Microarray manufacturing

The microarray technology was developed at the Stanford University in the early 1990s [2]. From the beginning, it was clear that this technique could have the same impact in biomedical and biotechnological research that the polymerase chain reaction (PCR) had in the 1980s. PCR reactions are now extensively used in microarray manufacturing. 

The microarray manufacturing method that enables microarray printing without direct contact to the surface is termed non-contact printing. Piezoelectric, bubble-generated, and microsolenoid driven pipettes as shown in Fig. 3 work with the same physical principle as ink-jet printers and are capa-... 

The widespread use of PCR amplification in microarray manufacture places much importance on the availability of informatics tools for automated primer design. A primer is a synthetic oligonucleotide that hybridizes to a complementary nucleic acid template, and expedites (primes) enzymatic synthesis by providing a starting point for enzyme. PCR primers bind to proximal and distal sites on cDNA templates, allowing target sequences... 

Spike-ins are usually RNA transcripts used to calibrate measurements in a DNA microarray experiment. Each spike-in is designed to hybridize with a specific control probe on the target array. Manufacturers of commercially available microarrays typically offer companion RNA spike-ins kits . Known amounts of RNA spike-ins are mixed with the experiment sample during preparation. Subsequently the measured degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA. 

The commercial success of the spotted microarray, like that of Affymetrix s GeneChip, is content-driven. In order to provide customers with comprehensive gene expression microarray products, manufacturers must obtain gene-specific annotated sequences covering genomes of major interest to the scienhfic community (e.g., genomes of humans, yeasts, and mice). 

In the following sections, the major types of substrates currently used for DNA and protein microarrays will be discussed. Much of what is known regarding microarray surface chemistry and the immobilization of biomolecules comes from work with DNA microarrays. Therefore, many of the examples cited here will be from these studies. Zhu and Snyder (2003) in their review provide good insight into the manufacture and utility of protein microarrays. Here are some points to consider when choosing a substrate for protein microarrays ... 

The manufacture and processing of the protein microarray should be conducted in such a manner that the arrayed proteins remain in their native and active state. For most proteins, this usually means the hydrated state in order to avoid surface denaturation. For antibody arrays which are perhaps more forgiving than other proteins, it has been our experience that while these could be stored cold and dry, it is most important to rehydrate them prior to use. This process is in sharp contrast to the preparation of nucleic acid arrays in which strand melting or denaturahon is necessary to achieve optimal binding to the solid support. While the hybridization process is well understood and can be controlled under thermodynamic principles, the folding and renaturation of proteins on planar (microarray) surfaces is under study. 

Photo-polymerization was conducted at 254 nm under a modified fluorescent microscope. Allyl-oligonucleotides were employed with methylene blue as the free radical initiator for crosslinking. In the case of proteins, acryloyl streptavidin was first immobilized so that biotinylated proteins could be applied to the gel pad (Vasiliskov et al., 1999). One of the major drawbacks with the gel pad approach was that separate pads had to be manufactured instead of coating the enhre slide with the gel and then printing down the microarray. 

Perhaps the least rmderstood factor in the process of microarraying is the print buffer (probe ink) composition. This may not be too much of a surprise because manufacturers of computer printers offer consumers a multitude of different inks (whose formulas are closely guarded trade secrets) for use with a particular printer and kind of paper. In fact, it can be argued that the ink is perhaps the most important piece of the consumable product stream for this manufacturing sector. 

Diehl, R, Grahlmann, S., Beier, M., and Hoheisel, J.D., Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acid Res., 29(7), 1-5, 2001. 

Martinsky, R.S., Microarray printing device including printing pins with flat tips and exterior channel and method of manufacture, US Patent 6,101,946, issued 2000. 

Scan microarray with ScanArray Express Microarray Scanner (PerkinElmer Life Science) following the manufacturer s instructions. 

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