There are two common types of fluorescent reporters used in qPCR assays, double-stranded DNA binding dyes and labeled primers or probes. Choosing the type of reporter for your qPCR assay depends on the objectives of your experiment.
Dyes bind to the double-stranded DNA produced as a result of the PCR amplification. The unbound dye fluoresces at a much lower level than bound dye, therefore the level of fluorescence is directly proportional to the amount of amplified DNA produced. One advantage of using these dyes is that they will work with standard PCR primers, eliminating the need to acquire specially labeled primers or probes. This does mean that the signal detected is not sequence-specific, and will require additional analysis to confirm that the correct sequence has been amplified. One method for verifying the amplified sequence is melt curve analysis.
Probe-based qPCR relies on a reporter-quencher mechanism. A sequence-specific probe that is labeled with a fluorescent reporter and a quencher molecule binds to the template. The fluorescent signal is not detected until the probe is degraded during amplification of the template. Primers are also needed, but using a probe makes the reaction more specific compared to dye-based chemistries. The primary advantage of using probe-based qPCR is that it provides the opportunity for multiplexing. By incorporating multiple probes with different colored fluorescent reporter dyes, this method can increase throughput by allowing several distinct sequences to be detected from the same qPCR.