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Spotted Arrays, Meet Sushi Arrays: Low Cost Gives Manufacturers Taste for These Chips

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In an effort to create low-cost microarrays using alternatives to spotting technology, at least three groups of researchers have developed what might be called sushi arrays: they fill the inside of a bunch of channels or rods with the DNA or protein samples, then slice the block cross-sectionally like a rice roll, yielding hundreds of virtually identical arrays.

Robert Star, senior investigator at the NIH, said he came up with his version of this technology, the cryo-array, more than a year ago when he was pondering how to screen a large number of protein samples “without needing access to high-tech, very expensive equipment” such as a spot arrayer. Instead he started with an ordinary block of tissue-embedding component, punched 25 steel needles into it before freezing the block, and pulled the needles out. He then filled each of the remaining wells with three microliters of liquid protein solution, let it freeze and cut the block into 10-micrometer slices with a cryostat, a device routinely used in hospitals for making tissue sections. He said he gets up to 800 slices from a single block, each of which includes spots of about 300 microns diameter containing 2.7 microliters of sample solution. He first transfers a slice to a piece of Scotch tape, then to a glass-backed nitrocellulose slide, and keeps them frozen and desiccated until they are used.

Star is publishing a proof-of-concept study on these arrays in an upcoming issue of the journal Proteomics. So far he has been able to detect a purified protein, down to a limit of 400 femtograms, and changes in concentration of a protein in a tissue homogenate on his arrays. “It’s like a dot blot,” Star said. “If you have a good antibody … this is a way of rapidly screening for a number of targets on the same set of samples.”

Apart from using this chip to screen biological samples, Star has considered applying it to biochemical or protein interaction assays, but has not tested it yet. These assays require the proteins to be in their native form, and although it is “protein friendly,” to process proteins while they are frozen, some of them might not survive the freeze-thaw cycle. Also, it remains to be seen if he can deposit enough protein on the membrane to do interaction studies.

But the main advantage of this technology is that it’s cheap. “This is all very low-tech, using things that are commonly around in most labs,” Star said. The technology is up for grabs for licensing from the NIH, which has filed a patent on it.

 Japan and California Also Do “Sushi” Arrays

The NIH is not the only inventor of “sushi-arrays”: both Mitsubishi Rayon of Japan and Vacaville, Calif.-based Large Scale Biology Corporation have been developing technologies based on the same principle.

Using more of a California-roll type approach, LSBC has bundled polymer rods, each containing a different antibody or other assay reagent. These rods are glued together with a polymer, and are sliced with a commercially available microtome. The rods serve as solid support systems; they are either filled with a porous material carrying the proteins or they come as hollow tubes coated with proteins on the inside, said Manfred Scholz, LSBC’s head of business development for the proteomics division. The company also has other undisclosed methods of loading the rods with probes, he said. Although the prototypes only consist of up to some dozen rods of a few centimeters length, they could be scaled up in number and length. Again, the main advantage would be the low cost. “You make it by the meter and sell it by the micrometer,” Scholz said, adapting the 3M business motto. But he cautioned that the technology is still years away from being ready for the market: “The need for a low-cost array is not there yet,” he said, but once a clinical array is required, “then cost becomes the main pressure.”

LSBC, Scholz said, mainly developed the array to “detect small quantities [of proteins] in very diverse samples,” but he can imagine other uses — for example to screen chemical libraries for compounds that bind to proteins on the array. The company’s patent application even covers the use of nucleic acids in the rods. So far, though, LSBC researchers have only tested the array in a few model assays to measure protein concentrations, he said.

But without a collaborrator who will help develop and market the array for a specific application, LSBC will not pursue the technology further. “For our own applications, we have decided we will not take it forward,” said Scholz. “It will only go forward if we have a partner.”

Mitsubishi Rayon, on the other hand, has more immediate marketing plans for its “fibrous DNA chips,” made by bundling hollow fibers that contain either cDNA or oligo probes with a hardening resin and slicing them into chips with a density of 100 to 10,000 spots per glass slide. “Currently we have a plan to commercialize our DNA microarrays within the next few months in Japan, and I hope to start global sales next year,” said Wataru Mizunashi, who manages the genomic device group in the company’s business planning and development division, in an e-mail. He sees their main advantages in high reproducibility and quality control. Applications include clinical testing, pharmaceutical development, food inspection, and environmental analysis.

— JK

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