PCR (Polymerase Chain Reaction) Glossary
Master the vocabulary of PCR — from basic thermal cycling to advanced techniques like multiplex and digital PCR.
Design primers for PCR →PCR
Polymerase chain reaction — the foundational technique for amplifying specific DNA sequences using thermal cycling and DNA polymerase.
Read definition →Hot-Start PCR
A PCR variant where polymerase activity is blocked until the first denaturation step, reducing non-specific amplification from primer mispriming at room temperature.
Read definition →Multiplex PCR
Simultaneous amplification of multiple target sequences in a single reaction using several primer pairs, requiring careful Tm matching and primer compatibility.
Read definition →Nested PCR
Two rounds of PCR where the second set of primers binds within the first amplicon, dramatically increasing sensitivity and specificity for rare targets.
Read definition →Real-time PCR
PCR monitored in real time using fluorescent reporters, enabling quantification of initial template concentration during the exponential phase.
Read definition →RT-PCR
Reverse transcription PCR — converts RNA to cDNA via reverse transcriptase, then amplifies the cDNA target. Essential for gene expression analysis.
Read definition →qPCR
Quantitative PCR — real-time PCR with absolute or relative quantification of target DNA using standard curves or comparative Ct methods.
Read definition →Digital PCR
Partitions a sample into thousands of individual reactions for absolute quantification without standard curves, detecting rare variants with high precision.
Read definition →Touchdown PCR
Starts with a high annealing temperature and decreases incrementally, enriching specific products early and reducing non-specific amplification.
Read definition →Taq Polymerase
A thermostable DNA polymerase from Thermus aquaticus that revolutionized PCR by eliminating the need to add fresh enzyme after each denaturation step.
Read definition →Thermal Cycler
The instrument that precisely controls temperature cycles for denaturation, annealing, and extension steps in PCR protocols.
Read definition →Thermocycling Profile
The specific temperature, time, and cycle count parameters that define a PCR protocol — typically 25–40 cycles of denature (94–98 °C), anneal (50–68 °C), extend (72 °C).
Read definition →DNA Polymerase
An enzyme that synthesizes new DNA strands by adding nucleotides complementary to a template in the 5′→3′ direction, requiring a primer to initiate synthesis.
Read definition →Amplicon
The specific DNA fragment produced by PCR amplification — the region between and including the forward and reverse primer binding sites.
Read definition →Amplicon Size
The length in base pairs of the PCR product, determined by the distance between primer binding sites on the template DNA.
Read definition →SYBR Green
A fluorescent dye that intercalates into double-stranded DNA, used in real-time PCR to monitor amplification — binds any dsDNA, requiring melt-curve analysis for specificity.
Read definition →TaqMan
A hydrolysis probe-based detection method using a fluorophore-quencher oligonucleotide that is cleaved during extension, releasing fluorescence proportional to target quantity.
Read definition →TaqMan Probe
An oligonucleotide with a reporter fluorophore at the 5′ end and a quencher at the 3′ end, designed to hybridize between the primers for specific detection.
Read definition →Probe Design
The process of selecting fluorescent probe sequences for real-time PCR, requiring Tm 8–10 °C above primer Tm, no secondary structures, and specific binding.
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