Understanding Genetic Fingerprinting (Part 2/3) Revision Notes | A Level AQA Biology

1. Why Every Person Leaves a Unique Molecular Signature

Picture two people standing side by side. Their genomes are roughly 99.9% identical — yet forensic scientists can tell them apart from a single hair root. The 0.1% difference is enough, and genetic fingerprinting is the tool that reads it.

In Part 1 of this series you met the idea that non-coding regions of DNA contain repeated sequences. Here in Part 2 we move from concept to technique: how scientists actually extract, amplify, separate, and read those repeats to produce a profile that can place a suspect at a crime scene, confirm a diagnosis, or resolve a paternity dispute.

2. The Raw Material: STRs and Why They Vary

The repeating units used in modern genetic fingerprinting are called short tandem repeats (STRs) — sequences of 2–7 base pairs repeated consecutively at a fixed chromosomal location (locus). A person might have 6 repeats of the sequence AGAT at one locus on chromosome 3, while their neighbour has 14 repeats at the same locus. Neither version affects protein production because STRs sit in non-coding DNA, but the difference is heritable and highly variable across the population.

Because STRs are inherited from both parents, every individual carries two alleles at each locus — one from each homologous chromosome. If both alleles have the same repeat number, the person is homozygous at that locus and shows one band; if the alleles differ, they are heterozygous and show two bands. Analysing 10–16 loci simultaneously makes the probability of two unrelated individuals sharing an identical profile astronomically small — typically less than one in a billion.

3. Producing a Genetic Fingerprint: The Four-Stage Process

The process moves through four clearly defined stages. Understanding each stage — and why it is necessary — is exactly what examiners test, so work through each one carefully.

• Stage 1: DNA extraction — isolate DNA from the sample
• Stage 2: PCR amplification — produce enough copies to analyse
• Stage 3: Gel electrophoresis — separate fragments by size
• Stage 4: Visualisation — reveal and interpret the banding pattern

3a. Stage 1 — DNA Extraction

Cells are lysed (broken open) using detergent, which disrupts the phospholipid bilayer of the cell membrane and nuclear envelope. Proteins are then removed by protease enzymes or by precipitation with salt, and the DNA is precipitated out of solution using cold ethanol. The result is a small pellet of relatively pure DNA.

Forensic samples — a bloodstain, a hair follicle, a saliva trace — often contain only nanogram quantities of DNA. This is far too little for direct analysis, which is why Stage 2 is essential.

3b. Stage 2 — PCR Amplification

PCR (polymerase chain reaction) uses short single-stranded DNA sequences called primers that are complementary to the regions flanking each STR locus. The primers bind either side of the repeat region, and DNA polymerase extends from them, copying the repeat region specifically. After 30 cycles, a single copy of the target sequence becomes over one billion copies — enough for reliable analysis.

Worked example: One PCR Cycle: Denaturation, Annealing, Extension

Describe what happens at the molecular level during a single PCR cycle targeting an STR locus.

1. Heat breaks hydrogen bonds between complementary base pairs. — The double helix unwinds into two single-stranded templates. High temperature is needed because hydrogen bonds, though individually weak, are numerous across the whole molecule.
2. Temperature is lowered; primers bind to complementary sequences flanking the STR locus on each template strand. — Primer specificity is critical — only the STR region of interest is targeted. The annealing temperature is optimised so primers bind their target but not random sequences elsewhere.
3. Taq DNA polymerase synthesises a new complementary strand from each primer in the 5' to 3' direction. — Taq polymerase is used because it is thermostable — it was isolated from the bacterium Thermus aquaticus, which lives in hot springs, so it is not denatured by the high temperatures used in earlier steps.
4. After n cycles: number of copies = $2^n$. After 30 cycles: $2^{30} \approx 1.07 \times 10^9$ copies. — Exponential amplification means even a degraded sample with very few intact molecules can yield enough product for analysis. This is why PCR is described as amplifying a 'needle in a haystack'.

Answer: One cycle produces two double-stranded copies from one template. After 30 cycles, approximately one billion copies of the target STR region are present.

A key feature of modern forensic PCR is that primers for multiple STR loci are included in the same reaction tube, each labelled with a different fluorescent dye. This multiplex PCR approach analyses all loci simultaneously, saving time and sample material.

3c. Stage 3 — Gel Electrophoresis

The amplified STR fragments are loaded into wells at one end of an agarose gel submerged in a buffer solution. An electric current is applied: DNA carries a negative charge (from its phosphate backbone), so fragments migrate towards the positive electrode. Smaller fragments experience less resistance from the gel matrix and travel further in a given time.

