Technology Affymetrix

While Affymetrix s early entry into the DNA microarray market afforded it a formidable position, the company has competitors. In order to commercialize the in situ array, it became clear that access to certain intellectual properties, especially the Southern patent (Oxford Gene Technologies or OGT), was required. Affymetrix obtained a license through a business relationship with Beckman Coulter which originally held the first and exclusive Southern license and later relinquished its exclusivity. Beckman Coulter and Affymetrix entered into a joint venture with Array Automation LLC to automate the processing of Affymetrix chips. Now that license to the Southern technology is available from OGT, others are permitted to commercialize in situ microarrays by alternative chemical S5mthesis approaches. 

An array of oligonucleotide which is composed of 20 80-mer oligos, or peptide nucleic acid probes, is synthesized either in situ (i.e., on-chip) or using conventional synthesis followed by on-chip immobilization. The resultant DNA array is then exposed to the labeled sample of DNA, hybridized, and the identity/abundance of complementary sequences determined. This method was developed at Affymetrix, Inc. and called DNA chips. Today, oligonucleotide-based chips are manufactured by many companies using alternative in situ synthesis or depositioning technologies. 

Alternative microarray approaches are available that involve the 3 tailing of the miRNA molecule with poly(A), followed by labeling and hybridization. The NCode miRNA microarray platform (Life Technologies) involves the addition of the poly(A) tail to the miRNA prior to ligation of fluorescent dye molecules and subsequent hybridization to the antisense miRNA probes on the microarray chip. In the case of Affymetrix GeneChip microRNA arrays, the poly(A)-tailed miRNAs are labeled with a biotinylated signal molecule. A limitation of hybridization-based microarrays is that because of the small size of miRNAs, the Tm of the probes has a wide range that may diminish specificity and/or sensitivity for miRNAs with a low GC content (10,56). 

FIGURE 23.1 Schematic representation of genome-scale gene expression analysis with DNA microarrays, (a) DNA microarrays produced by probe deposition (b) Oligonucleotide microarrays produced by in situ probe synthesis (Affymetrix technology). 

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