Simulation · Biology · Class 12

Agarose gel electrophoresis: small fragments run farther

From the lesson Gel electrophoresis in Biotechnology: Principles and Processes. Change the values and watch what happens.

The idea behind it

NCERT §9.2.1 (separation and isolation of DNA fragments)

Cutting DNA with restriction enzymes gives fragments, and these are separated by gel electrophoresis.
DNA fragments carry a negative charge, so under an electric field they are forced through a matrix towards the anode (positive electrode).
The matrix most used today is agarose, a natural polymer extracted from seaweeds.
The gel acts as a sieve, so fragments separate (resolve) by size: the smaller the fragment, the farther it moves.
Pure DNA cannot be seen in visible light without staining. The gel is stained with ethidium bromide and exposed to UV light, and the DNA shows as bright orange bands.
Undigested DNA and digested DNA run in separate lanes, so the gel shows whether an enzyme has cut the sample.
The wanted bands are cut out of the gel and the DNA is extracted from the gel piece. This step is elution, and the purified fragments are then joined to cloning vectors.

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