Polymerase chain reaction microarray analysis

Levels of RNA (usually specific mRNAs) in a cell can be measured by well-established techniques such as Northern blot analysis or by polymerase chain reaction (PCR) analysis. However, the recent advent of DNA microarray technology has converted the identification and measurement of specific mRNAs (or other RNAs if required) into a high-throughput process. DNA arrays are also termed oligonucleotide arrays , gene chip arrays or simply, chips . 

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

The methods used for the evaluation of regulation of gene expression are too numerous to be described in detail here. They include Northern analysis to determine levels of a particular mRNA, nuclear run on to determine whether an increase in mRNA is due to an increase in the rate of transcription, and promoter deletion analysis to identify specific elements in the promoter region responsible for the control of expression. Of much current interest is the use of microarrays that permit the study of the expression of hundreds to thousands of genes at the same time. Reverse transcriptase-polymerase chain reaction and RNase protection assay techniques are used to amplify and quantitate mRNAs, while the electrophoretic mobility shift assay is used to measure binding of a transcription factor to its specific DNA consensus sequence. 

The techniques that have proven most valuable in toxicology include those of molecular cloning, the polymerase chain reaction, and the production of genetically modified mice. Microarrays, used to evaluate gene expression under various conditions, including exposure to toxicants, are becoming more important and, in concert with other molecular techniques, are being considered as potentially useful in such applied areas as hazard assessment and risk analysis. 

Alternatively, microchip technologies offer other platforms for HTS such as microarrays and microfluidic devices. Microarrays allow the simultaneous analysis of thousands of parameters within a single experiment and for this reason have become cracial tools in drug discovery and life sciences research. They consist of immobilized biomolecules spatially addressed on planar surfaces, microchannels or microweUs, or an array of beads immobilized with different biomolecules. Biomolecules commonly immobilized on microarrays include oligonucleotides, polymerase chain reaction (PCR) products, proteins, lipids, peptides, and carbohydrates. Currently, in situ synthesized microarrays can be purchased or... 

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