Separating DNA fragments by gel electrophoresis

Microbiology, Immunity and Forensics · Decay, DNA techniques and forensics · note 3 of 5

Spec 6.18

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Separating DNA fragments by gel electrophoresisSpec 6.18

In short

Gel electrophoresis separates DNA fragments by length. DNA is negatively charged because of its phosphate groups, so in an electric field it moves through an agarose gel towards the positive electrode. Shorter fragments move faster and further, and fragments are made visible with a fluorescent dye or probe.

DNA is cut into fragments with restriction enzymes (or amplified by PCR).
A gel made of agarose (a porous polysaccharide) is covered with a buffer solution that conducts electricity. Samples, mixed with loading dye to make them dense and visible, are put into wells at the negative end. A mixture of fragments of known lengths (a DNA ladder) is put in one well.
An electric current is applied. DNA is negatively charged because of the phosphate groups, so it moves through the gel towards the positive electrode (anode).
The gel acts as a mesh. Shorter fragments move through it more easily, so they travel further in a given time, and longer fragments move more slowly. Fragments of the same length form a band.
The DNA is made visible by staining with a fluorescent dye that binds to DNA and is viewed in UV light, or by DNA probes that carry a fluorescent or radioactive label.

The length of a fragment is estimated by comparing how far its band has moved with the bands of the DNA ladder. A graph of log₁₀ fragment length against distance moved is roughly a straight line.

Exam tip:

The two key ideas are charge (negative phosphate groups, so moves to the anode) and size (smaller fragments move further through the gel). Fragments are separated by length, not by mass of the whole sample.

Gel electrophoresis: wells near the cathode, DNA moving through agarose gel towards the anode, a DNA ladder and sample lanes, with smaller fragments travelling further. — **Gel electrophoresis**: DNA is negatively charged, so it moves towards the anode; smaller fragments move further.

Written and checked against the Edexcel International A Level Biology (YBI11) specification · Updated October 2026

Frequently asked questions

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Saprotrophic bacteria and fungi secrete extracellular enzymes that digest dead organisms and waste, then absorb the soluble products. They respire some of this, releasing carbon dioxide into the atmosphere. Producers can then take up this carbon dioxide in photosynthesis, so carbon returns to the living world.

How does PCR work?

PCR copies a section of DNA using repeated cycles. At about 95 °C the strands separate, at about 55 to 65 °C primers anneal, and at about 72 °C Taq polymerase builds new strands from free nucleotides. Each cycle doubles the amount of DNA, giving millions of copies after 30 cycles.

How does gel electrophoresis separate DNA?

DNA is negatively charged because of its phosphate groups. In an electric field it moves through an agarose gel towards the positive electrode. The gel is a mesh, so shorter fragments move faster and further than longer ones, separating the fragments by length into bands.

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