Protein microarrays mature: choices multiply, but developers still grapple with engineering issues.(Technology)

while not as ubiquitous as their DNA counterparts, protein arrays are starting to hold their own, appearing as the key technology in a growing number of published research papers and even starring in their own new textbook. And their potential to be major players in the proteomics field appears boundless. "The protein field is about 10 times the size of the DNA field, so ... I think we can probably expect the protein microarray field to be much larger than the DNA microarray field," says Mark Schena, visiting scholar at TeleChem International, ArrayIt Division, Sunnyvale, Calif., and editor of the book Protein Microarrays (Jones and Bartlett, 2005).

If protein arrays have not yet reached DNA microarray status, it may be in part due to bad P.R. Proteomicists have been wary to accept the technology because of proteins' reputation for instability. Indeed, when highly diluted in a nonphysiological buffer and then purified under pressure or through metal-affinity columns, proteins are unstable, Schena notes. "But when configured into a microarray where the concentrations are very high, preparations are pure, and the proteins are free of proteases, metal ions, oxidizing agents, and the other things that disrupt protein function, we find that proteins are actually extremely stable," he says.

As researchers overcome initial skepticism, protein array developers continue to address problems such as manufacturing cost and sensitivity. The range of options is growing to meet increased demand, and scientists can now choose among various ready-made antibody- or protein-profiling arrays. For those so inclined, tools and kits for do-it-yourself arrays are also available. Or, researchers can pick up complete turnkey systems based on traditional arrays, microfluidics, surface plasmon resonance, and even mass spectrometry.

MANUFACTURING HURDLES Victor Morozov of the National Center for Biodefense at George Mason University, Manassas, Va., says that in order for protein arrays to be competitively priced, developers will have to turn to parallel, industrial-scale manufacturing technologies similar to those employed in the production of microelectronic chips. Or, they will need to develop in situ synthesis methods such as that pioneered by DNA array manufacturer Affymetrix of Santa Clara, Calif.

With current technologies, though, on-chip synthesis of whole proteins is impractical, as the chemistry involved is more complex and cosily than oligonucleotide synthesis. Further, proteins synthesized on-chip may lose tertiary structure during the multistep fabrication process. "In situ [synthesis] doesn't really work," says Schena. "You really …