Abstract
Many aspects of molecular genetics necessitate the detection of nucleic acid sequences. Current approaches involving target amplification (in situ PCR, Primed in situ Labeling, Self-Sustained Sequence Replication, Strand Displacement Amplification), probe amplification (Ligase Chain Reaction, Padlock Probes, Rolling Circle Amplification) and signal amplification (Tyramide Signal Amplification, Branched DNA Amplification) are summarized in the present review, together with their advantages and limitations.
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Southern, E. M. (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503–507.
Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985) Individual-specific “fingerprints” of human DNA. Nature 316, 76–79.
Wang, D. G., Fan, J.-B., Siao, C.-J., et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082.
Winn-Deen, E. S. (1996) Automation of molecular genetic methods-Part 2: DNA amplification techniques. J. Clin. Ligand Assay 19, 21–26.
Haase, A. T., Retzel, E. F., and Staskus, K. A. (1990) Amplification and detection of lentiviral DNA inside cells. Proc. Natl. Acad. Sci. USA 87, 4971–4975.
Nuovo, G., MacConnell, P., Forde, A., and Delvenne, P. (1991) Detection of human papillomavirus DNA in formalin-fixed tissues by in situ hybridization after amplification by polymerase chain reaction. Am. J. Pathol. 139, 847–854.
Ray, R., Komminoth, P., Machado, M., and Wolfe, H. J. (1991) Combined polymerase chain reaction and in situ hybridization for the detection of single copy genes and viral genomic sequences in intact cells. Mod. Pathol. 4, 124A.
Spann, W., Pachman, K., Zabinienska, H., Pielmeier, A., and Emmerich, B. (1991) In situ amplification of single copy gene segments in individual cells by the polymerase chain reaction. Infection 19, 242–244.
Komminoth, P. and Werner, M. (1997) Target and signal amplification: approaches to increase the sensitivity of in situ hybridization. Histochem. Cell Biol. 108, 325–333.
Nuovo, G. (1992) PCR in situ hybridization. Raven Press, New York.
Chen, R. H. and Fuggle, S. V. (1993) In situ cDNA polymerase chain reaction. A novel technique for detecting mRNA expression. Am. J. Pathol. 143, 1527–1534.
Komminoth, P., Adams, V., Long, A. A., et al. (1994) Evaluation of methods for hepatitis C virus (HCV) detection in liver biopsies: comparison of histology, immunochemistry, in situ hybridization, reverse transcriptase (RT) PCR and in situ RT PCR. Pathol. Res. Pract. 190, 1017–1025.
Isaacson, S. H., Asher, D. M., Godec, M. S., Gibbs, C. J., and Gajdusek, D. C. (1996) Widespread, restricted low-level measles virus infection of brain in a case of subacute sclerosing panencephalitis. Acta Neuropathol. 91, 135–139.
Levin, M. C., Fox, R. J., Lehky, T., et al. (1996) PCR-in situ hybridization detection of human T-cell lymphotropic virus type 1 (HTLV-1) tax proviral DNA in peripheral blood lymphocytes of patients with HTLV-1-associated neurologic disease. J. Virol. 70, 924–933.
Bagasra, O., Seshamma, T., and Pomerantz, R. (1993) Polymerase chain reaction in situ: intracellular amplification and detection of HIV-1 proviral DNA and other specific genes. J. Immunol. Methods 158, 131–145.
Cao, Y., Kopplow, K., and Liu, G. Y. (2000) In situ immuno-PCR to detect antigens. Lancet 356, 1002, 1003.
Embretson, J., Zupancic, M., Beneke, J., et al. (1993) Analysis of human immunodeficiency virus-infected tissue by amplification and in situ hybridization reveals latent and permissive infections at single-cell resolution. Proc. Natl. Acad. Sci. USA 90, 357–361.
Long, A. A., Komminoth, P., Lee, E., and Wolfe, H. J. (1993) Comparison of indirect and direct in situ polymerase chain reaction in cell preparations and tissue sections. Detection of viral DNA, gene rearrangements and chromosomal translocations. Histochemistry 99, 151–162.
Koch, J., Hinhkjaer, J., Mogensen, J., Kolvraa, S., and Bolund, L. (1991) An improved method for chromosome-specific labeling of alpha satellite DNA in situ by using denaturated double-stranded DNA probes as primers in a primed in situ labeling (PRINS) procedure. Genet. Anal. Tech. Appl. 8, 171–178.
