Quantitative PCR

Quantitative PCR, also called real-time PCR or qPCR, is a version of the polymerase chain reaction that measures DNA while the reaction runs instead of only at the end. Ordinary PCR is usually checked on a gel once cycling is over, when the reaction has leveled off, so it shows whether a sequence is present but not reliably how much there was to begin with.

Each reaction holds a fluorescent reporter whose glow the instrument reads after every cycle. The reporter may be a dye such as SYBR Green, which binds any double-stranded DNA, or a sequence-specific probe such as a TaqMan probe, which lights up only as its target is copied. The cycle at which the signal crosses a set threshold is the quantification cycle (Cq, often written Ct). The more template a sample starts with, the earlier it crosses, so the lower its Cq. Amounts are read from a standard curve or compared with a reference gene.

RT-PCR, or reverse transcription PCR, is a different method that starts from RNA: the enzyme reverse transcriptase copies it into DNA, which PCR then amplifies. Combined as RT-qPCR, the two measure messenger RNA in gene expression studies and detect RNA viruses such as SARS-CoV-2. Because RT is easily misread as real-time, qPCR is the preferred short form for real-time PCR.