Not exactly brute force -- but rather carefully metered dynamic force -- is the key to pulling apart two strands of the DNA "zipper" and popping loose restriction enzymes and other proteins along the way. A report in the journal Physical Review Letters (PRL Vol.91, No.2, July 11, 2003) by Steven J. Koch and Michelle D. Wang, titled "Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA," tells how to do it and predicts future applications of the technique.

"This could be used for restriction mapping, the first critical step in genomic sequencing, and for actual sequencing where the sequence of DNA is determined with a large number of restriction enzymes," says Wang, Cornell assistant professor of physics, of a handy technique with an unwieldy name: unzipping force analysis of protein association, or UFAPA.

"We're still in the laboratory-development stage now," Wang adds, "but the process could be automated so that in drug development, for example, pharmaceutical companies could use UFAPA to screen libraries of small molecules for affinity to DNA." The other PRL author, Koch, was a physics graduate student at Cornell at the time of the research and now is a postdoctoral researcher at Sandia National Laboratories. UFAPA is simplicity itself, given the right equipment and a light touch on the controls. As described in the PRL report:

• One strand of the DNA is anchored to a microscope cover slip;
• the other strand is attached to a microsphere (a tiny ball of polystyrene) that is held in an optical trap (by a laser beam);
• the DNA is unzipped as the microscope cover slip is moved away from the trapped microsphere;
• when the un
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