AmpArray™ is designed to detect expression of genes in different
samples. Each AmpArray™ is a 96-well PCR plate format that is
arrayed with duplicated 48 pairs of primers to amplify specific fragments of
genes (Fig. 1). Among them, one pair primers specific to
the house-keeping gene, G3PDH, works as control, and the rest of primer pairs
are specific to the individual genes, which are grouped by biological relevance
such as biological pathway, disease related genes or gene family. These primers
are meticulously designed by using a highly reliable primer designing algorithm
which provides an uniform annealing temperature and similar sizes of PCR products
so that one set of PCR condition works for all primer pairs.
RT-PCR is a simple and reliable method to compare the expression levels in
different samples for a given gene of interest, however, it is difficult to
successfully amplify multiple gene products in a 96-well by using one PCR condition.
It requires that all of primer pairs, which are used to amplify specific fragments
of a group of genes, are suitable for a PCR condition . To that end, we have put
extreme effort to select optimal primer pairs so that high successful rate of
PCR for every pair of primers used in AmpArray™ can be achieved.
One example of using the AmpArray™ for the MAP kinase pathway
is shown in Fig. 2.
Application of AmpArray™
- Focus on gene profiling with selected groups of the genes
- Detect expression change of the genes with low copy number
- Be able to detect and discover alternative splicing forms of gene expression
- Validate data from high density gene chips.
- Detect effect of RNAi on expression of related genes
Advantages of using AmpArray™
- Easy-to-use and timesaving: no radioactive labeling, no hybridization, obtain
data in one or two days.
- Affordable: no expensive equipment required, only a 96-well regular PCR.
- High-sensitivity: the number of PCR cycles can be adjusted based on the
levels of transcripts in the sample.
- High-specificity: each pair of primers is well-selected, and results are
confirmable with predicted sizes.
- Total RNA can be used: only two reverse transcription reaction are required
for hundreds of genes. The primer pairs are selected to minimize the effect
of possible genomic DNA contamination.
- Discovery of alternative spliced forms of specific genes (Fig.
2).
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