​A single-molecule imaging technique, called protein-induced fluorescence enhancement (PIFE), has gained traction in recent years as a popular tool for observing DNA–protein interactions with nanometer precision. Yet, according to a new KAUST study, research laboratories have not been using the technique to its fullest potential.

The PIFE assay is predicated on the idea that DNA tagged with a fluorescent dye will glow brighter when proteins are bound in the vicinity. In many instances, this is true—which has led many scientists to adopt PIFE over other more labor-intensive techniques that rely on dual labeling of proteins and DNA.

But Samir Hamdan's graduate students Fahad Rashid, Manal Zaher and Vlad-Stefan Raducanu  realized that protein binding to DNA-dye complexes could sometimes have the opposite effect as well. Instead of enhancing the fluorescent signal, protein interactions can sometimes dampen the glow, depending on certain properties of the system.

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Image: Manal Zaher holds up the DNA-dye complex.
© 2019 KAUST