Fluorescence quenching is any process that decreases the fluorescence intensity of a sample. Many molecular interactions can result in quenching including excited-state reactions, molecular rearrangements, energy transfer, ground-state complex formation, and collisional quenching. The efficiency of fluorescence quenching is distance dependent. If the reporter fluorophore and quencher are far apart, fluorescence occurs. However, if the reporter and quencher are close together in space fluorescence is suppressed and does not occur.
In oligonucleotide probes, the reporter and quencher are typically placed such that a change in distance will produce a maximal change in fluorescence. The observed fluorescent signal monitors the event, for example, a hybridization or nuclease activity. In this case the oligonucleotide sequence acts as a flexible tether or link between the fluorescent reporter and quencher. Since, many dyes are known to aggregate, self-associate, form dimers, trimers, or polymers, the tendency for dyes to aggregate is the basis of the static quenching mechanism.
In static quenching or contact quenching a reporter such as FAM and a quencher such as BHQ-1 label can bind together to form a new, nonfluorescent intramolecular dimer. Furthermore, the efficiency of static quenching is dependent on the affinity of the reporter and quencher for each other. Often the reporter and quencher are planar, hydrophobic molecules that stack together to avoid contact with water.