Researchers Stretch DNA on Chip, Lay Track for Future Computers
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Newswise — Researchers at Purdue University are making it easier to read life's genetic blueprint.
They have precisely placed strands of DNA on a silicon chip and then stretched out the strands so that their encoded information might be read more clearly, two steps critical to possibly using DNA for future electronic devices and computers.
Findings about the research are detailed in a paper posted online this month and will appear in an upcoming issue of the journal Advanced Materials. The paper was written by Albena Ivanisevic, an assistant professor of biomedical engineering at Purdue, and physics graduate student Dorjderem Nyamjav.
Ivanisevic and Nyamjav created templates containing charged lines of commercially available polymer. The positively charged polymer has the opposite charge as DNA, so when the genetic material is dropped onto the chip, it is attracted to the lines automatically. Then the researchers used a syringe to drag the DNA, uncoiling the strands along the template surface.
"The charged structures enable us to direct biological molecules in a certain location," Ivanisevic said.
Although other researchers have deposited DNA onto similar templates, Ivanisevic is the first to demonstrate how to also stretch strands of DNA in specific locations on such templates, which contain features so small they are measured in nanometers. This step could lead to the ability to stretch DNA molecules in specific locations on electronic chips, which is critical in harnessing the storage capacity of DNA for future computers.
"We don't want to have DNA coiled on the surface," Ivanisevic said. "We want to be able to extend it and stretch it so that you can read what's on the strand. You can think about a variety of DNA computing strategies. But you have to have the strand extended, and you have to have the ability to place it in a specific location."
Researchers also would like to be able to place DNA strands directly between two electrodes to perform consistent, precise measurements and determine certain electronic characteristics of genetic material.
"If you can actually demonstrate that you can do that, then you can think about making real molecular devices where DNA is used as a construction material," Ivanisevic said. "At this point, however, this is certainly a very basic nanofabrication problem."
Theoretically, future computers might tap the vast storage capacity that enables DNA to hold the complex blueprints of living organisms. These new computers would be based on DNA's four-letter code instead of a computer's customary two digits and would offer advantages in speed, memory capacity and energy efficiency over conventional electronics for solving certain types of complex problems.
The researchers used an instrument called an atomic force microscope and a device called a cantilever to lay down the lines of polymer in a process called dip-pen nanolithography. Each of the lines of polymer is about as wide as 100 nanometers, and each centimeter-square chip contains numerous templates.
"Nano" is a prefix meaning one-billionth, so a nanometer is one-billionth of a meter, or roughly the length of 10 hydrogen atoms strung together. A single DNA molecule is about 2 nanometers wide.
The same technique can be used to precisely place a variety of biological molecules, including proteins and viruses, onto such templates. It is not necessary to dry out or stain the molecules, meaning they can be kept in their natural state and still function as they would in living organisms.
Because the polymer is commercially available, the procedure can be readily studied by researchers and industry.
Ivanisevic is associated with two centers in Purdue's Discovery Park: the Birck Nanotechnology Center and Bindley Bioscience Center, which funded the research.
Related Web sites:
Purdue University Home Page: http://www.purdue.edu
Albena Ivanisevic: https://Engineering.Purdue.edu/BME/People/viewPersonById?resource_id=2251
Advanced Materials: http://www.wiley-vch.de/publish/en/journals/alphabeticIndex/2089/
This diagram depicts the process of depositing DNA onto a chip containing lines of a polymer that has the opposite charge as DNA, causing the genetic material to be attracted automatically to the polymer. The researchers then stretched the DNA along the lines of polymer, uncoiling the genetic material so that its coded information might be read clearly. Inset images taken with an atomic force microscope show the lines and the DNA molecules. The work was done by Albena Ivanisevic, an Purdue University assistant professor of biomedical engineering, and physics doctoral student Dorjderem Nyamjav. Results are being published in the journal Advanced Materials. (Purdue University Department of Biomedical Engineering/Albena Ivanisevic)
A publication-quality image is available at ftp://ftp.purdue.edu/pub/uns/ivanisevic.DNA2.jpeg.
Physics doctoral student Dorjderem Nyamjav, left, and Albena Ivanisevic, an assistant professor of biomedical engineering at Purdue University, review an image taken with an atomic force microscope. The researchers have developed a method for precisely placing strands of DNA on a silicon chip and then stretching out the strands so that their encoded information might be clearly read, two steps critical to possibly using DNA for future electronic devices and computers. (Purdue News Service photo/David Umberger)
A publication-quality image is available at ftp://ftp.purdue.edu/pub/uns/ivanisevic.DNA.jpeg.
Alignment of Long DNA Molecules on Templates Generated via Dip-Pen Nanolithography
Dorjderem Nyamjav and Albena Ivanisevic
A methodology to place and stretch long DNA molecules by coupling Dip-Pen Nanolithography with molecular combing is presented. Templates were fabricated on SiOx surfaces using a positively charged polymer, poly(allylamine hydrochloride). Upon molecular combing, DNA molecules elongate on the surface and are localized by the presence of the charged lithographically defined structures.