Koch, J., Mongensen, J., Pedersen, S., et al. (1992) Fast one-step procedure for the detection of nucleic acids in situ by primer-induced sequence-specific labeling with fluorescein-12-dUTP. Cytogenet. Cell Genet. 60, 1–3.
Pellestor, F., Girardet, A., Coignet, L., Andreo, B., and Charlieu, J. P. (1996) Assessment of aneuploidy for chromosomes 8, 9, 13, 16 and 21 in human sperm by using in situ labeling technique. Am. J. Hum. Genet. 58, 797–802.
Wilkens, L., Komminoth, P., Nasarek, A., von Wasielewski, R., and Werner, M. (1997) Rapid detection of karyotype changes in interphase bone marrow cells by oligonucleotide primed in situ labeling (PRINS). J. Pathol. 181, 368–373.
Hindkjaer, J., Hammoudah, S. A., Hansen, K. B., Jensen, P. D., Koch, J., and Pedersen, B. (1995) Translocation (1;16) identified by chromosome painting, and PRimed IN Situ-labeling (PRINS). Report of two cases and review of the cytogenetic literature. Cancer Genet. Cytogenet. 79, 15–20.
Therkelsen, A. J., Nielsen, A., Koch, J., Hindkjaer, J., and Kolvraa, S. (1995) Staining of human telomeres with primed in situ labeling (PRINS). Cytogenet. Cell Genet. 63, 235–237.
Kubalakova, M., Lysak, M. A., Vrana, J., Simkova, H., Cihalikova, J., and Dolezel, J. (2000) Rapid identification and determination of purity of flow-sorted plant chromosomes using c-PRINS. Cytometry 41, 102–108.
Terkelsen, C., Koch, J., Kolvraa, S., Hindkjaer, J., Pedersen, S., and Bolund, P, (1993) Repeated primed in situ labeling: formation and labeling of specific DNA sequences in chromosomes and nuclei. Cytogenet. Cell Genet. 63, 235–237.
Gosden, J. and Lawson, D. (1995) In situ cyclic amplification of oligonucleotide primed synthesis (cycling PRINS). In: PCR application manual, Boehringer Mannheim Corporation, Mannheim, pp. 115–118.
Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., and Gingeras, T. R. (1989) 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.
Guatelli, J. C., Whitfield, K. M., Kwoh, D. Y., Barringer, K. J., Richman, D. D., and Gingeras, T. R. (1990) Isothermal in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA 87, 1874–1878.
Compton, J. (1991) Nucleic acid sequence-based amplification. Nature 350, 91–92.
Gingeras, T. R., and Kwoh, D. Y. (1992) In vitro nucleic acid target amplification techniques: issues and benefits. Praxis Biotechnol. 4, 403–429.
Miller, N., Hernandez, S. G., and Cleary, T. J. (1994) Evaluation of Gen-Probe amplified Mycobacterium tuberculosis direct test and PCR for direct detection of Mycobacterium tuberculosis in clinical specimens. J. Clin. Microbiol. 32, 393–397.
Zaaijer, H. L., Kok, W., ten-Veen, J. H., et al. (1995) Detection of HIV-1 RNA in plasma by isothermal amplification (NASBA) irrespective of the stage of HIV-1 infection. J. Virol. Methods 52, 175–181.
Vandamme, A. M., Van-Dooren, S., Kok, W., et al. (1995) Detection of HIV-1 RNA in plasma and serum samples using the NASBA amplification system compared to RNA-PCR. J. Virol. Methods 52, 121–132.
Simpkin, S. A., Chan, A. B., Hays, J., Popping, B., and Cook, N. (2000) An RNA transcription-based amplification technique (NASBA) for the detection of viable Salmonella enterica. Lett. Appl. Microbiol. 31, 186,187.
Voisset, C., Mandrand, B., and Paranhos-Baccala, G. (2000) RNA amplification technique, NASBA, also amplifies homologous plasmid DNA in non-denaturing conditions. Biotechniques 29, 236.
Walker, G. T., Little, M. C., Nadeau, J. G., and Shank, D. D. (1992) Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc. Natl. Acad. Sci. USA 89, 392–396.
