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).

Detection	Visualization
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 digestion	-Agarose or polyacrylamide gel -HPLC
Dot blots	Hybridization with labeled probe
High-pressure liquid chromatography	UV detection
Electrochemiluminescence	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 borek@leucine.ibch.poznan.pl
Department of Crystallography
Faculty of Chemistry
Adam Mickiewicz University
Grunwaldzka 6
Poznan, Poland