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Aptamers in the Attic

By Laura Lee, biology '12

Abigail Miller

Photo of Professor Miller with her FCCS apparatus by Laura Lee.

Professor Abigail Miller, the newest addition to American University’s Department of Chemistry, is changing the way we look at molecules—literally. Way up on the fourth floor of Beeghly, Miller refers to her workspace as “Beeghly’s secret floor.”

“No one seems to know that the fourth floor is here,” she says.

In her isolated and windowless laboratory, Miller works in the ideal dark and quiet conditions in order to do something incredible: count individual molecules. Traditional techniques in chemistry allow for the quantification of large numbers of molecules. For the purposes of context one mole, a standard measure used in chemistry, is defined roughly as 6.022x1023 molecules. However, the information gained from this kind of research is only representative of the average states of these molecules. Dr. Miller, an analytical chemist, narrows this scope using a fairly new technique to study molecular interactions: fluorescence cross- correlation spectroscopy, or FCCS. Through FCCS, she can determine highly specific quantities of product and reactant at any given time, ultimately lending her the ability to characterize chemical reactions.

What is even more impressive is the fact that Miller constructed the machine she uses to conduct FCCS. Miller’s homemade FCCS apparatus allows her to count individual proteins in a reaction that has been marked with a fluorescent tag. The proteins are tagged using aptamers, which can be anywhere from 20 to 100 base pairs long. The short length of these aptamers lends them high specificity in their interactions with proteins. These aptamers have a fluorescent tag that responds to the excitation from specific wavelengths of light emitted by red and green lasers, not much more powerful than a standard laser pointer, from the FCCS apparatus. Upon excitation, the fluorescent tags emit characteristic photons that are captured by a camera connected to a microscope, which is in turn connected to a computer containing specialized hardware that enables it to detect the single photon. The characteristics of the photon will change based on state of the aptamer—specifically, whether or not it is bound to the target protein.

Examining reactions at very low concentrations has several advantages. For one, doing so is highly efficient. Miller is able to use as little as 10 microliters of solution at a time. “Because of that, my samples can last me for years,” she notes. Through the exact control over low concentrations of solution, Miller is able to ensure that only one molecule is within the scope of the apparatus at any given time. Most importantly, this technique also allows her to model how these proteins behave in a solution with much greater clarity than traditional techniques would allow, giving researchers a better understanding of how and why natural systems behave.

The use of aptamers instead of antibodies offers Miller a significant medical research advantage as well. Proteins are traditionally fluorescently labeled using antibodies. “Aptamers are more flexible than antibodies, and they offer more control with fluorescent tags,” she explains. Furthermore,antibodies are part of a body’s inflammatory response. Aptamers are highly useful as an in vitro technique because they will not cause nearly as much rejection from the cell. This, in combination with the ability to measure reactions at very low concentrations, means that Miller’s work has the potential to make a substantial contribution to medical research.

Having been at American University for more than a year now, Miller is up and running. With the completion of her FCCS apparatus, she can now detect molecules in different environments and characterize what factors in the solution dynamics can cause shifts in the protein binding process. Now, Miller can complete the shift from antibody to aptamer use and begin studying multiple systems. With the rapid development of Miller’s work, perhaps her hidden fourth-floor laboratory won’t stay hidden for much longer.