A Ruler of Gold and DNA

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PostPosted: Thu Dec 21, 2006 2:38 pm    Post subject: A Ruler of Gold and DNA Reply with quote

A Ruler of Gold and DNA

New tool could expedite scientists’ push to learn how genetic information is processed.

Scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California at Berkeley have developed a ruler made of gold nanoparticles and DNA that can measure the smallest of life’s phenomena, such as precisely where on a DNA strand a protein attaches itself.

The molecular ruler, detailed in the October premier issue of the journal Nature Nanotechnology, offers label-free and real-time measurement of a range of protein-DNA interactions at an extremely high resolution. As such, it promises to play a key role in the current push in biology to understand how genetic information flows from DNA to RNA to gene expression. Today, scientists involved in this research typically examine the final products of this chain of events by cataloging the expression levels of various genes and proteins.

The newly developed molecular ruler, however, can give scientists a much earlier glimpse into this process by measuring the initial protein-DNA binding interactions that unleash the flow of information which, in turn, sparks gene expression.

“We can use the ruler to look at this process much more upstream. We can measure the beginning stages of DNA-binding activities,” says Fanqing Frank Chen, a scientist in Berkeley Lab’s Life Sciences Division who was a member of the research team that, for the first time, used the molecular ruler to map protein-DNA interactions.

The existing techniques used to measure protein-DNA interactions involve labeling DNA and proteins with either radioactive or fluorescent compounds. But radioactive labels require tedious sample preparation and incur radiation-use restrictions, and fluorescent labels are short-lived and unable to measure complex protein-DNA interactions that measure more than 8 nanometers in length.

“Our work promises to be a fast and convenient alternative for mapping DNA-protein interactions. We can measure precisely how a protein interacts with the information inscribed in the DNA and begins to regulate genetic information,” says Chen. “We can also measure large protein-DNA interactions that span up to 17 nanometers in length, and, in theory, span as much as 70 nanometers in length.”

The molecular ruler was developed by a team of scientists that includes UC Berkeley Bioengineering Professor Luke Lee, UC Berkeley Ph.D. student Gang Liu, and Paul Alivisatos, Director of Berkeley Lab's Materials Sciences Division and an Associate Laboratory Director. It’s composed of gold nanoparticles that are coated with a substance that makes the nanoparticles soluble. Next, about 100 double-stranded DNA segments are tethered to the gold nanoparticle in a configuration that resembles a many-legged spider.

The ruler works because of plasmon resonance, which is the collection of electrons that resonate in a metallic particle, in this case the gold-DNA conjugate. Plasmon resonance changes as a particle changes, leading to differences in scattering wavelength. For example, if the gold particle’s spidery DNA strands, which are 54 base pairs long, are shortened for whatever reason, then the gold-DNA particle’s scattering wavelengths also shift — and this shift can be easily detected using spectroscopy. This method is so sensitive that scientists can use it to detect whether a DNA strand has been shortened by as little as one base pair in length, which opens the door for mapping the exact location of protein-DNA interactions.

Chen and colleagues put the ruler to the test by using it to conduct DNA footprinting, a process in which scientists identify where on a DNA strand a particular protein attaches itself. DNA footprinting is most commonly performed on proteins that are thought to play a significant functional role, such as in regulating gene expression.

Source : http://www.lbl.gov/

This story was first posted on 12th October 2006.
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