Microscopic antenna unzips DNA

By Kimberly Patch, Technology Research News

Life on earth has borne out DNA's potential to organize molecules. Scientists looking to co-opt the ability for computing and microscopic machine construction, however, must first find ways to organize the molecule itself.

Researchers from the Massachusetts Institute of Technology and Engeneos, Inc. have come up with a method of precisely separating portions of the double helix of a short DNA molecule, causing it to unzip into two strands. The process can be controlled remotely, works through human tissue, and is reversible.

The researchers achieved the feat by chemically attaching a metal nanocrystal antenna to a DNA molecule, then bombarding the antenna with radio waves.

They put the DNA in a solution surrounded by a coil that generates an alternating magnetic field, which heats the gold by induction. "This magnetic field causes currents to change direction in the gold particle [one billion] times per second, which generates heat," said Kimberly Hamad-Schifferli, a researcher at MIT's Media Lab.

DNA is made up of strings of four types of paired bases attached to phosphate backbones. The method causes heat from the crystal to transfer to the DNA molecule. Once the DNA heats up, its paired bases separate, breaking the double helix into its two single strands.

When the radio waves stop, the heat dissipates and the process is reversed. "Once the magnetic field is turned off, the particle and the DNA dissipate the heat, and the DNA zips up its bonds again," said Hamad-Schifferli.

Portions of biological DNA regularly unzip in order to expose the exact order of a certain segment of bases, which serves as a template for making proteins.

The researchers' method leaves molecules surrounding the targeted DNA molecule relatively unaffected, according to Hamad-Schifferli. The 1.4-nanometer metal particle acts as a point heat source which heats anything in its vicinity, she said. But "because the metal particle is so small [and] since the molecule you want to control is directly linked to the particle, the heat is largely localized to it," she said. "We believe that this radius is about 10 nanometers, though we are currently doing experiments to determine this value," she said. A nanometer is a millionth of a millimeter; a line of 10 carbon atoms measures about one nanometer.

The reaction takes place relatively quickly; in the researchers experiments the DNA molecules dissipated the heat in less than 50 billionths of a second. The researchers are looking into the limits of how fast the process can work, Hamad-Schifferli added.

The researchers hit upon the method because they were looking for a way to control biomolecules in solution using an antenna, said Hamad-Schifferli. There are already ways of switching molecules on and off by using light to control a light-sensitive molecule, but the drawback with light is that it cannot penetrate tissue, said Hamad-Schifferli.

Induction heating is used in industry as a non-contact method of heating metals, and it can penetrate tissue. "We thought to extend it to nanometer-scale antennas," she said.

The method could be used to manipulate DNA molecules, which in biological settings regularly and efficiently execute mechanical tasks. "We believe that this work may be useful for diagnostics," said Hamad-Schifferli. "For example, it can be used to reversibly turn on protein expression. So if you have a system where you'd like to determine the role of a protein, you can temporarily turn it off to view the effect on the system."

The method could also be used to manipulate other types of protein molecules. It is relatively easy to attach a nanocrystal antenna to any type of protein, and the heat could be used to affect processes like enzymatic activity, biomolecular assembly, and gene regulation, according to Hamad-Schifferli. Enzymes act as catalysts, binding to certain portions of molecules in order to hasten biological reactions by as many as 20 orders of magnitude.

The research is impressive, said Jens-Christian Meiners, an assistant professor of physics and biophysics at the University of Michigan. The researchers "have come up with a novel method of locally heating a DNA molecule," he said. "While separating DNA strands through heating is a routine practice in biochemistry, the truly new aspect is that this heating can be confined to a spot that small on a molecular scale by using the nano-antenna as a heat source."

The technique has potential not only for DNA molecules, "but also... other biologically relevant molecules such as proteins," Meiners said. "The authors speculate that this technique could be used to turn selectively an individual enzyme on or off, or control the expression of individual genes. Both [seem] entirely possible and would allow large numbers of very specific experiments in molecular and cell biology," he said.

The technique could also be used in conjunction with nanoscale devices that use DNA, Meiners said. "For DNA-based machinery this technique may be away not only to bring energy into the system, but to bring [it] exactly to the spot where it is needed to drive it," said Meiners.

It is likely to take at least 10 years before the method can be used practically for therapeutic applications, said Hamad-Schifferli.

Hamad-Schifferli's research colleagues were Aaron T. Santos, Shuguang Zhang and Joseph M. Jacobson from MIT and John J. Schwartz from Engeneos Inc. They published the research in the January 10, 2002 issue of the journal Nature. The research was funded by the Media Lab Things That Think Consortium and the Defense Advanced Research Projects Agency (DARPA).

Timeline:   >10 years
Funding:   Corporate; Government
TRN Categories:   Biology; Biotechnology; Biological, Chemical, DNA and Molecular Computing; Nanotechnology; Physics
Story Type:   News
Related Elements:  Technical paper, "Remote Electronic Control of DNA Hybridization through Inductive Coupling to an Attached Metal Nanocrystal Antenna," Nature, January 10, 2002.


February 27, 2002

Page One

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Microscopic antenna unzips DNA

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