The Northwestern researchers used the tip of an atomic force microscope (AFM) to deposit oligonucleotides onto the substrates, producing spots of DNA as small as 50 nm in diameter. To pattern onto gold, they modified the DNA with hexanethiol groups, while for the silica surfaces they used oligonucleotides with 5'-terminal acrylamide groups.
"With this new tool, we can take a normal chip that's made and sold today for studying a problem in genomics and miniaturize it to 1/100,000th of its size," said Chad Mirkin, director of Northwestern's Institute for Nanotechnology and leader of the research team. "In a normal chip with 100,000 different spots of DNA, each spot is 20 to 40 µm in diameter. Using state-of-the-art dip-pen nanolithography we can prepare 100,000 DNA spots in the area occupied by a single spot in a conventional gene chip."
The scientists found that they could tailor the DNA deposition rate by controlling the humidity. For example, on a gold substrate, a relative humidity change of 15% altered the size of a spot created by holding the AFM tip for 10 s from 50 to 100 nm.
The researchers also prepared a two-component DNA array on an oxidized silicon substrate. Then they exposed it to a mixture of 5 and 13 nm diameter gold nanoparticles that were modified with DNA that was complementary to one of the two patterns. The particles selectively assembled themselves onto the appropriate pattern according to their size.
"Our direct-write patterning of multiple DNA strands also opens up new possibilities for building and studying nanoscale architectures," said Mirkin. "By taking advantage of DNA as a type of biochemical Velcro, we should be able to build a circuit, a catalyst, a sensor or a transistor from the bottom up, instead of the top down."
"If one uses the analogy of building a house, the deposited DNA is not only an architectural blueprint for a structure but also the construction worker who directs where each brick goes," added Mirkin. "Because single-stranded DNA molecules have a natural preprogrammed chemical match and attract complementary molecules, we can use them to control material and device fabrication."