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Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than Förster resonance energy transfer (FRET).

The cover picture shows a 96-well plate illuminated by a UV lamp and viewed through a cutoff filter. All wells contain a Cy3.5-BHQ1 (reporter quencher) dual-labeled oligonucleotide probe in buffer. Complementary sequence was added to three columns. The probe is virtually nonfluorescent due to static quenching through formation of an intramolecular dimer. Addition of complement separates the dye and quencher, causing fluorescence. Intramolecular dimers as a new design strategy for fluorescence-quenched probes is discussed by M. K. Johansson and R. M. Cook in the Concepts article on p. 3466 ff.