A DNA size ladder (a mixture of fragments of known length) is run alongside the samples. By comparing band positions to the ladder, the size — and therefore the number of STR repeats — at each locus can be determined. In capillary electrophoresis, the modern forensic standard, fluorescently labelled fragments pass a laser detector and the output is an electropherogram showing peaks rather than visible bands.

3d. Stage 4 — Visualisation and Interpretation

In traditional Southern blotting (the original Jeffreys method), DNA fragments were transferred from the gel to a nylon membrane, then hybridised with radioactively labelled probes complementary to the repeat sequences. Exposure to X-ray film produced an autoradiograph — the characteristic ladder of dark bands that became the iconic image of genetic fingerprinting.

Modern forensic laboratories use capillary electrophoresis with fluorescent detection instead. The output is a digital electropherogram: a series of peaks whose positions correspond to fragment sizes. Software compares the peak positions to an internal size standard and assigns an allele number (the repeat count) at each locus. The result is a numerical profile — for example, 14,17 at locus D3S1358 — that can be stored in and searched against a national DNA database.

4. Reading and Comparing Profiles

Comparing profiles is the analytical heart of genetic fingerprinting. Each individual shows up to two bands per locus (one per allele). When comparing a crime scene sample to a suspect, scientists look for a match across all loci in the profile — not just one or two.

In the table above, Suspect A matches the crime scene profile at all four loci shown. Suspect B differs at every locus. Across a full 16-locus profile, a complete match between two unrelated individuals has a probability of less than 1 in 109, making the evidence highly compelling — though not mathematically certain.

There is one important biological exception: identical (monozygotic) twins share the same DNA sequence and therefore produce identical genetic fingerprints. Genetic fingerprinting cannot distinguish between identical twins — a limitation worth knowing for evaluation questions.

5. Applications: Forensics, Paternity, and Medical Diagnosis

Genetic fingerprinting is not confined to crime scenes. The same underlying technique — compare STR profiles across individuals — underpins three major application areas that AQA expects you to discuss with precision.

• Forensic science: matching biological material (blood, saliva, semen, hair roots) from a crime scene to a suspect or eliminating innocent individuals from enquiries.
• Paternity testing: a child inherits one allele at each locus from each biological parent. If the child's allele at a given locus is not present in the alleged father's profile, paternity is excluded. A match across all loci provides statistical support for paternity.
• Medical and research applications: identifying genetic variants linked to inherited disease, confirming the identity of tissue donors and recipients in transplantation, and tracking the spread of infectious disease strains.

In paternity testing, the logic is straightforward: at each locus, one of the child's two alleles must have come from the biological father. If the alleged father does not carry the allele the child must have inherited paternally, he is excluded. If his profile is consistent across all loci, paternity is supported — though not proven with absolute certainty, because an unrelated individual could theoretically share the same profile by chance.

6. Ethical Considerations and Limitations

The power of genetic fingerprinting raises genuine ethical questions that AQA includes in evaluation-style questions. These are not peripheral concerns — they are part of the specification and examiners expect you to engage with them analytically, not just list them.

National DNA databases (such as the UK's NDNAD) store profiles from convicted individuals and, in some jurisdictions, from those merely arrested but not convicted. The central tension is between public safety — a larger database increases the chance of matching crime scene DNA to a perpetrator — and individual privacy and civil liberties, particularly for those who were never found guilty of any offence.

A further concern is the risk of misinterpretation. A DNA match is probabilistic, not absolute. Juries may overestimate the certainty of a match (the 'prosecutor's fallacy'), treating a 1 in a billion probability as equivalent to proof. Scientists and legal professionals must communicate the statistical nature of the evidence clearly to avoid wrongful convictions.

7. Exam Technique: Securing Every Mark

Genetic fingerprinting questions appear across a range of command words. The marks available and the depth of answer expected shift significantly depending on which command word is used — so recognising the command word is the first step before you write a single sentence.

For describe questions about the process, work through the stages in order: extraction, PCR, electrophoresis, visualisation. Name each stage and state what happens — do not explain why at this point. For explain questions, add the mechanism: why does DNA move towards the positive electrode? Because the phosphate backbone carries a negative charge. For evaluate questions, you must present evidence on both sides and reach a conclusion — a one-sided answer will not access the top mark band.

Genetic fingerprinting sits at the intersection of molecular biology, statistics, and ethics — and AQA questions reflect all three dimensions. Secure the process stages first, then practise the evaluation structure, and you will be well placed to access marks across the full range of question types in this topic.