Walker, G. T., Fraiser, M. S., Schram, J. L., Little, M. C., Nadeau, J. G., and Malinowski, D. P. (1992) Strand displacement amplification — an isothermal, in vitro DNA amplification technique. Nucl. Acids Res. 20, 1691–1696.
Spargo, C. A., Haaland, P. D., Jurgensen, S. R., Shank, D. D., and Walker, G. T. (1993) Chemiluminiscent detection of strand displacement amplified DNA from species comprising the Mycobacterium tuberculosis complex. Mol. Cell Probes 7, 395–404.
Walker, G. T., Nadeau, J. G., Spears, P. A., Schram, J. L., Nycz, C. M., and Shank, D. D. (1994) Multiplex strand displacement amplification (SDA) and detection of DNA sequences from Mycobacterium tuberculosis and other mycobacteria. Nucl. Acids Res. 22, 2670–2677.
Walker, G. T. and Linn, C. P. (1996) Detection of Mycobacterium tuberculosis DNA with termophilic strand displacement amplification and fluorescent polarization. Clin. Chem. 42, 1604–1608.
Nycz, C. M., Dean, C. H., Haaland, P. D., Spargo, C., and Walker, G. T. (1998) Quantitative reverse transcription strand displacement amplification: quantitation of nucleic acids using an isothermal amplification technique. Anal. Biochem. 259, 226–234.
Nadeau, J. G., Pitner, J. B., Linn, C. P., Schram, J. L., Dean, C. H., and Nycz, C. M. (1999) Real-time, sequence-specific detection of nucleic acids during strand displacement amplification. Anal. Biochem. 276, 177–187.
Wu, D. Y. and Wallace, R. B. (1989) The ligation amplification reaction (LAR) — amplification of specific DNA sequences using sequential rounds of template-dependant ligation. Genomics 4, 560–569.
Barany, F. (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88, 189–193.
Barany, F. (1991) The ligase chain reaction in a PCR world. PCR Methods Appl. 1, 5–16.
Birkenmeyer, L. G. and Mushahwar, I. K. (1991) DNA probe amplification methods. J. Virol. Methods 35, 117–126.
Segev, D. (1992) Amplification of nucleic acid sequences by the repair chain reaction, In Nonradioactive Labeling and Detection of Biomolecules (Kessler, C., ed.), Springer Verlag, Berlin, pp. 212–218.
Abravaya, K., Carrino, J. J., Muldoon, S., and Lee, H. H. (1995) Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucl. Acid Res. 23, 675–682.
Reyes, A. A., Carrera, P., Cardilla, E., et al. (1997) Ligase chain reaction assay for human mutations: the sickle cell by LCR assay. Clin. Chem. 43, 40–44.
Birkenmeyer, L. G. and Armstrong, A. S. (1992) Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae. J. Clin. Microbiol. 30, 3089–3094.
van Doornum, G. J. J., Buimer, M., Prins, M., et al. (1995) Detection of Chlamydia trachomatis infection in urine samples from men and women by Ligase Chain Reaction. J. Clin. Microbiol. 33, 2042–2047.
Kapala, J., Copes, D., Sproston, A., et al. (2000) Pooling cervical swabs and testing by ligase chain reaction are accurate and cost-saving strategies for diagnosis of Chlamydia trachomastis. J. Clin. Microbiol. 38, 2480–2483.
Rohner, P., Jahn, E. I., Ninet, B., et al. (1988) Rapid diagnosis of pulmonary tuberculosis with the LCx Mycobacterium tuberculosis assay and comparison with conventional diagnostic techniques. J. Clin. Microbiol. 36, 3046,3047.
Viinanen, A. H., Soini, H., Marjamaki, M., Liippo, K., and Viljanen, M. K. (2000) Ligase chain reaction assay is clinically useful in the discrimination of smear-positive pulmonary tuberculosis from atypical mycobacterioses. Ann. Med. 32, 279–283.
Nilsson, M., Malmgren, H., Samiotaki, M., Kwiatkowski, M., Cowdhary, B. P., and Landegren, U. (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265, 2085–2088.
Landegren, U. and Nilsson, M. (1997) Locked on the target: strategies for future gene diagnostics. Ann. Med. 29, 585–590.
