LightCycler^® probes from metabion are synthesized in our ISO-certified manufacturing facility using processes licensed by Roche. Unlike the TaqMan® assay where a self-quenching fluorogenic probe is cleaved to generate a fluorescent signal, the LightCycler^® hybridisation probe system is based on two oligonucleotide probes that hybridize, in a head-to-tail arrangement, to adjacent sequences of the target DNA. Each probe carries a different marker dye, the first one 3'Fluorescein, the second one either 5'LC610, 5'LC640, 5`LC670 or 5'LC705.

Additionally, LC probes' 3'OH terminus is "capped" by a phosphate group to prevent polymerase from extending the primer during PCR reaction. As the marker dyes are in close proximity, there can be a fluorescence resonance energy transfer (FRET) between them which allows a specific and quantitative real time detection of the amplification of a nucleic acid template. To avoid sterical problems between the 3' Fluo and 5' LCRed end labels of the probes there should be a spacer of 1 to 5 nucleotides (4 to 25 Å distance) to separate the two probes from each other.