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A ruler of gold and DNA

BERKELEY, CA -- 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
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Contact: Dan Krotz
dakrotz@lbl.gov
510-486-4019
DOE/Lawrence Berkeley National Laboratory
11-Oct-2006


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