Fire, A. and Xu, S-Q. (1995) Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92, 4641–4645.
Liu, D., Daubendiek, S. L., Zillman, M. A., Ryan, K., and Kool, E. T. (1996). Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerases. J. Am. Chem. Soc. 118, 1587–1594.
Lizardi, P. M., Huang, X., Zhu, Z., Bray-Ward, P., Thomas, D. C., and Ward, D. C. (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19, 225–232.
Banér, J., Nilsson, M., Mendel-Hartvig, M., and Landegren, U. (1998) Signal amplification of padlock probes by rolling circle replication. Nucl. Acids Res. 26, 5073–5078.
Schweitzer, B., Wiltshire, S., Lambert, J., et al. (2000) Immunoassays with rolling circle DNA amplification: A versatile platform for ultrasensitive antigen detection. Proc. Natl. Acad. Sci. USA 97, 10,113–10,119.
Urdea, M., Running, J., Horn, T., Clyne, J., Ku, L., and Warner, B. (1987) A novel method for the rapid detection of specific nucleotide sequences in crude biological samples without blotting or radioactivity; application to the analysis of hepatitis B virus in human serum. Gene 61, 253–264.
Horn, T. and Urdea, M. (1989) Forks and combs and DNA: The synthesis of branched oligodeoxyribonucleotides. Nucl. Acids Res. 17, 6959–6967.
Horn, T., Chang, C-A., and Urdea, M. S. (1997) Chemical synthesis and characterization of branched oligodeoxynucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucl. Acids Res. 25, 4842–4849.
Collins, M. L., Irvine, B., Tyner, D., et al. (1997) A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/mL. Nucl. Acids Res. 25, 2979–2984.
Martell, M., Esteban, J. I., Quer, J., and Genesca, J. (1992) Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J. Virol. 66, 3225–3239.
Lau, J. Y., Davis, G. L., Kniffen, J., and Qian, K. P. (1993) Significance of serum hepatitis C virus RNA levels in chronic hepatitis. Lancet 341, 1501–1504.
Hendricks, D. A., Stowe, B. J., Hoo, B. S., et al. (1995) Quantitation of HBV DNA in human serum using a branched DNA (bDNA) signal amplification assay. Am. J. Clin. Pathol. 104, 537–546.
Cao, Y., Ho, D. D., Todd, J., et al. (1995) Clinical evaluation of branched DNA signal amplification for quantifying HIV type 1 in human plasma. AIDS Res. Hum. Retrovir. 11, 353–361.
Urdea, M. (1993) Synthesis and characterization of branched DNA (bDNA) for the direct quantitative detection of CMV, HBV, HCV and HIV. Clin. Chem. 39, 725,726.
Iqbal, S. S., Chambers, J. P., Brubaker, R. R., Goode, M. T., and Valdes, J. J. (1999) Detection of Yersinia pestis using branched DNA. Mol. Cell Probes 13, 315–320.
Bobrow, M. N., Harris, T. D., Shaughnessy, K. J., and Litt, G. J. (1989) Catalysed reporter deposition, a novel method of signal amplification. Application to immunoassays. J. Immunol. Methods 125, 279–285.
Adams, J. C. (1992) Biotin amplification of biotin and horseradish peroxidase signals in histochemical stains. J. Histochem. Cytochem. 40, 1457–1463.
Raap, A. K., van de Corput, M. P. C., Vervenne, R. A. W., van Gijlswijk, R. P. M., Tanke, H. J., and Wiegant, J. 1995 Ultra-sensitive FISH using peroxidase-mediated deposition of biotin or fluorochrome tyramides. Hum. Mol. Gen. 4, 529–534.
van Gijlswijk, R. P. M., Zijlmans, H. J. M. A. A., Wiegant, J., et al. (1997) Fluorochrome-labeled tyramides: use in immuno-cytochemistry and fluorescent in situ. J. Histochem. Cytochem. 45, 375–382.
NEN Life Science Products web site: http://www.nen.com/
Merz, H., Malisius, R., Mannweiler, S., et al. (1995) ImmunoMax. A maximized immunohistochemical method for the retrieval and enhancement of hidden antigens. Lab. Invest. 73, 149–156.
