Interpreting Gel Electrophoresis Results (Part 1/3) Revision Notes | A Level AQA Biology

1. Why Every Person's DNA Tells a Unique Story

Two humans share roughly 99.9% of their DNA sequence. Yet forensic scientists can tell two people apart from a single hair follicle, and paternity tests can confirm biological relationships with near-certainty. The 0.1% that differs is doing a lot of work — and genetic fingerprinting is the technique that reads it.

This lesson focuses on the biological principles behind genetic fingerprinting and how gel electrophoresis is used to visualise and interpret the results. By the end, you will be able to read a banding pattern and draw conclusions about genetic relationships and population variability — exactly the kind of analysis AQA examiners ask for.

2. The Biological Principles: Why Fingerprints Differ

The key to genetic fingerprinting lies in regions of non-coding DNA called variable number tandem repeats (VNTRs). These are short sequences — typically 10 to 100 base pairs long — that repeat head-to-tail at specific locations (loci) on chromosomes. The critical point is that the number of repeats at each locus varies enormously between individuals.

Picture a locus on chromosome 7 where the sequence AGCT repeats. One person might have 14 repeats at that locus; another might have 31. Because humans are diploid, each person carries two alleles at every locus — one inherited from each parent. The combination of repeat numbers across multiple loci produces a pattern so statistically unique that the probability of two unrelated individuals sharing an identical profile is vanishingly small (often cited as less than one in a billion).

This polymorphism arises from errors during DNA replication and recombination events in meiosis. Over generations, different numbers of repeats accumulate in different lineages. Because VNTRs are inherited in a Mendelian fashion — one allele from each parent — close relatives share more VNTR alleles than unrelated individuals, which is precisely what makes the technique useful for determining genetic relationships.

3. From Sample to Profile: The Genetic Fingerprinting Technique

Now that you understand why individuals differ at VNTR loci, the next question is: how do we actually detect those differences? The technique involves four key stages, and each one connects directly to biological principles you have already studied.

• Stage 1 — DNA extraction: cells are lysed and DNA is isolated from the sample (blood, saliva, hair root, semen, or any nucleated cell source).
• Stage 2 — PCR amplification: specific VNTR loci are amplified using the polymerase chain reaction, producing millions of copies of the target regions from even a tiny starting sample.
• Stage 3 — Gel electrophoresis: the amplified fragments are separated by size through an agarose gel under an electric field.
• Stage 4 — Visualisation and interpretation: the resulting banding pattern is compared between individuals or against a reference ladder to determine fragment sizes.

PCR is essential here because real-world samples — a blood spot at a crime scene, a cheek swab — often contain only nanogram quantities of DNA. PCR amplifies the VNTR regions of interest to a quantity large enough to be detected after electrophoresis. Without amplification, the bands would be too faint to visualise reliably.

During PCR, primers are designed to flank the VNTR region at each locus. The number of base pairs in the amplified product depends directly on how many repeats are present — more repeats means a longer fragment. This is the link between the biological variation at the DNA level and the physical separation you observe on the gel.

4. Gel Electrophoresis: How the Separation Works

Gel electrophoresis exploits two properties of DNA: it carries a net negative charge (due to the phosphate groups in its backbone), and smaller fragments move through a porous medium more easily than larger ones. When an electric field is applied across an agarose gel, all DNA fragments migrate towards the positive electrode. The gel acts as a molecular sieve — larger fragments are slowed more by the gel matrix and travel a shorter distance, while smaller fragments travel further.

After electrophoresis, the gel is treated with a fluorescent dye (such as ethidium bromide or a safer modern alternative) or the DNA is transferred to a membrane and probed with labelled complementary sequences. Under UV light, each band becomes visible as a bright stripe. The position of each band corresponds to a specific fragment length, which in turn reflects the number of VNTR repeats at that locus.

A DNA size ladder — a mixture of fragments of known length — is always run alongside the samples. By comparing band positions to the ladder, you can estimate the size (in base pairs) of each fragment. This is the reference standard that makes quantitative interpretation possible.

5. Reading the Banding Pattern: Genetic Relationships

Here is where interpretation becomes the central skill. Each band on a gel represents one allele at one VNTR locus. Because humans are diploid, a heterozygous individual will show two bands per locus (one from each chromosome); a homozygous individual will show one band (both alleles have the same number of repeats, so the fragments co-migrate to the same position).

