Probe based assays for quantitative PCR (qPCR) contain a reporter molecule and a quencher molecule. These probes utilize FRET (fluorescent resonance energy transfer) technology. The basic idea is that if the two molecules are close enough to each other, the quencher will mask the fluorescence from the reporter by itself absorbing the energy emitted by the reporter molecule in the form of an electron transfer. An emission from the quencher should not be detected. When a sufficient distance separates the reporter molecule from the quencher, fluorescence is detected.

 

The number of fluorescence carrying reporter molecules is proportional to the number of amplicons. The technique can be used to measure, among other things, gene expression levels and viral load. FRET also provides a method for screening known and unknown mutations and SNPs.