November 16, 2007

New technique measures molecular interactions

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Darryl Bornhop, Ph.D., and colleagues have developed a technique to measure interactions between molecules. (photo by Daniel Dubois)

New technique measures molecular interactions

When biological molecules kiss, a new kind of biosensor can tell.

A new and deceptively simple technique has been developed by chemists at Vanderbilt that can measure the interactions between free-floating, unlabeled biological molecules including proteins, sugars, antibodies, DNA and RNA.

That is precisely the kind of capability needed to capitalize on the new avenues of research that have been opened up by the 15-year-plus effort to sequence the human genome.

DNA is the blueprint of all living creatures. But, just as the blueprint of a building is much simpler than the actual structure, so too is DNA far simpler than the myriad of molecules that make up living bodies. As a result, scientists need powerful new methods to study the actual behavior of all these molecules, particularly how they work together.

The new method is called back-scattering interferometry (BSI). By shining a red laser like those used in barcode scanners into a microscopic, liquid-filled chamber where two kinds of molecules are mixed, the instrument can measure the strength with which they react, even when the interactions are extremely weak.

In a report in the Sept. 21 issue of the journal Science, the researchers demonstrated it is sensitive enough to detect the process of protein folding.

“Pharmaceuticals depend on reactions between proteins and small molecules or between pairs of proteins or between interactions between RNA and DNA or pairs of DNA molecules,” said Darryl Bornhop, Ph.D., professor of Chemistry, who headed the 12-year development process. “So the ability to measure how that happens is very advantageous.”

Bornhop collaborates with two researchers in the Vanderbilt Center for Structural Biology: Hassane Mchaourab, Ph.D., professor of Molecular Physiology and Biophysics; and Jens Meiler, Ph.D., assistant professor of Chemistry, Pharmacology and Biomedical Informatics.

The method represents an entirely new application of interferometry, a powerful technique that combines light from multiple sources to make precise measurements. Interferometry is used in everything from astronomy to holography to geodetic surveys to inertial navigation.

The equipment required for the new biosensor is surprisingly modest: a helium-neon laser like those used in grocery store scanners, a mirror, a CCD detector like those used in digital cameras and a special glass microfluidic chip.

The chip contains a channel about one-fiftieth the size of a human hair. There is a “Y” at one end that allows the researchers to inject two solutions simultaneously, each containing a different kind of molecule.

Each time a laser beam strikes the channel, some of the light is transmitted back up to the mirror where it is directed to the detector. There it forms a line of alternating light and dark spots called an interference pattern.

It turns out that the interference pattern is very sensitive to what the molecules are doing. If the molecules begin sticking together, for example, the pattern begins to shift. This allows the system to measure interaction forces that vary a millionfold. That includes the entire range of binding forces found in living systems.

Vanderbilt has applied for and received two patents on the process and has several other patents pending. The university has issued an exclusive license to develop the technology to Molecular Sensing Inc.

Bornhop is one of the founders of the start-up and serves as its chief scientist. The company plans on completing a prototype system this fall.

Co-authors on the Science paper were graduate students Joey Latham, Amanda Kussrow and Dmitry Markov; Richard Jones, Ph.D.; and Henrik Sørensen, Ph.D. Latham and Markov are now post-doctoral fellows at Vanderbilt, Jones is working in industry and Sørensen is at the Risø National Laboratory in Denmark.