Skip to main content
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1989 Dec;86(23):9178–9182. doi: 10.1073/pnas.86.23.9178

Detection of specific DNA sequences by fluorescence amplification: a color complementation assay.

F F Chehab 1, Y W Kan 1
PMCID: PMC298457  PMID: 2594760

Abstract

We have developed a color complementation assay that allows rapid screening of specific genomic DNA sequences. It is based on the simultaneous amplification of two or more DNA segments with fluorescent oligonucleotide primers such that the generation of a color, or combination of colors, can be visualized and used for diagnosis. Color complementation assay obviates the need for gel electrophoresis and has been applied to the detection of a large and small gene deletion, a chromosomal translocation, an infectious agent, and a single-base substitution. DNA amplification with fluorescent oligonucleotide primers has also been used to multiplex and discriminate five different amplified DNA loci simultaneously. Each primer set is conjugated to a different dye, and the fluorescence of each dye respective to its amplified DNA locus is scored on a fluorometer. This method is valuable for DNA diagnostics of genetic, acquired, and infectious diseases, as well as in DNA forensics. It also lends itself to complete automation.

Full text

PDF
9179

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bakker E., Hofker M. H., Goor N., Mandel J. L., Wrogemann K., Davies K. E., Kunkel L. M., Willard H. F., Fenton W. A., Sandkuyl L. Prenatal diagnosis and carrier detection of Duchenne muscular dystrophy with closely linked RFLPs. Lancet. 1985 Mar 23;1(8430):655–658. doi: 10.1016/s0140-6736(85)91325-x. [DOI] [PubMed] [Google Scholar]
  2. Chamberlain J. S., Gibbs R. A., Ranier J. E., Nguyen P. N., Caskey C. T. Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res. 1988 Dec 9;16(23):11141–11156. doi: 10.1093/nar/16.23.11141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chehab F. F., Doherty M., Cai S. P., Kan Y. W., Cooper S., Rubin E. M. Detection of sickle cell anaemia and thalassaemias. Nature. 1987 Sep 24;329(6137):293–294. doi: 10.1038/329293b0. [DOI] [PubMed] [Google Scholar]
  4. Chehab F. F., Xiao X., Kan Y. W., Yen T. S. Detection of cytomegalovirus infection in paraffin-embedded tissue specimens with the polymerase chain reaction. Mod Pathol. 1989 Mar;2(2):75–78. [PubMed] [Google Scholar]
  5. Conner B. J., Reyes A. A., Morin C., Itakura K., Teplitz R. L., Wallace R. B. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci U S A. 1983 Jan;80(1):278–282. doi: 10.1073/pnas.80.1.278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cotton R. G., Rodrigues N. R., Campbell R. D. Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4397–4401. doi: 10.1073/pnas.85.12.4397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Crescenzi M., Seto M., Herzig G. P., Weiss P. D., Griffith R. C., Korsmeyer S. J. Thermostable DNA polymerase chain amplification of t(14;18) chromosome breakpoints and detection of minimal residual disease. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4869–4873. doi: 10.1073/pnas.85.13.4869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Farrall M., Estivill X., Williamson R. Indirect cystic fibrosis carrier detection. Lancet. 1987 Jul 18;2(8551):156–157. doi: 10.1016/s0140-6736(87)92354-3. [DOI] [PubMed] [Google Scholar]
  9. Gitschier J., Drayna D., Tuddenham E. G., White R. L., Lawn R. M. Genetic mapping and diagnosis of haemophilia A achieved through a BclI polymorphism in the factor VIII gene. 1985 Apr 25-May 1Nature. 314(6013):738–740. doi: 10.1038/314738a0. [DOI] [PubMed] [Google Scholar]
  10. Goossens M., Kan Y. Y. DNA analysis in the diagnosis of hemoglobin disorders. Methods Enzymol. 1981;76:805–817. doi: 10.1016/0076-6879(81)76159-7. [DOI] [PubMed] [Google Scholar]
  11. Gusella J. F., Wexler N. S., Conneally P. M., Naylor S. L., Anderson M. A., Tanzi R. E., Watkins P. C., Ottina K., Wallace M. R., Sakaguchi A. Y. A polymorphic DNA marker genetically linked to Huntington's disease. Nature. 1983 Nov 17;306(5940):234–238. doi: 10.1038/306234a0. [DOI] [PubMed] [Google Scholar]
  12. Horn G. T., Bugawan T. L., Long C. M., Erlich H. A. Allelic sequence variation of the HLA-DQ loci: relationship to serology and to insulin-dependent diabetes susceptibility. Proc Natl Acad Sci U S A. 1988 Aug;85(16):6012–6016. doi: 10.1073/pnas.85.16.6012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hu E., Trela M., Thompson J., Lowder J., Horning S., Levy R., Sklar J. Detection of B-cell lymphoma in peripheral blood by DNA hybridisation. Lancet. 1985 Nov 16;2(8464):1092–1095. doi: 10.1016/s0140-6736(85)90686-5. [DOI] [PubMed] [Google Scholar]
  14. Innis M. A., Myambo K. B., Gelfand D. H., Brow M. A. DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9436–9440. doi: 10.1073/pnas.85.24.9436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kan Y. W., Dozy A. M. Polymorphism of DNA sequence adjacent to human beta-globin structural gene: relationship to sickle mutation. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5631–5635. doi: 10.1073/pnas.75.11.5631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kazazian H. H., Jr, Boehm C. D. Molecular basis and prenatal diagnosis of beta-thalassemia. Blood. 1988 Oct;72(4):1107–1116. [PubMed] [Google Scholar]
