What are quenchers and why are they used in Real-Time PCR? Are quenchers required when using LUX primers?
Quenchers are moieties attached to primers or probes that can quench the emission from a fluorophore that is also attached to that probe. They usually do this by FRET (Fluorescence Resonance Energy Transfer). Quenchers are generally used in probe-based assays to extinguish or change the wavelength of the fluorescence emitted by the fluorophore when both are attached to the same oligo. When the fluorophore gets excited it passes on the energy to the quencher, which emits the light at a different wavelength (higher wavelength). TAMRA is an example of a quencher. Other quenchers, known as dark quenchers, capture the fluorescence of the fluorophore but give off heat instead of a fluorescence emission. This is advantageous because there is less contaminating fluorescence that could possibly be detected in a qPCR assay and contribute to background. Dabcyl, Eclipse, and Black Hole (BHQ) quenchers are dark quenchers. LUX primers do not need a quencher because they form a hairpin loop that quen
