Detection and analysis of PCR products

Detection and analysis of PCR products

The product of a PCR should be a fragment or fragments of DNA of defined length. Many techniques can be used to detect amplified sequences (see Table).

Agarose gel and/or polyacrylamide

gel electrophoresis

-EtBr staining (UV transilluminator, image analyzer)

-Southern blotting (hybridization with labeled probe)

-Incorporation of label into amplifying sequence

-Silver staining

Restriction endonuclease


-Agarose or polyacrylamide gel


Dot blots
Hybridization with labeled probe
High-pressure liquid chromatography
UV detection
Voltage-initiated chemical reaction/photon detection
Direct sequencing
Radioactive or fluoescent-based DNA sequencing
The simplest and commonly used technique is electrophoresis of the PCR product on an agarose gel with EtBr (ethidium bromide). EtBr is a fluorescent dye that intercalates into the DNA. Size markers can be electrophoresed on the gel to allow size determination of the PCR product. An example of detection of PCR products on the agarose gel with EtBr is shown in Figure below.

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Dominika Borek
Department of Crystallography
Faculty of Chemistry
Adam Mickiewicz University
Grunwaldzka 6
Poznan, Poland