Rapid generation of homologous internal standards and evaluation of data for quantitation of messenger RNA by competitive polymerase chain reaction

Abstract

Sensitive and quantitative measurement of messenger RNA (mRNA) is important for accurate assessment of gene expression. Conventional methods of mRNA measurement frequently lack the sensitivity required to detect mRNA expressed at low level, such as mRNA encoding receptors and intracellar signaling molecules. Thus, the extremely sensitive RT-PCR has become the method of choice for examination of gene expression. However, quantitation of mRNA by PCR is difficult because small variations in amplification efficiencies among sample tubes can lead to substantial differences in product yield, thereby rendering direct comparisons between samples invalid. Development of protocols for quantitative RT-PCR has relied on internal standards to monitor the efficiency of the RT-PCR in different reaction tubes. Technically, the two most serious limitations to routine successful application of competitive quantitative PCR is ready access to competitive internal standards and efficient methods for accurate quantitative analysis of the data. In the present manuscript, application and validation of a simple approach to generate homologous internal competitive standards and to quantitate data for rapid, accurate determination of the expression level of genes by quantitative PCR is described. Generation of the competitive standard from a previously amplified PCR product by the methods described requires only one additional primer pair, and an additional two-step reaction; it can be completed in 1–2 days. Analyzing the results of the competitive PCR reaction via phosphoimager analysis provides a simple, rapid method for accurate quantitation of results. Data presented here clearly illustrate that the methods described have been successfully applied, and that they should have wide application for competitive quantitative PCR analysis of gene expression.