Purdue researchers use enzyme to clip 'DNA wires'

March 1, 2005
'DNA wires'

Researchers at Purdue University have attached magnetic "nanoparticles" to DNA and then cut these "DNA wires" into pieces, offering the promise of creating low-cost, self-assembling devices for future computers. Findings are detailed in a paper published online in February in the Journal of the American Chemical Society. The paper was written by Purdue graduate student Joseph M. Kinsella and Albena Ivanisevic, an assistant professor of biomedical engineering and chemistry at Purdue.

DNA, or deoxyribonucleic acid, has an overall negative charge, so it might be used in a process called self-assembly to create electronic devices. When placed in a solution with magnetic particles that have a positive charge, the particles are automatically attracted to the DNA strands, which act as tiny scaffolds for creating wires.

Other researchers have "metalized" DNA by coating it with copper, gold and platinum, but no other researchers have coated DNA and then cut the strands into smaller pieces using a "restriction enzyme," a class of enzyme that causes DNA to fragment, Kinsella said.

Because magnetic components are essential for today's computer memory, the findings represent potential future applications for DNA-based structures in computers created with "molecular electronics," in which biological molecules might be harnesses to create devices for computers, sensors and other uses. Self-assembly might be used in the future to create electronic devices at lower cost than is possible with conventional manufacturing processes.

Purdue researchers had previously developed a technique for precisely placing strands of DNA on a silicon chip and then stretching out the strands so that their encoded information might be read more clearly. The current work by Ivanisevic's team builds on that previous research.

Kinsella created the magnetic particles, which are made from a ceramic iron oxide material about 4 nanometers in diameter. A nanometer is one billionth of a meter, or roughly 10 times the size of a hydrogen atom.

The Purdue researchers sliced the DNA wires with an enzyme called BamH1, one of numerous restriction enzymes that are used in standard genetic engineering techniques to snip DNA so that scientists can alter the genetic structures of organisms like bacteria.

DNA molecules contain "bases" called guanine, adenine, thymine and cytosine, represented as G, A, T and C. The bases combine in numerous sequences, and various restriction enzymes attach to and cut specific sequences, enabling scientists to isolate and snip DNA segments of differing lengths. The enzyme used in the Purdue research cuts segments of DNA containing a sequence of GGATCC.

"We incubate the particles and DNA in a solution, and the electric charge brings them together to form the wire," Ivanisevic said. "Then we basically make smaller wire segments with magnetic particles attached to this DNA sequence."

Because hundreds of different restriction enzymes snip segments containing specific sequences of genetic material, the method might be used in the future to cut DNA wires of varying lengths for building electronic devices.

Ivanisevic and former Purdue physics graduate student Dorjderem Nyamjav were the first to coat DNA with magnetic particles two years ago. Kinsella and Ivanisevic are the first to show that the BamH1 enzyme cuts DNA wires.

"We weren't sure the enzyme would be able to recognize the DNA sequence covered with particles," Kinsella said. "We thought the particles might hinder the process."

The researchers found, however, that the particles did not interfere with the process, possibly because the electrical charges are strong enough to hold the particles firmly in place, but weak enough to enable the enzyme to push them out of the way.

"The entire strand of DNA used in this research has been stretched onto silicon oxide surfaces at lengths up to 35 microns, or millionths of a meter, and 2 nanometers wide," Kinsella said. "When coated with particles and fragmented by the enzyme, we were able to distinguish that the once-single DNA wire was clipped into smaller wires."

In future work, the Purdue researchers plan to stretch DNA coated with magnetic particles between electrodes and test the coated genetic material for electrical properties.

Source: Purdue University

Explore further: Sugar-coated world

Related Stories

Sugar-coated world

December 18, 2017

Glycans are essential to virtually every biological process in the body. These complex structures—composed of interlocking sugar molecules—adorn the surfaces of cells in fuzzy profusion. Glycans are a crucial part of ...

DNA repair enzyme mapped in atomic detail

December 11, 2015

An enzyme crucial to the process of DNA repair in our cells has been mapped in atomic detail by researchers at the University of Dundee, the UK's top-rated University for Biological Sciences.

New Method Offers Insight into Radiation Damage to DNA

March 21, 2008

A new technique for assessing the damage radiation causes to DNA indicates that the spatial arrangement of damaged sites, or lesions, is more important than the number of lesions in determining the severity of the damage. ...

A Ruler of Gold and DNA

October 12, 2006

Scientists from the U.S. Department Energy’s Lawrence Berkeley National Laboratory and the University of California at Berkeley have developed a ruler made of gold nanoparticles and DNA that can measure the smallest of ...

Recommended for you

Quantum dot ring lasers emit colored light

January 22, 2018

Researchers have designed a new type of laser called a quantum dot ring laser that emits red, orange, and green light. The different colors are emitted from different parts of the quantum dot—red from the core, green from ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.