  17. Kirmaier C., Holten D., Bylina E. J., Youvan D. C. Electron transfer in a genetically modified bacterial reaction center containing a heterodimer. Proc Natl Acad Sci U S A. 1988 Oct;85(20):7562–7566. doi: 10.1073/pnas.85.20.7562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kogan S. C., Doherty M., Gitschier J. An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences. Application to hemophilia A. N Engl J Med. 1987 Oct 15;317(16):985–990. doi: 10.1056/NEJM198710153171603. [DOI] [PubMed] [Google Scholar]
  19. Lee M. S., Chang K. S., Cabanillas F., Freireich E. J., Trujillo J. M., Stass S. A. Detection of minimal residual cells carrying the t(14;18) by DNA sequence amplification. Science. 1987 Jul 10;237(4811):175–178. doi: 10.1126/science.3110950. [DOI] [PubMed] [Google Scholar]
  20. Lidsky A. S., Güttler F., Woo S. L. Prenatal diagnosis of classic phenylketonuria by DNA analysis. Lancet. 1985 Mar 9;1(8428):549–551. doi: 10.1016/s0140-6736(85)91208-5. [DOI] [PubMed] [Google Scholar]
  21. Mullis K. B., Faloona F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335–350. doi: 10.1016/0076-6879(87)55023-6. [DOI] [PubMed] [Google Scholar]
  22. Myers R. M., Larin Z., Maniatis T. Detection of single base substitutions by ribonuclease cleavage at mismatches in RNA:DNA duplexes. Science. 1985 Dec 13;230(4731):1242–1246. doi: 10.1126/science.4071043. [DOI] [PubMed] [Google Scholar]
  23. Myers R. M., Lumelsky N., Lerman L. S., Maniatis T. Detection of single base substitutions in total genomic DNA. Nature. 1985 Feb 7;313(6002):495–498. doi: 10.1038/313495a0. [DOI] [PubMed] [Google Scholar]
  24. Orkin S. H., Kazazian H. H., Jr, Antonarakis S. E., Goff S. C., Boehm C. D., Sexton J. P., Waber P. G., Giardina P. J. Linkage of beta-thalassaemia mutations and beta-globin gene polymorphisms with DNA polymorphisms in human beta-globin gene cluster. Nature. 1982 Apr 15;296(5858):627–631. doi: 10.1038/296627a0. [DOI] [PubMed] [Google Scholar]
  25. Pirastu M., Kan Y. W., Cao A., Conner B. J., Teplitz R. L., Wallace R. B. Prenatal diagnosis of beta-thalassemia. Detection of a single nucleotide mutation in DNA. N Engl J Med. 1983 Aug 4;309(5):284–287. doi: 10.1056/NEJM198308043090506. [DOI] [PubMed] [Google Scholar]
  26. Pressley L., Higgs D. R., Clegg J. B., Weatherall D. J. Gene deletions in alpha thalassemia prove that the 5' zeta locus is functional. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3586–3589. doi: 10.1073/pnas.77.6.3586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Saiki R. K., Bugawan T. L., Horn G. T., Mullis K. B., Erlich H. A. Analysis of enzymatically amplified beta-globin and HLA-DQ alpha DNA with allele-specific oligonucleotide probes. Nature. 1986 Nov 13;324(6093):163–166. doi: 10.1038/324163a0. [DOI] [PubMed] [Google Scholar]
  28. Saiki R. K., Chang C. A., Levenson C. H., Warren T. C., Boehm C. D., Kazazian H. H., Jr, Erlich H. A. Diagnosis of sickle cell anemia and beta-thalassemia with enzymatically amplified DNA and nonradioactive allele-specific oligonucleotide probes. N Engl J Med. 1988 Sep 1;319(9):537–541. doi: 10.1056/NEJM198809013190903. [DOI] [PubMed] [Google Scholar]
  29. Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350–1354. doi: 10.1126/science.2999980. [DOI] [PubMed] [Google Scholar]
  30. Saiki R. K., Walsh P. S., Levenson C. H., Erlich H. A. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A. 1989 Aug;86(16):6230–6234. doi: 10.1073/pnas.86.16.6230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Shibata D. K., Arnheim N., Martin W. J. Detection of human papilloma virus in paraffin-embedded tissue using the polymerase chain reaction. J Exp Med. 1988 Jan 1;167(1):225–230. doi: 10.1084/jem.167.1.225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Spritz R. A., Jagadeeswaran P., Choudary P. V., Biro P. A., Elder J. T., deRiel J. K., Manley J. L., Gefter M. L., Forget B. G., Weissman S. M. Base substitution in an intervening sequence of a beta+-thalassemic human globin gene. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2455–2459. doi: 10.1073/pnas.78.4.2455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Treisman R., Orkin S. H., Maniatis T. Specific transcription and RNA splicing defects in five cloned beta-thalassaemia genes. Nature. 1983 Apr 14;302(5909):591–596. doi: 10.1038/302591a0. [DOI] [PubMed] [Google Scholar]
  34. Wu D. Y., Wallace R. B. The ligation amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics. 1989 May;4(4):560–569. doi: 10.1016/0888-7543(89)90280-2. [DOI] [PubMed] [Google Scholar]
  35. Zhang J. Z., Cai S. P., He X., Lin H. X., Lin H. J., Huang Z. G., Chehab F. F., Kan Y. W. Molecular basis of beta thalassemia in south China. Strategy for DNA analysis. Hum Genet. 1988 Jan;78(1):37–40. doi: 10.1007/BF00291231. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES