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For Immediate Release
January 02, 2007

DNA on Surfaces: from DNA Letters to DNA Chips

"A simple test in the doctor's office reveals not only what is making a patient sick, but also what drug will work best to treat the disease. A similar test quickly checks a suspicious powder or a city's water supply for dangerous biowarfare agents. If this sounds like science fiction, it is only because the latest biotech marvel—the 'DNA chip'—still needs a few more years to become part of everyday life," says Dr. Dmitri Petrovykh, a scientist at the University of Maryland.

Dr. Petrovykh is a leading member of a team of scientists whose goal is to understand how DNA molecules attach to solid surfaces and thus to bring the promise of novel biotech devices like DNA chips closer to reality. The multi-disciplinary team includes participants from the U.S. Naval Research Laboratory (NRL), the National Institute of Standards and Technology (NIST), the University of Wisconsin (UW) and the University of Maryland (UMD). The most recent results of their research are described in a paper appearing in the January 2 issue of the Proceedings of the National Academy of Sciences (PNAS) co-authored by Aric Opdahl (UW and NIST), Dmitri Petrovykh (UMD and NRL), Hiromi Kimura-Suda (NIST), Michael Tarlov (NIST) and Lloyd Whitman (NRL). Earlier this year, in a paper published in the Journal of the American Chemical Society (JACS) the above co-authors, together with Virginia Pérez-Dieste (UW), Franz Himpsel (UW) and James Sullivan (NRL), described how methods developed to analyze surfaces of silicon chips can be adapted to comprehensively study the DNA molecules on surfaces. The scientists have now used these methods to discover that when placed near a gold surface certain DNA sequences unexpectedly abandon their typical behavior and instead form nanoscale "brushes" and other unusual structures.

DNA Letters and DNA Chips

The four letters most closely associated with DNA designate the nucleobases that encode the genetic information: A (adenine), C (cytosine), G (guanine), and T (thymine). A key property of these four "DNA letters" is their ability to form "complementary" (matching) pairs: A-T and C-G. If two strands of DNA have sequences composed of complementary bases in matching locations along the sequence, they can combine to form the famous DNA double-helix by a process called "hybridization".
DNA chips are devices that provide scientists with a convenient way to observe and study the process of DNA hybridization. DNA chips start with a piece of glass or silicon (sometimes coated with a thin layer of gold) about the size of a light-sensitive chip from a digital camera. Instead of electronic pixels that sense light, however, DNA chips are covered with up to half a million "pixels" of precisely positioned microscopic droplets of DNA. Each pixel contains strands of "probe DNA" that are designed to recognize a particular "target DNA" signature. The recognition process involves placing a drop of solution that needs to be analyzed onto the surface of the chip; target DNA molecules present in that solution will eventually encounter and hybridize with matching probes. This process works best, however, when each probe DNA strand is firmly attached to the chip on only one end and stands upright on the surface of the chip. In other words, the DNA molecules literally must stand up to be counted.

Creating a DNA-based "Surface Alphabet"

In their PNAS paper, Drs. Opdahl, Petrovykh, and their collaborators describe how the shapes and positions of DNA strands on the surface can be controlled by using a certain DNA sequence, a special property of which the scientists had previously discovered. Dr. Kimura-Suda explains the results of an earlier study, published in 2003 in JACS: "We were surprised to find that DNA strands composed of just one of the DNA letters—A or adenine—show a very strong preference for sticking to gold. The preference, in fact, is so strong that even the normally stable A-T combination breaks apart, leaving only A on the gold surface."
"Our method of creating complex DNA structures on gold surfaces exploits the 'sticky' nature of DNA strands with an all-A sequence," continues Dr. Aric Opdahl. "One or more such all-A segments can be incorporated in well-defined locations within a synthetic DNA strand. When this strand comes into contact with a gold surface, the all-A segments readily stick to the surface and act as anchors for the rest of the molecule."
Dr. Opdahl describes the resulting DNA structures by comparing them to letters that have similar shapes. "A strand with one sticky end forms an 'L-shape', a strand with a sticky segment in the middle forms a 'U-shape' (or a 'J-shape' if that segment is off-center)." Expanding the alphabet analogy to DNA strands with two sticky regions results in W- and Ω-shaped molecules, and so on.
"Usually," continues Dr. Petrovykh, "if the DNA molecules are far apart on the surface they fall down. If, on the other hand, the molecules are packed closely together, the target strands can not easily get close enough for hybridization to occur. The L-shaped DNA molecules offer the best combination of properties, because they stand up on their own and maintain well defined spacing. The idea of using these L-shaped DNA molecules is similar to bending the bottom of a stiff cardboard cutout into an L-shape in order to make it stand up by itself." The bases at the bottom of DNA L-shapes have the added advantages of readily sticking to the surface and keeping the DNA molecules from getting too close together.

Possible Applications

Biologically, DNA is most interesting and important as part of the molecular machinery inside living cells. But in the rapidly-growing fields of biotechnology and nanotechnology, DNA is often studied and used in distinctly non-biological environments. DNA molecules may be attached to solid surfaces, embedded in composite materials, bombarded with energetic x-rays or charged particles in vacuum, or stretched mechanically or by electric fields. One major practical benefit expected soon from such applications is the development of novel bio-medical devices (such as DNA chips) that make use of the unusual combination of biological, chemical, and physical properties that DNA molecules possess.
The methods described in the series of papers by the UMD, NRL, and NIST team provide a way to obtain detailed information about how DNA strands are attached to solid surfaces. The resulting ability to control and scrutinize the details of DNA structures on these surfaces will become increasingly important for the development of future generations of smaller and more complex DNA chips and related devices. Dr. Whitman notes that "the special properties of 'letter-shaped' DNA molecules also suggest their possible applications as nanoscale 'Velcro® fasteners' that might be used to selectively attach more complex nanostructures to a particular area on a surface." He concludes, "We hope to work with industrial partners on commercial applications of our new scheme for attaching and controlling DNA on surfaces."
The research was sponsored by the Air Force Office of Scientific Research and the Office of Naval Research.

PNAS article information

Independent control of grafting density and conformation of single-stranded DNA brushes,
Aric Opdahl, Dmitri Y. Petrovykh, Hiromi Kimura-Suda, Michael J. Tarlov, and Lloyd J. Whitman
(2007) Proc Natl Acad Sci USA 104:9–14, doi:10.1073/pnas.0608568103

Link to the article:

Links to additional information

Homepage of Dmitri Petrovykh:

NIST Tech Beat: "Adenine 'Tails' Make Tailored Anchors for DNA"

ALS Science Highlight: "When DNA Needs to Stand Up and Be Counted"




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