DNA: Switch and Detect
DNA can act as an electronic switch that is “flipped” by analyte-specific binding and, thus, can function as a chemical sensor, according to a recent report by scientists from Simon Fraser University (SFU) in British Columbia.

Switch designs. Two DNA aptamer “switches” that can be used for electronic detection of analytes.

DNA electrical conductivity, via long-range electron transport through the double helix, has been the subject of much research over the past 5–10 years. One of the significant observations is the large effect that disruptions in the base-stacking have on the efficiency of electric current flow. Even single base mismatches have been shown to cut off the flow considerably.

To take advantage of this behavior for developing an electronic chemical-specific sensor, Richard Fahlman and Dipanker Sen from SFU used a DNA aptamer, a sequence isolated by special in vitro selection techniques that contains a ligand-specific binding “pocket”. The pocket, which, in this case, was specific for binding the neuromodulator adenosine, is a bulge that interrupts the regular helical pattern. It therefore inhibits electron transport.

The Canadian team coupled anthraquinone (AQ), a photosensitizer that can oxidize guanine bases via charge transport, to one end of the aptamer and irradiated the molecule (J. Amer. Chem. Soc. 2002, 124 (17), 4610–4616). By using electrophoresis gels, they measured at what points along the helix guanine oxidized to determine where transport had taken place. Oxidation clearly was detected for the guanines that were on the same side of the bulge as AQ, but no oxidation was observed on the opposite side of the bulge (see Figure, a). This signified that charge flow was “blocked”. With addition of adenosine, significant oxidation was observed at all of the guanines, indicating that the bulge was pulled into a more tightly stacked helical structure from adenosine binding, allowing for less impeded charge transfer.

Fahlman and Sen also developed another sensor design in which the adenosine-binding bulge was one base pair away from a three-way junction of double helices, as shown in b. The shape of the junction was disfigured by the protuberance, limiting charge transfer to only AQ-adjacent guanines. With the addition of adenosine, transport was observed throughout the main helical chain. By separating the analyte from the electron flow, this approach makes the technique applicable to a wider range of aptamer binders that don’t inherently permit charge transfer through their structure. Thus, this method can potentially be used for the detection of almost any compound, from small molecules to proteins.

Ideally, say the authors, for rapid, automated analyte detection, these types of DNA sensors should be functionalized onto electrodes, allowing direct current flow measurements of conformational changes in a chip-based design.

L. James Lee, professor of chemical engineering at Ohio State University (Columbus), described his research in a presentation at the Materials Research Society’s annual meeting in San Francisco. He and his team found that by adding nanometer-sized clay particles to liquid plastic during the foam manufacturing process, they could increase plastic foam’s density and strength.

While most structural-grade plastic foam contains bubbles close to several hundred micrometers across, the bubbles in Lee’s nanocomposite foams were as small as 5 µm across. With a foam that contained 5% clay particles, the engineers were able to create boards that were just as strong, but only two-thirds as thick, as typical foam.

In addition to upping the foam strength, Lee and his colleagues, along with several industrial partners, are working to develop standard foams with carbon dioxide instead of CFCs.

Padma Venkatraman, a postdoctoral fellow in the Department of Geography and Environmental Engineering, presented the first part of the group’s two-part findings at the American Chemical Society national meeting in Orlando, FL.

The first part consisted of a survey of the estimated environmental concentration of the 200 drugs that are sold and prescribed most often in the United States. The survey was based on total over-the-counter drug sales and prescriptions, as well as a search of the medical literature available on each drug’s biochemistry and metabolism.

Because some drugs are not metabolized before elimination, the researchers calculated probable environmental concentrations with and without metabolism. They also noted that many medications aren’t metabolized because they never are ingested, but instead are flushed down the toilet after expiration.

Michael L. Blumenfeld, an undergraduate student, presented the second part of the group’s findings, a new gas chromatography-mass spectrometry technique that the team used to test several water samples for their drugs of interest. The new technique involves adding a unique derivatizing agent, pentafluorobenzylbromide, to the samples. This reagent improves the sample’s volatility and chromatography peak shape and introduces a functional group to increase detection sensitivity.

“There’s always been a problem with carryover of excess reagent and then the derivatization catalyst. This way, we actually destroy the excess derivatizing agent and we don’t end up with any derivatization catalysts. We get beautiful peak shapes and extremely low detection limits,” said A. Lynn Roberts, who headed the research team.