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ARS Home » Research » Publications at this Location » Publication #126496
Title: QUANTITATIVE ANALYSIS OF GENE EXPRESSION BY REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION AND CAPILLARY ELECTROPHORESIS WITH LASER- INDUCED FLUORESCENCE DETECTION

Author
item Richards, Mark
item Poch, Stephen

Submitted to: Molecular Biology and Biotechnology Encyclopedia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2001
Publication Date: 5/1/2002
Citation: Molecular Biotechnology 21:19-38, 2002.

Interpretive Summary: There has been a dramatic expansion of DNA sequence information compiled over the past several years for a variety of eukaryotic and prokaryotic genomes. Accompanying this increase in knowledge of genomic structure and organization has been a growing interest in studying the function of individual genes including regulation of their expression. To do this, it is important to be able to accurately monitor gene expression at the level of nucleic acid. In this article, we discuss how reverse transcription and polymerase chain reaction can be combined with capillary electrophoresis and laser-induced fluorescence detection to develop new methods that can accurately measure gene expression by quantifying the level of messenger RNA (mRNA) present in a sample of total RNA extracted from tissues and cells. The ability to measure mRNA allows researchers to study individual gene activity and function, which ultimately contributes to our understanding of the phenotype of an organism or the total effect of all o its expressed genes.

Technical Abstract: There has been a dramatic expansion of DNA sequence information compiled over the past several years for a variety of eukaryotic and prokaryotic genomes. Accompanying this increase in knowledge of genomic structure and organization has been a growing interest in studying the function of individual genes including regulation of their expression. A number of methods such as Northern blotting, ribonuclease protection assay, and hybridization arrays have been developed to analyze gene expression at the transcriptional (mRNA) level. Although quantitative estimates of mRNA transcripts can be obtained from each of these methods, often times they lack sufficient sensitivity or the methodology is too costly or too labor- intensive to be applied to the analysis of a large number of samples. The most sensitive method for analyzing gene expression at the mRNA level involves the combination of reverse transcription and polymerase chain reaction (RT-PCR). However, in order to provide accurate quantitative estimates of gene expression, a rapid and efficient method is required for separation and detection of the double-stranded DNA (dsDNA) products of RT- PCR. Recent advances in capillary electrophoresis with laser-induced fluorescence detection (CE/LIF) have made this method suitable for the automated analysis of large numbers of RT-PCR samples. An overview of the application of CE/LIF to quantitative analysis of gene expression by RT-PCR is presented along with selected protocols and examples. Both relative- quantitative (RQ) and quantitative-competitive (QC) approaches to RT-PCR are discussed in conjunction with the use of CE/LIF for rapid and accurate quantitative analysis of PCR products.