Werner, M., von Wasielewski, R., and Komminoth, P. (1996) Antigen retrieval, signal amplification and intensification in immunohistochemistry. Histochem. Cell. Biol. 105, 253–260.
Adler, K., Erickson, T., and Bobrow, M. (1997) High sensitivity detection of HPV- 16 in SiHa and CaSki cells using FISH enhanced by TSA. Histochem. Cell Biol. 108, 321–324.
Wiedorn, K. H., Kuhl, H., Galle, J., Caselitz, J., and Vollmer, E. (1999) Comparison of in situ hybridization, direct and indirect in situ PCR as well as tyramide signal amplification for detection of HPV. Histochem. Cell Biol. 111, 89–95.
Yang, H., Wanner, I. B., Roper, S. D., and Chaudhari, N. (1999) An optimized method for in situ hybridization with signal amplification that allows the detection of rare mRNAs. J. Histochem. Cytochem. 47, 431–445.
Acar, H., Copeland, N. G., Gilbert, D. J., Jenkins, N. A., and Largaespada, D. A. (2000) Detection of integrated murine leukemia viruses in a mouse model of acute myeloid leukemia by fluorescence in situ hybridization combined with tyramide signal amplification. Cancer Genet. Cytogenet. 121, 44–51.
Klockars, T., Isosomppi, J., Laan, M., Kakko, N., Palotie, A., and Peltonen, L. (1997) The visual assignment of genes by Fiber-FISH: BTF3 protein homologue gene (BTF3) and a novel pseudogene of human RNA helicase A (DDX9P) on 13q22. Genomics 44, 355–357.
Horelli-Kuitunen, N., Aaltonen, J., Yaspo, M-L., et al. (1999) Mapping ESTs by FIBER-FISH. Genome Methods 9, 62–71.
Mayer, G. and Bendayan, M. (1997) Biotinyl-tyramide: A novel approach for electron microscopic immunocytochemistry. J. Histochem. Cytochem. 45, 1449–1454.
Stanarius, A., Faber-Zuschratter, H., Topel, I., Schulz, S., and Wolf, G. (1999) Tyramide signal amplification in brain immunocytochemistry: adaptation to electron microscopy. J. Neurosci. Methods 88, 55–61.
Kohler, A., Lauritzen, B., and Van Noorden, C. J. F. (2000) Signal amplification in immunochemistry at the light microscopic level using biotinylated tyramide and nanogold-silver staining. J. Histochem. Cytochem. 48, 933–941.
Prichard, C. G. and Stefano, J. E. (1991) Detection of viral nucleic acids by Qb replicase amplification. Med. Virol. 10, 67–80.
Cahil, P., Foster, K., and Mahan, D. E. (1991) Polymerase chain reaction and Qb replicase amplification. Clin. Chem. 37, 1482–1485.
Isaksson, A. and Landegren, U. (1999) Accessing genomic information: alternatives to PCR. Curr. Opin. Biotechnol. 10, 11–15.
Ray, R. A. and Shaikh, H. (2000) The progress and promise of intracellular nucleic acid amplification in histopathology. Microscopy Anal. 78, 7–9.
Raap, A. K., Marijnen, J. G. J., Vrolijk, J., and van der Ploeg, M. (1986) Denaturation, renaturation and loss of DNA during in situ hybridisation procedures. Cytometry 7, 235–242.
Andras, S. C., Hartman, T. P. V., Marshall, J. A., et al. (1999) A drop-spreading technique to produce cytoplasm-free mitotic preparations from plants with small chromosomes. Chromosome Res. 7, 641–647.
Andras, S. C., Hartman, T. P. V., Alexander, J., et al. (2000) Combined PI-DAPI staining (CPD) reveals NOR asymmetry and facilitates karyotyping of plant chromosomes. Chromosome Res. 8, 387–391.
Pastinen, T., Perola, M., Niini, P., et al. (1988) Array-based multiplex analysis of candidate genes reveals two independent and additive genetic risk factors for myocardial infarction in the Finnish population. Hum. Mol. Genet. 7, 1453–1462.
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Andras, S.C., Power, J.B., Cocking, E.C. et al. Strategies for signal amplification in nucleic acid detection. Mol Biotechnol 19, 29–44 (2001). https://doi.org/10.1385/MB:19:1:029
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DOI: https://doi.org/10.1385/MB:19:1:029