The chipping news: protein arrays and biochips speed up protein functional analysis and expression profiling. (Lab Consumer).

Recent months have seen a surge of activity in the field of protein microarrays. No wonder: Gene expression-profiling is faster and more powerful thanks to improvements in DNA microarray technology. Now researchers want to apply these benefits to boost the speed of proteomics research.

But developing these tools is not easy, as protein arrays present technical challenges not faced by DNA microarray manufacturers. "You can attach any two pieces of DNA the same way and expect [them] to behave the same way," explains Nick Naclerio, chief business officer of Zyomyx (www.zyomyx.com), a Hayward, Calif.-based company offering protein arrays and microfluidics-based chip production. But proteins are heterogeneous, he adds, thus making it difficult to develop methods to attach them to biochips and have them remain functional. Proteins are also more difficult to synthesize than DNA and are more likely to lose structural or functional properties in different environments or when modified. Unlike DNA, where the sequence is all that matters, a protein's three-dimensional structure must be preserved.

Despite these problems, researchers and biotech companies have successfully developed protein arrays, most based on conventional DNA microarray technology. For example, Brian Haab, working in the laboratory of DNA microarray pioneer Patrick Brown of the Stanford University School of Medicine, designed protein microarrays for the detection and quantitation of 115 proteins in solution. Haab spotted the proteins onto poly-L-lysine-coated microscope slides using a robotic arrayer, and visualized protein binding using a standard DNA microarray scanner. (1) Similarly, HarVard University researchers Gavin MacBeath and Stuart Schreiber recently described the design and use of high-density protein microarrays for high-throughput screening of protein function using an automated contact printer to spot 150-200-[micro]m spots onto glass slides coated with an aldehyde-containing silane reagent. (2)

Protein arrays offer distinct advantages over conventional techniques for quantitating proteins in a complex mixture. Haab, now at the Van Andel Research Institute in Grand Rapids, Mich., explains that antibody assays using protein arrays are much quicker than those using two-dimensional gel electrophoresis or liquid chromatography. He adds that protein arrays facilitate data analysis because each spot is a separate entity. "With 2-D gels, matching up spots is quite difficult from gel to gel," Haab says.

Protein arrays also improve upon standard protein-protein interaction …