Detecting Bulging DNA

Courtesy of C.C. ChengBulged structures are crucial motifs in the recognition of DNA by nucleic acid-binding proteins, says Chien-Chung Cheng of Academia Sinica, Taipei, Taiwan. So, they're important as potential targets for antiviral drugs. They also are known to be intermediates in the process of frame-shift mutagenesis.But unlike RNA, says Cheng, "it has been difficult to obtain detailed structural information about DNA bulges, because they are relatively unstable." The most common detection

Sep 27, 2004
Ivan Oransky
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Courtesy of C.C. Cheng

Bulged structures are crucial motifs in the recognition of DNA by nucleic acid-binding proteins, says Chien-Chung Cheng of Academia Sinica, Taipei, Taiwan. So, they're important as potential targets for antiviral drugs. They also are known to be intermediates in the process of frame-shift mutagenesis.

But unlike RNA, says Cheng, "it has been difficult to obtain detailed structural information about DNA bulges, because they are relatively unstable." The most common detection method, the gel mobility shift assay, has low sensitivity, explains Cheng. Other methods employ reagents that have difficulty distinguishing one secondary structure of single-stranded regions from another.

Cheng and a colleague have developed a method of detecting nucleic acid bulges. The method makes use of metal complexes that are DNA bulge-specific, exhibiting low affinity toward double-stranded DNA and low reactivity toward single-stranded DNA. The method, which was recently awarded US patent 6,770,760, is also quick, says Cheng, taking just 5–10 minutes in the presence of hydrogen peroxide.

He and his colleagues have published on the method, and at least four projects are ongoing, including study of bulge structures in Streptomyces and creation of diagnostic agents for genetic diseases. For licensing details, contact the Academia Sinica patent office at http://ip@gate.sinica.edu.tw.

- Ivan Oransky