gnirke, A., and Kwok, P. Y. Fluorescence energy transfer detection as a homogeneous DNA diagnostic method. Proc. Natl. Acad. Sci. USA 94, 10756–10761, 1997.Google Scholar
  101. 101.
    Nazarenko, I. A., Bhatnagar, S. K., and Hohman, R. J. A closed tube format for amplification and detection of DNA based on energy transfer. Nucleic Acids Res. 25, 2516–2521, 1997.CrossRefGoogle Scholar
  102. 102.
    Chiang, P. W., Song, W. J., Wu, K. Y, Korenberg, J. R., Fogel, E. J., Van Keuren, M. L., Lashkari, D., and Kurnit, D. M. Use of a fluorescent-PCR reaction to detect genomic sequence copy number and transcriptional abundance. Genome Res. 6, 1013–1026, 1996.Google Scholar
  103. 103.
    Whitcombe, D., Theaker, J., Guy, S. P., Brown, T., and Little, S. Detection of PCR products using self-probing amplicons and fluorescence. Nature Biotechnol. 17, 804–807, 1999.CrossRefGoogle Scholar
  104. 104.
    Walker, G. T, Linn, C. P., and Nadeau, J. G. DNA detection by strand displacement amplification and fluorescence polarization with signal enhancement using a DNA binding protein. Nucleic Acids Res. 24, 348–353, 1996.CrossRefGoogle Scholar
  105. 105.
    Walker, G. T., and Linn, C. P. Detection of Mycobacterium tuberculosis DNA with thermophilic strand displacement amplification and fluorescence polarization. Clin. Chem. 42, 1604–1608, 1996.Google Scholar
  106. 106.
    Walker, G. T., Nadeau, J. G., Linn, C. P., Devlin, R. F., and Dandliker, W. B. Strand displacement amplification (SDA) and transient-state fluorescence polarization detection of Mycobacterium tuberculosis DNA [see comments]. Clin. Chem. 42, 9–13, 1996.Google Scholar
  107. 107.
    Spears, P. A., Linn, C. P., Woodard, D. L., and Walker, G. T. Simultaneous strand displacement amplification and fluorescence polarization detection of Chlamydia trachomatis DNA. Anal. Biochem. 247, 130–137, 1997.CrossRefGoogle Scholar
  108. 108.
    Gibson, N. J., Gillard, H. L., Whitcombe, D., Ferrie, R. M., Newton, C. R., and Little, S. A homogeneous method for genotyping with fluorescence polarization. Clin. Client. 43,1336–1341, 1997.Google Scholar
  109. 109.
    Walter, N. G., Schwille, P., and Eigen, M. Fluorescence correlation analysis of probe diffusion simplifies quantitative pathogen detection by PCR. Proc. Natl. Acad. Sci. USA 93,12805–12810, 1996.Google Scholar
  110. 110.
    Higuchi, R., Fockler, C., Dollinger, G., and Watson, R. Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions. Biotechnology (New York) 11, 1026–1030, 1993.Google Scholar
  111. 111.
    Ishiguro, T., Saitoh, J., Yawata, H., Yamagishi, H., Iwasaki, S., and Mitoma, Y. Homogeneous quantitative assay of hepatitis C virus RNA by polymerase chain reaction in the presence of a fluorescent intercalater. Anal. Biochem. 229, 207–213, 1995.CrossRefGoogle Scholar
  112. 112.
    Livache, T., Fouque, B., and Teoule, R. Detection of HIV1 DNA in biological samples by an homogeneous assay: Fluorescence measurement of double-stranded RNA synthesized from amplified DNA. Anal. Biochem. 217, 248–254, 1994.CrossRefGoogle Scholar
  113. 113.
    Kyger, E. M., Krevolin, M. D., and Powell, M. J. Detection of the hereditary hemochromatosis gene mutation by real-time fluorescence polymerase chain reaction and peptide nucleic acid clamping. Anal. Biochem. 260, 142–148, 1998.CrossRefGoogle Scholar
  114. 114.
    Ririe, K. M., Rasmussen, R. P., and Wittwer, C. T. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245, 154–160, 1997.CrossRefGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Larry E. Morrison
    • 1
  1. 1.Vysis, Inc.Downers Grove

Personalised recommendations