When comparing profiles, the rule is straightforward: shared bands indicate shared alleles. A child must inherit one allele at every locus from their biological mother and one from their biological father. So every band in a child's profile must be present in either the mother's or the father's profile. If a band in the child's profile cannot be matched to either proposed parent, that individual is excluded as a biological parent.

Worked example: Interpreting a Paternity Gel: Step-by-Step

A gel shows profiles for a child (C), a mother (M), and two candidate fathers (F1 and F2). At locus 1, the child shows bands at positions corresponding to 400 bp and 700 bp. The mother shows bands at 400 bp and 550 bp. F1 shows bands at 700 bp and 900 bp. F2 shows bands at 300 bp and 600 bp. Determine which candidate is the biological father and justify your answer.

1. Child (C): bands at 400 bp and 700 bp — Each band represents one allele at this locus. The child is heterozygous here.
2. Mother (M): bands at 400 bp and 550 bp. The child's 400 bp band matches the mother's 400 bp band. — The child inherited the 400 bp allele from the mother. This accounts for one of the child's two bands.
3. The child's remaining band is at 700 bp. This must have been inherited from the biological father. — Every allele in the child's profile must come from one parent or the other. The 700 bp band is unaccounted for by the mother.
4. F1: bands at 700 bp and 900 bp. F1 carries a 700 bp allele. — F1 could have contributed the 700 bp allele to the child. F1 is not excluded.
5. F2: bands at 300 bp and 600 bp. F2 does not carry a 700 bp allele. — F2 cannot have contributed the 700 bp allele. F2 is excluded as the biological father at this locus.
6. F1 is consistent with being the biological father; F2 is excluded. — In a real case, this analysis would be repeated across multiple loci to increase statistical confidence. Exclusion at even one locus is sufficient to rule out a candidate.

Answer: F1 is consistent with being the biological father because the child's 700 bp paternal allele is present in F1's profile. F2 is excluded because neither of F2's alleles (300 bp, 600 bp) matches the child's paternal allele (700 bp).

Notice the logic here: you are not proving that F1 is the father — you are showing that F1 cannot be excluded, while F2 can be excluded. This distinction matters in exam answers. The more loci analysed, the smaller the probability that a non-parent would match by chance, so in practice, profiles spanning 10 or more loci are used to achieve near-certainty.

6. Genetic Variability Within a Population

Genetic fingerprinting is not only used to identify individuals or resolve paternity disputes. It is also a powerful tool for measuring genetic variability within a population — a concept that connects directly to evolutionary biology and conservation genetics.

When profiles from many individuals in a population are compared, the diversity of banding patterns reflects the allelic diversity at VNTR loci. A population with high genetic variability will show many different band positions across individuals; a population with low genetic variability — perhaps due to a bottleneck event or inbreeding — will show fewer distinct patterns, with many individuals sharing the same bands.

This has direct applications in conservation biology. If a captive breeding programme is being managed for an endangered species, genetic fingerprinting can identify which individuals are most closely related. Breeding closely related individuals reduces genetic variability further, increasing the risk of inbreeding depression. By selecting less-related pairs, conservationists maximise the genetic diversity of the offspring population.

At the population level, genetic fingerprinting data can also be used to infer evolutionary relationships between populations or species. Populations that share more VNTR alleles are likely to have diverged more recently or to have experienced gene flow between them. This connects the technique to phylogenetics and the broader study of how populations change over time.

8. Practical Skills: Safe, Accurate, and Critical Electrophoresis (AQA PS2–PS4)

Genetic fingerprinting is not just a theoretical concept — it is also a practical skill assessed in the AQA specification. Competence in the laboratory involves: \n\n- Using equipment safely (such as micropipettes, electrophoresis tanks, and stains)\n- Recording and interpreting results methodically\n- Evaluating the quality of evidence and sources of error. \n\nYou must also show awareness of health and safety (e.g. wearing gloves when handling stains and gels, using UV shields when visualising DNA bands) and good scientific practice.

Safe handling: When preparing and running agarose gels, always wear gloves and safety goggles. Many DNA stains (like ethidium bromide) are hazardous — use less-toxic alternatives if available, and follow COSHH guidance. UV transilluminators (for visualising bands) can cause skin and eye damage: use the UV shield and never look directly at the light. Dispose of gels and used tips in designated biohazard waste.

Recording results: Photograph the gel under UV light before removing samples. Draw and label the banding pattern, including the orientation (positive/negative electrodes), size ladder, and all sample lanes. Record the sizes of bands (in base pairs) by comparison to the ladder, and keep a clear record of which sample was loaded into each well.