There are two general approaches used to obtain a fluorescent signal from the synthesis of product in Real-time PCR. The first depends upon the property of fluorescent dyes such as SYBR Green I to bind to double stranded DNA and undergo a conformational change that results in an increase in their fluorescence. The second approach is to use fluorescent resonance energy transfer (FRET).

These methods use a variety of ways to alter the relative spatial arrangement of photon donor and acceptor molecules. These molecules are attached to probes, primers or the PCR product and are usually selected so that amplification of a specific DNA sequence brings about an increase in fluorescence at a particular wavelength.

A major advantage of the real-time PCR instruments and signal transduction systems currently available is that it is possible to characterise the PCR amplicon in situ on the machine. This is done by analysis of the melting temperature and/or probe hybridisation characteristics of the amplicon within the PCR reaction mixture.

In the intercalating dye system, the melting temperature of the amplicon can be estimated by measuring the level of fluorescence emitted by the dye as the temperature is increased from below to above the expected melting temperature. The methods that rely upon probe hybridisation to produce a fluorescent signal are generally less liable to produce false positive results than alternative methods such as the use of intercalating dyes to detect net synthesis of double stranded DNA (dsDNA) followed by melting analysis of the product.

Hybridisation, ResonSense and hydrolysis probe systems give fluorescent signals that are only produced when the target sequence is amplified and are unlikely to give false positive results. An additional feature of the hybridisation, ResonSense and related methods is the possibility to measure the temperature at which the probes disassociate from their complementary sequences.

This measurement gives a further verification of the specificity of the amplification reaction. An important feature of many of the probe systems is their compatibility with multiplexing due to the availability of fluorophores with resolvable emission spectra.