SOUTH SAN FRANCISCO Coming up with the optimal array spot diameter size was a key point in developing BioForce Nanosciences' NanoArrayer system, and the spot size has been a key selling point for the year-old instrument, which will be placed in about 10 academic institutions this year, according to BioForce CEO Eric Henderson.
The question that BioForce scientists asked when designing the system was how big should a spot be in order for researchers to use a minimal amount of sample while assaying enough molecules so that results have statistical significance, said Saju Nettikadan who spoke about the NanoArrayer System at Select Bioscience's OncoProteomics conference held here last week.
The scientists determined that the optimal array spot diameter size is in the range of one to 20 microns, said Nettikadan, who is director of the Research and Application Development group at BioForce. That answer was applied to the NanoArrayer, which was launched in February 2005.
"Our arrays print [spots] larger than a micron. If you go smaller than that, there are not enough biomolecules there," said Nettikadan.
An experiment using a hypothetical 10 nm spot with up to 10 proteins would be based on too few proteins to produce statistically significant results, explained Henderson.
"At the time that I was looking, NanoForce had the only commercially available system to print in small areas that would complement the sizes of our [nanohole array sensor] apertures. So the decision to buy the NanoArrayer was totally spot-size driven, in my case."
"The smaller you get, the less dynamic range there is," he said. "We have built arrays with spots smaller than a micron, but we don't pursue that commercially because we don't believe there's a need for that yet."
On the other end of the scale, traditional array printers print spots with diameters of 100 microns or more, said Dale Larson, the director of the Technology and Engineering Center at Harvard Medical School, which purchased a NanoArrayer System that was just installed last week. For Larson, 100-micron spots are much too large to be used for his purposes.
About a year ago, Larson and his colleagues started looking for an array printer that would complement the lab's nanohole array sensor a machine that can make nanometric apertures in a glass plate coated with chrome or gold.
"At the time that I was looking, NanoForce had the only commercially available system to print in small areas that would complement the sizes of our apertures," said Larson. "So the decision to buy the NanoArrayer was totally spot-size driven, in my case."
The nanohole array sensor determines biomolecule concentrations and binding kinetics by measuring the amount of light transmitted through nanoaperatures. Researchers at Harvard plan to use the NanoArrayer to "functionalize" the surface of nanohole sensors so that they are specific for certain biomolecules.
"One application we are pursuing is a large-scale protein array of protein drug targets that people are interested in," said Larson. "We plan to print the protein targets on the [sensor's] surface, and then watch as various drug candidates bind to them."
At the Johns Hopkins School of Medicine, researchers in Jan Hoh's laboratory are using the NanoArrayer for a different purpose. They are using the arrayer as a "little pen" for writing extracellular matrix molecules so that they can test how cells interpret their local environment.
"Let's say you put mice in a box, and you put [in] some cheese and some doors, and then the next day you move the doors around and you see how fast they can learn the new path to the cheese," said Hoh, who is a professor in the Department of Physiology at JHSM. "We're kind of doing the same thing. We're changing the pattern [of the extracellular matrix molecules], and asking how sensitive the cell is to those changes."
For Hoh, it is important that array spot sizes be small relative to the dimensions of cells, which typically measure tens of microns across.
"Conventional arrayers' spots are too large, to the point of being useless," said Hoh, who has been using the NanoArrayer for about 18 months. "Using the NanoArrayer, we print micrometer spots with a five-micron separation. You can print arbitrarily complex patterns, though we've been printing some relatively simple patterns. We're incredibly excited about [the instrument]. It allows us to make patterns of proteins that are not possible by other means that are going to give really new and exciting insight into how cells interpret their environment."
The NanoArrayer costs about $140,000, said Henderson.
Technologies that compete with the NanoArrayer include scanning probe lithography and electrospray technologies, but neither of those do quite the same thing as the NanoArrayer, Henderson said.
BioForce's long-term vision is to place the NanoArrayer chips in clinics.
"What it would certainly be appropriate for is, for example, if you have 10 diagnostic proteins for stomach cancer, and you want to use just one drop of blood for the assay," said Henderson. "We've done prostate specific antigen tests on four cells."
The NanoArrayer is not designed for the initial high-throughput discovery phase of proteomics, Henderson noted.
"We can't print a very highly complex array, like 10,000 different molecules on a surface," he said. "But we can print six molecules 10,000 times."
Tien-Shun Lee ([email protected])