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COMPETITIVE PCR FOR QUANTITATION OF mRNA
8 COMPETITIVE PCR FOR QUANTITATION OF mRNA Gary Gilliland, Steven Perrin, and H. Franklin Bunn
PCR has proved useful in amplifying specific mRNAs, especially those present in low copy number. For example, it has been possible to amplify, subclone, and characterize low-abundance m R N A (Froh man et al. 1988) and to detect unique m R N A transcripts from abnor mal cells in a background of normal cells (Chelly et al 1988; Ka wasaki et al 1988; Lee et al 1987). Although it has been possible to detect and amplify large amounts of rare m R N A transcripts, it has been more difficult to quantitate the amount of m R N A present in the starting material. T h i s has pre cluded, for example, the use of P C R in the analysis of induction of m R N A in response to exogenous stimuli. T h e main constraint in obtaining quantitative data is inherent in the amplification process. Because amplification is (at least initially) an exponential process, small differences in any of the variables that control the reaction rate will dramatically affect the yield of PCR product. Variables that influence the rate of the P C R include the concentrations of polymer ase, dNTPs, Mg, DNA, and primers; annealing, extension, and de naturing temperatures; cycle length and cycle number; ramping times; rate of "primer-dimer" formation; and presence of contami-
60
PCR Protocols: A Guide to Methods and Applications Copyright © 1990 by Academic Press, Inc. All rights of reproduction in any form reserved.
PCR has proved useful in amplifying specific mRNAs, especially those present in low copy number. For example, it has been possible to amplify, subclone, and characterize low-abundance m R N A (Froh man et al. 1988) and to detect unique m R N A transcripts from abnor mal cells in a background of normal cells (Chelly et al 1988; Ka wasaki et al 1988; Lee et al 1987). Although it has been possible to detect and amplify large amounts of rare m R N A transcripts, it has been more difficult to quantitate the amount of m R N A present in the starting material. T h i s has pre cluded, for example, the use of P C R in the analysis of induction of m R N A in response to exogenous stimuli. T h e main constraint in obtaining quantitative data is inherent in the amplification process. Because amplification is (at least initially) an exponential process, small differences in any of the variables that control the reaction rate will dramatically affect the yield of PCR product. Variables that influence the rate of the P C R include the concentrations of polymer ase, dNTPs, Mg, DNA, and primers; annealing, extension, and de naturing temperatures; cycle length and cycle number; ramping times; rate of "primer-dimer" formation; and presence of contami-
60
PCR Protocols: A Guide to Methods and Applications Copyright © 1990 by Academic Press, Inc. All rights of reproduction in any form reserved.