Abstract
Numerous techniques have been developed to measure gene expression in tissues and cells. These include coupled reverse transcription and polymerase chain reaction amplification (RT-PCR), Northern blot (see Chapter 20), in situ hybridization (see Chapter 21), RNase protection assays, dot blots, and S1 nuclease assays. Of these methods, RT-PCR is the most sensitive and versatile (1–bi1-5). PCR allows amplification of a DNA or cDNA template by greater than one million-fold quickly and reliably (6). Starting with minute amounts of DNA, PCR generates sufficient material for subsequent experimental analyses such as cloning, restriction digestion, electrophoresis, and sequencing. The entire amplification process is performed in just a few hours.
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Saiki, R. K., Scharf. S., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., and Arnheim, N. (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.
Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G., and Erlich, H. (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51, 263–273.
Bell, J. (1989) The polymerase chain reaction. Immunol Today, 10, 351–355.
Gibbs, R. A. (1990) DNA amplification by the polymerase chain reaction. Anal. Chem. 62, 1202–1214.
Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G., and Erlich, H. (1992) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. 1986.Biotechnology 24, 17–27.
Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.
Templeton, N.S. (1992) The polymerase chain reaction. History, methods, and applications. Diagn. Mol. Pathol. 1, 58–72.
Frohman, M. A. and Martin, G. R. (1989) Cut, paste and save: New approaches to altering specific genes in mice. Cell 56, 145–147.
Dieffenbach, C. W. and Dveksler, G. S. (1993) Setting up a PCR laboratory. PCR Methods Appl. 3, S2–S7.
Blumberg, D. D. (1987) Creating a ribonuclease-free environment. Meth. Enzymol. 152, 20–24.
Rychlik, W., Spencer, W. J., and Rhoads, R. E. (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res. 18, 6409–6412.
Williams, J. F. (1989) Optimization strategies for the polymerase chain reaction. Biotechniques 7, 762–769.
Wittwer, C. T. and Garling, D. J. (1991) Rapid cycle DNA amplification: time and temperature optimization. Biotechniques 10, 76–83.
Harris, S. and Jones, D. B. (1997) Optimization of the polymerase chain reaction. Br. J. Biomed. Sci. 54, 166–173.
Roux, K. H. (1995) Optimization and troubleshooting in PCR. PCR Methods Appl. 4, S185–S194.
Sellner, L. N. and Turbett, G. R. (1998) Comparison of three RT-PCR methods. Biotechniques 25, 230–234.
Sellner, L. N., CoelenR. J., and Mackenzie, J. S. (1992) A one-tube, one manipulation RT-PCR reaction for detection of Ross River virus. J. Virol. Methods 40, 255–263.
Mallet, F., Oriol, G., Mary, C., Verrier, B., and Mandrand, B. (1995) Continuous RT-PCR using AMV-RT and Taq DNA polymerase: characterization and comparison to uncoupled procedures. Biotechniques 18, 678–687
Birch, D.E. (1996) Simplified hot start PCR. Nature 381, 445–446.
D’Aquila, R. T., Bechtel, L. J., Videler, J. A., Eron, J. J., Gorczyca, P., and Kaplan, J. C. (1991) Maximizing sensitivity and specificity of PCR by pre-amplification heating. Nucleic Acids Res. 19, 3749.
Bassam, B. J., and Caetano-Anolles, G. (1993) Automated “hot start” PCR using mineral oil and paraffin wax. Biotechniques 14, 30–34.
Sharkey, D. J., Scalice, E. R., Christy, K. G., Atwood, S. M., Daiss, J. L. (1994) Antibodies as thermolabile switches: high temperature triggering for the polymerase chain reaction. Biotechnology (NY) 12, 506–509.
Kaijalainen, S., Karhunen, P. J., Lalu, K., Lindstrom, K. (1993) An alternative hot start technique for PCR in small volumes using beads of wax-embedded reaction components dried intrehalose. Nucleic Acids Res. 21, 2959–2960.
Kwok, S., and Higuchi, R. (1989) Avoiding false positives with PCR. Nature (London) 339, 237–238.
Victor, T., Jordaan, A., du Toit, R., Van Helden, P. D. (1993) Laboratory experience and guidelines for avoiding false positive polymerase chain reaction results. Eur. J. Clin. Chem. Clin. Biochem. 31, 531–535.
Grillo, M., Margolis, F. L. (1990) Use of reverse transcriptase polymerase chain reaction to monitor expression of intronless genes. Biotechniques 9, 266–268.
Huang, Z., Fasco, M. J., Kaminsky, L. S. (1996) Optimization of Dnase I removal of contaminating DNA from RNA for use in quantitative RNA-PCR. Biotechniques 20, 1012–1014, 1016, 1018-1020.
Hengen, P. N. (1995) Fidelity of DNA polymerases for PCR. Trends Biochem. Sci. 20, 324–325.
Longley, M. J., Bennett, S. E., and Mosbaugh, D. W. (1990) Characterization of the 5′ to 3′ exonuclease associated with Thermus aquaticus DNA polymerase. Nucleic Acids Res. 18, 7317–7322.
Bell, D. A., DeMarini, D. M. (1991) Excessive cycling converts PCR products to random-length higher molecular weight fragments. Nucleic Acids Res. 19, 5079.
Eckert, K. A., and Kunkel, T. A. (1990) High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. Nucleic Acids Res. 18, 3739–3744.
Eckert, K. A., and Kunkel, T. A. (1991) DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1, 17–24.
Ellsworth, D. L., Rittenhouse, K. D., Honeycutt, R. L. (1993) Artifactual variation in randomly amplified polymorphic DNA banding patterns. Biotechniques 14, 214–217.
Baldino, F., Chesselet, M. F., Lewis, M. E. (1989) High resolution in situ hybridization histochemistry, Methods Enzymol. 168, 761–777.
Sellner, L. N., Coelen, R. J., Mackenzie, J. S. (1992) Reverse transcriptase inhibits Taq polymerase activity. Nucleic Acids Res. 20, 1487–1490.
Chumakov, K. M. (1994) Reverse transcriptase can inhibit PCR and stimulate primer-dimer formation. PCR Meth. Appl. 4, 62–64.
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© 2001 Humana Press Inc., Totowa, NJ
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Haddad, EB., Rousell, J. (2001). Analysis of Gene Expression. In: Rogers, D.F., Donnelly, L.E. (eds) Human Airway Inflammation. Methods in Molecular Medicine, vol 56. Humana Press. https://doi.org/10.1385/1-59259-151-5:229
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DOI: https://doi.org/10.1385/1-59259-151-5:229
Publisher Name: Humana Press
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