Real Time PCR: RT-PCR also known as quantitative PCR is used to amplify and simultaneously quantify a target DNA. It differs from standard PCR in a way that it can detect the amplified product as the reaction progresses with time but in standard PCR the amplified product is detected at the end of the reaction by agarose gel electrophoresis. RT-PCR is widely used in expression profiling, to determine the expression of a gene or to identify the sequence of an RNA transcript, including transcription start and termination sites.

Many probes are used for detection of amplified product in RT-PCR such as TaqMan probe, Molecular beacons, ds DNA binding dyes (eg.SYBR green) of which TaqMan probes are most widely used. TaqMan probes are oligonucleotide probes which have a fluorophore at its 5' end and a quencher at its 3' end. The quencher molecule quenches the fluorescence emitted by the fluorophore when excited by the light source of the cycler via FRET (Fluorescence Resonance Energy Transfer).

When DNA polymerase starts synthesizing the new strand, it degrades the probe (due to its 5'-3' exonuclease activity) which releases the fluorophore. This inhibits quenching effect of the quencher and allows fluorescence of the fluorophore. Hence fluorescence detected in RT-PCR is directly proportional to the amount of DNA template.

Inverse PCR - Inverse Polymerase Chain Reaction is a variant of PCR, and is used when only one internal sequence of the target DNA is known. It is therefore very useful in identifying flanking DNA sequences of genomic inserts.