Scientists in Switzerland have shown that pyrene excimer fluorescence can be effectively quenched by perylene diimide (PDI) upon DNA duplex formation.

Molecular probes have many biological applications and are important for genetic diagnostics. Probes that already exist rely on the interplay between the light emitting (fluorescence) and light absorbing (quenching) molecules. 

Robert Häner and his colleagues from the University of Bern, in Switzerland, have developed a probe, which consists of a fluorophore (pyrene) and a quenching unit (PDI). The fluorescence is dependant upon the distance between these two units. In the presence of a target molecule (DNA) the probe undergoes a structural change which results in quenching of the fluorescence.

Quenching occurs due to the good spectral overlap between the PDI absorbance and the pyrene excimer emission, which results in efficient energy transfer. The pairs of pyrene and PDI units were also found to interact via interstrand stacking which indicates PDI physically interferes with the pyrene excimer unit resulting in the quenched fluorescence. Previous reports have shown that an efficient quencher of pyrene excimer fluorescence is usually difficult to achieve.

For future goals 'probes not only have to be highly sensitive, but they also have to be reliable and widely applicable. The ultimate probe will recognize its genetic target sequence with absolute specificity. The remainder part of the molecule, which includes the fluorophores and quenchers, must not interfere with this recognition,' said Häner.

Häner added that 'one of the driving forces for our research is the increasing demand for molecular genetic probes. However, the design of a simple, yet reliable concept still remains a challenge.' 

Emma Shiells