Biochip sprouts DNA strands

By Kimberly Patch, Technology Research News

In addition to DNA's natural role of manufacturing the proteins that drive many of life's processes, the molecule has serious potential as a scientific tool. Researchers have found it invaluable for sensing and identifying microbes and chemicals, and there are many possibilities that involve using DNA to construct structures molecule by molecule.

The key to expanding DNA's sensor function is being able to quickly expose DNA molecules that contain different sequences of nucleotides to a solution containing substances to be tested. And the key to using DNA to build molecular structures is finding efficient ways to position and connect the molecules.

Researchers from the University of California at Davis and Wayne State University have addressed both issues with a method for attaching DNA strands to a gold surface so that the molecules stand up like a thick forest of branchless trees.

The method also allowed the researchers to precisely position lines of vertical DNA strands in patterns as narrow as 10 nanometers, or about 100 times the width of a hydrogen atom. "We succeeded in grafting DNA molecules with nanometer precision at desired positions on surfaces," said Gang-yu Liu, an associate professor of chemistry at the University of California at Davis. A nanometer is one millionth of a millimeter.

Because the molecules are standing up, chemicals introduced into a surrounding solution would have access to the full strands, which stretch to heights of around 700 nanometers. This makes the method a good candidate for making biological microarrays that would use different types of DNA to test very small samples of many different substances at the same time.

Such closely packed, miniature arrays could speed gene identification, disease diagnoses, drug discovery and toxicological research, said Liu. "Further miniaturization could provide [better] performance in a shorter time," she said. For instance, larger portions of an organism's genome could be incorporated into a single chip.

The ability to control exactly where DNA molecules attach also makes the method useful for producing molecular-scale devices for applications like quantum computing, she said. Many quantum computing schemes, which exploit the traits of particles like atoms and electrons to store and manipulate information, require devices small enough to direct small numbers of particles, or even single atoms or electrons.

The researchers made their DNA patterns using chemistry and an atomic force microscope that directly manipulates molecules using an extremely sharp tip as narrow as one nanometer.

They prepared a surface for the DNA to attach to by making a sandwich of mica, a thin layer of gold and a single layer of organic molecules. They added a solution containing short, single-stranded segments of DNA that were thiolated, meaning they contained a segment on one end capable of adsorbing, or chemically attaching to, the gold.

When the researchers used an atomic force microscope to etch patterns into the molecule layer, exposing the gold, strands of DNA attached to the exposed areas. "Molecules in selected regions of the surface are shaved away [and] the resist molecules are removed, [DNA molecules] immediately adsorb onto these newly exposed areas following the scanning track of the AFM tip," said Liu.

Using the same microscope tip, but less pressure, the researchers were able to confirm that the DNA had attached by sensing the height of the molecules on the surface. "DNA molecules are densely packed in, and adopt a standing-up configuration," said Liu.

The ability to construct patterns of DNA and examine the results as the patterns are being constructed is unusual, said Liu. It makes the process easier by allowing patterns to be extended without the need to change masks or repeat the entire fabrication process, said Liu.

The DNA the researchers used, in contrast to the variety found in living beings, was single-stranded and very short, containing between 12 and 35 of the four bases that make up the bulk of DNA. Biological DNA stored in the nuclei of cells contains billions of bases and is wound into a double-stranded helix; the two strands separate to access segments of bases that act as blueprints for building proteins.

There are two challenges to using the method practically, said Liu. The first is to stabilize the DNA nanostructures over time. This is a necessary step in being able to produce nano-sized features without the structures deforming, she said.

The second is to make the structures more quickly and efficiently by making the fabrication process parallel and more automatic. The current scanning probe lithography process is "serial... with relatively low throughput," she said.

The researchers are looking to eventually use the method to form complicated two- and three-dimensional nanostructures, said Liu. At the same time, they will determine how the DNA nanostructures react to various agents, she said. "Our ultimate goal is to construct designed nanostructures of DNA, and to demonstrate their unique physical and biochemical reactivities," she said.

The technique is potentially useful, and could allow for smaller bioarrays that are around 10,000 times more complex than those made using conventional processes like robotic spotting and photolithography, said Linette Demers, a chemist at NanoInk, Inc.

In contrast to the 10-nanometer-thick lines produced by the researchers, robotic spotting equipment cannot currently make dots smaller than several hundred thousand nanometers, said Demers. At the same time, the most advanced commercial photolithography processes cannot make feature smaller than 130 nanometers.

Bioarrays -- patterns of DNA spots arranged on chips -- are widely used to study gene structure and expression in basic research areas like oncology, toxicology, neurology and pharmacogenomics.

The technique could also be used to improve on-the-spot diagnosis, said Demers. Even "modest improvements in understanding and implementation of DNA patterning and readout technologies... have an impact in biomedicine," she said.

There is work to be done before the researchers' technique can be implemented in widely used real-world applications, Demers added. In its present form, nanografting is a serial technique and thus inherently very slow. "Speed, and the ability to lay down tens of thousands of different DNA sequences on a chip" are needed to use the technique to miniaturize genetic arrays, she said.

However, even slow nanografting is potentially useful for niche applications like examining the effects of nanoscale confinement of protein molecules, investigating new readout methods for miniaturized bioanalysis devices, and preliminary research into bioelectric circuits, she said.

It is difficult to predict when the method could be ready for use because of the rapid pace of change in nanotechnology development, said Liu. "We hope to have it ready in five to fifteen years," she said.

Liu's research colleagues were Christine S. Chow of Wayne State University, and Maozi Liu and Nabil A. Amro of the University of California at Davis. They published the research in the August 14, 2002 issue of Nano Letters. The research was funded by the National Science Foundation (NSF) and the University of California at Davis.

Timeline:   5-15 years
Funding:   Government, University
TRN Categories:  Chemistry; Nanotechnology
Story Type:   News
Related Elements:  Technical paper, "Production of Nano Structures of DNA on Surfaces," Nano Letters, August 14, 2002.


November 13/20, 2002

Page One

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Webs within Web boost searches

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Method measures quantum quirk

Biochip sprouts DNA strands


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