Applications of PCR and gel electrophoresis

Molecules (Continuity and change) · DNA replication · note 4 of 6

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Applications of PCR and gel electrophoresisSpec D1.1.5

In short

DNA profiling is the main application of PCR and gel electrophoresis: regions of DNA that vary in length between people are amplified and separated, giving a pattern of bands. Profiles are compared in paternity tests and forensic investigations. Using more markers makes the test more reliable, because it reduces the probability that two unrelated people match by chance.

Because PCR can amplify a chosen sequence from a tiny sample and gel electrophoresis can separate fragments by length, the two techniques have a broad range of applications.

DNA profiling for paternity and forensic investigations.
Detecting pathogens: PCR detects DNA (or RNA copied into DNA) of a virus or bacterium in a patient sample, as in tests for viral infections.
Genetic screening: testing for alleles that cause genetic conditions.
Research: amplifying genes for sequencing or for comparing species.

DNA profiling

Some regions of the genome contain short tandem repeats (STRs): a short base sequence repeated many times. The number of repeats at each region varies between individuals, so the length of the region varies. In DNA profiling, several of these regions are amplified by PCR and the fragments are separated by gel electrophoresis, giving a pattern of bands (a DNA profile) that is almost unique to each person.

Using DNA profiles
Use	How profiles are compared
Paternity	A child inherits one allele of each region from each parent. Every band in the child's profile must match a band in the mother's or in the father's profile. A man whose profile lacks the non-maternal bands cannot be the father.
Forensic investigation	DNA from blood, hair or skin cells at a crime scene is amplified and profiled, then compared with profiles from suspects. A match links a person to the scene; a mismatch excludes them.

Exam tip:

Nature of science: reliability is enhanced by increasing the number of measurements. In DNA profiling, using more markers (more STR regions) reduces the probability of a false match between two different people.

Paternity test: each band in the child comes from one parent, so Man 2 is the father and Man 1 is excluded.

Written and checked against the IB Biology HL specification · Updated October 2026

Frequently asked questions

Why is DNA replication semi-conservative?

DNA replication is semi-conservative because the two strands of the original molecule separate and each acts as a template for a new strand. Each daughter molecule therefore keeps one original strand and gains one new strand. Complementary base pairing makes the new strand match the old partner, so both copies have identical base sequences.

What are the three stages of PCR?

The three stages of PCR are denaturation, annealing and extension. At about 95 °C hydrogen bonds break and the strands separate; at about 55 °C primers bind to the ends of the target sequence; at about 72 °C heat-stable Taq polymerase builds new strands. Each cycle doubles the number of copies.

How does gel electrophoresis separate DNA fragments?

Gel electrophoresis separates DNA fragments by length. DNA is negatively charged because of its phosphate groups, so when a voltage is applied it moves through the gel towards the positive electrode. Smaller fragments move through the gel mesh more easily, so they travel further than larger fragments in the same time.

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