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More Bang for Your Microarray Buck

January 2007--Microarrays are already winning applause despite their relative infancy. Combined with advances in DNA sequencing, the small silicon wafers have opened up the field of functional genomics, giving us a better glimpse into the dynamic nature of gene activity. Think of them as gene phone books that you can peruse to see which genes are or aren't "home" under different conditions. Want to know which genes are turned on or off when a muscle cell gets hit with adrenaline? Within their fluorescent haze of multicolored lights, microarrays hold the answer.

Like its electrical cousin, the microprocessor, microarray technology needs to improve on multiple fronts, expand capabilities, hasten production time and increase cost-effectiveness for consumer appeal. Researchers Jef Boeke and Heng Zhu at Hopkins High Throughput Biology (HiT) Center have taken on the challenge.

For Boeke, who co-directs the HiT Center, the priority is adding all the unlisted phone numbers.

"Most microarrays hold DNA or RNA segments that represent a particular set of genes," Boeke says. "They're extremely useful, but they don't tell the whole story."

In higher organisms, he notes, genes make up only a tiny percentage of the genome. The largely ignored non-coding DNA is just as vital.

Transposons, in particular, pique Boeke's interest. The bits of DNA that jump among and around genes admirably increase organisms genetic variety, but can wreak havoc if they land in a bad spot.

"Transposon insertions may contribute significantly to heart disease and cancer predisposition, among other common diseases," says Boeke, "but without a way to search comprehensively for such needles in a haystack, we can't know to what extent."

To get a better grasp, Boeke has developed the TIP (for transposon insertion point) chip, which stores evenly spaced segments of the yeast genome. By adding DNA probes amplified from the transposon borders of any yeast strain, the TIP chip reveals transposon terrain. Currently, the chips' value lies in monitoring transposon activity in yeast, but Boeke hopes to design human TIP chips in the future. This is not a trivial step, however, since yeast carries around 50 transposon copies, while humans have hundreds of thousands.

Human complexity, then, requires microarrays with better storage capacity, and Boeke has developed one both simple and ingenious. While standard microarrays hold single DNA fragments in each section, his model layers two half-size fragments on top of each other. The bottom layer reads from left to right and the top layer goes north to south, producing either a horizontal or vertical series of lights. "They're just as easy to read as single-layer arrays," he says, "so I think we can expand them to hold three or four times as much data by adding diagonal layers."

Years ago, Heng Zhu wondered if DNA microarray technology could be applied to proteins: "I knew there would be technical obstacles, but with protein chips, we could study binding activity, enzyme kinetics or novel drug screening. They would be flexible, yet so powerful."

Zhu, then a postdoc at Yale, and his colleagues stepped up to create the first protein array, a modestly sized chip holding the 120 yeast kinases (enzymes that add phosphates to proteins). A larger array containing all 5,800 yeast proteins followed, and in 2004, Zhu arrived at Hopkins, ready to tackle human proteins.

"The real challenge is getting enough protein," he says. "Separately purifying proteins is too rigorous."

So, why not just synthesize the protein right on the chip? Zhu placed the RNA template for each protein in the appropriate section, then added a specially modified protein synthesis kit. The kicker was attaching puromycin to each section. This antibiotic, which kills cells by latching onto proteins before their construction is complete, was an ideal molecule to hold the newly synthesized proteins so they wouldn't fall off the slide.

Now Zhu's tests of the technique on cell fundamentals is ballooning. He's completed an array for all known human transcription factors, for example. Probing the chip with various DNA fragments gives Zhu a global picture of which sequence motifs the gene-activating proteins recognize. Lectin proteins will form the next array. He'll use that chip to see how cells talk to each other. Soon, he thinks, a chip of the whole human proteome will be within reach.

Because Zhu envisions that scientists around the world could hold these powerful chips in their hands, he believes that collaborations HiT's set up to disseminate microarray advances are as important as the research itself. Just as the microprocessor revolution placed a computer in almost every American home and office, someday a microarray scanner may be a mainstay of every biology lab.

--Nick Zagorski

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