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[Biochemistry](https://durgical.com/en/biochemistry/) · Topic

# Polymerase chain reaction (PCR)

PCR copies one chosen piece of DNA millions of times in a few hours; it underpins molecular diagnosis of infections and genetic diseases.

Updated 2026-11-01

## Key facts

- Ingredients: template DNA, two primers flanking the region, the four dNTPs, Mg²⁺ and a heat-stable DNA polymerase (Taq, from Thermus aquaticus).
- Each cycle has three steps: denaturation (~95 °C), primer annealing (~50–65 °C) and extension (~72 °C).
- Exponential growth: about 30 cycles give on the order of a billion copies (2³⁰).
- RT-PCR: RNA is first copied into cDNA with reverse transcriptase (RNA viruses, gene expression).
- Real-time PCR (qPCR): a fluorescent probe or dye measures the product each cycle; fewer cycles to turn positive = more starting template.

## In detail

- Specificity comes from the primers: about 18–25 nucleotides complementary to the ends of the target region.
- The product is seen by agarose gel electrophoresis: bands separate by size and are stained with a DNA-binding dye.
- The qPCR Ct value (threshold cycle) is inversely related to the amount of starting template; this is how viral load is measured.
- Variants: multiplex PCR (several targets at once), digital PCR (counts molecules one by one), allele-specific PCR (detects a point mutation).
- Pitfalls: contamination with previously amplified DNA (false positives) and inhibitors in the sample (false negatives); hence positive, negative and internal controls.

**Also called**
PCR, RT-PCR, qPCR

## Clinical notes

- Viral load for HIV, hepatitis B and C; diagnosis of dengue, COVID-19 and other infections by RT-PCR.
- Rapid detection of Mycobacterium tuberculosis and of rifampicin resistance (rpoB mutations) with automated molecular tests.
- Genetic diagnosis: point mutations, deletions (Duchenne), repeat expansions (fragile X, Huntington), forensic identification and paternity tests.

## Related conditions

- [HIV infection and AIDS](https://durgical.com/en/conditions/hiv-infection-and-aids/)
- [Tuberculosis](https://durgical.com/en/conditions/tuberculosis/)
- [Dengue](https://durgical.com/en/conditions/dengue/)

## Related

- [DNA polymerases](https://durgical.com/en/biochemistry/enzymes/dna-polymerases/)
- [DNA sequencing](https://durgical.com/en/biochemistry/topics/dna-sequencing/)
- [Recombinant DNA and cloning](https://durgical.com/en/biochemistry/topics/recombinant-dna-and-cloning/)
- [Trinucleotide repeat expansion disorders](https://durgical.com/en/biochemistry/topics/trinucleotide-repeat-expansion-disorders/)
- [DNA structure and chromatin](https://durgical.com/en/biochemistry/topics/dna-structure-and-chromatin/)

## Test yourself

Think of the answer, then tap the question to see it.

## Why does PCR need a heat-stable DNA polymerase?

Each cycle heats to about 95 °C to separate the strands; an ordinary polymerase would denature.

## What extra step does RT-PCR have, and what is it for?

A prior reverse transcription that copies RNA into cDNA; it lets you detect RNA viruses or measure gene expression.

## In qPCR, what does a low Ct value mean?

Plenty of starting template: the product crosses the fluorescence threshold in few cycles (e.g. high viral load).

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Educational information, not medical advice. For any symptom, see a health professional.

Sources: [Polymerase Chain Reaction (PCR) Fact Sheet](https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-Reaction-Fact-Sheet) (National Human Genome Research Institute (NHGRI), 2026); [Polymerase Chain Reaction (PCR)](https://www.genome.gov/genetics-glossary/Polymerase-Chain-Reaction-PCR) (National Human Genome Research Institute (NHGRI), 2026); [HIV Viral Load: MedlinePlus Medical Test](https://medlineplus.gov/lab-tests/hiv-viral-load/) (MedlinePlus, US National Library of Medicine, 2026); Textbook of Biochemistry for Medical Students, 6th ed. (Jaypee Brothers Medical Publishers (Vasudevan DM, Sreekumari S, Vaidyanathan K), 2011).

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