Interpreting Gel Electrophoresis Results (Part 2/3) Revision Notes | A Level AQA Biology

1. Reading a Gel: What the Bands Are Actually Telling You

Picture a gel electrophoresis result as a photograph of a race. DNA fragments all start at the same line — the wells — and migrate through the gel towards the positive electrode. The smallest fragments travel furthest because they slip through the gel matrix most easily. The result is a series of bands, each representing a group of DNA fragments of the same size.

To make sense of where each band sits, scientists always include a DNA ladder (also called a marker) in one lane. This contains fragments of precisely known sizes — for example, 100 bp, 200 bp, 500 bp, 1000 bp. By comparing the position of an unknown band to the ladder, you can estimate the size of that fragment in base pairs (bp).

The relationship between fragment size and migration distance is not linear — it is logarithmic. Larger fragments show a compressed pattern near the wells, while smaller fragments are more spread out near the bottom of the gel. This is why reading a gel accurately requires comparing to the ladder rather than measuring distance with a ruler alone.

Notice how the 100 bp fragment has migrated nearly to the end of the gel, while the 2000 bp fragment has barely moved. This inverse relationship — larger size, shorter distance — is the single most important rule when interpreting any gel result.

2. Interpreting Banding Patterns: A Step-by-Step Method

Exam questions on gel electrophoresis almost always ask you to do one of three things: estimate a fragment size, compare lanes to identify a match, or explain what a pattern tells you about genetic relationships. There is a reliable method for each of these tasks.

Worked example: Estimating Fragment Size from a Gel

A gel is run with a DNA ladder containing bands at 100 bp, 250 bp, 500 bp, and 1000 bp. An unknown fragment (lane 2) produces a band that migrates slightly further than the 250 bp ladder band but not as far as the 100 bp band. Estimate the size of the unknown fragment.

1. Ladder bands: 1000 bp (closest to well), 500 bp, 250 bp, 100 bp (furthest from well) — Always orient yourself using the ladder first. Confirm which end is the well (top) and which is the positive electrode (bottom).
2. Unknown band is between the 250 bp and 100 bp ladder bands, but closer to the 250 bp band. — The unknown has migrated further than 250 bp (so it is smaller than 250 bp) but not as far as 100 bp (so it is larger than 100 bp).
3. Fragment size is approximately 150-200 bp — Because the band sits closer to the 250 bp marker than to the 100 bp marker, an estimate of around 150-200 bp is reasonable. In an exam, stating the range and justifying by reference to the ladder earns the mark.
4. The unknown fragment is approximately 150-200 bp in length. — Avoid claiming false precision. Gel electrophoresis gives an estimate, not an exact value. Examiners reward candidates who acknowledge this.

Answer: The unknown fragment is approximately 150-200 bp, based on its position between the 250 bp and 100 bp ladder bands, closer to the 250 bp marker.

Comparing lanes to identify a match follows a similar logic. Two samples are considered to match if their band patterns — the number of bands and the position of each band — are identical across all lanes examined. A single band that differs in position is sufficient to rule out a match.

3. Genetic Fingerprinting: Why Scientists Use It

The banding patterns you have been reading are not arbitrary — they arise from regions of DNA called Variable Number Tandem Repeats (VNTRs). At specific loci across the genome, short DNA sequences are repeated end-to-end. The number of repeats varies enormously between individuals, so in the RFLP-based approach, these regions are cut with restriction enzymes and separated by gel electrophoresis, each person produces a unique pattern of bands.

The probability that two unrelated individuals share an identical genetic fingerprint across multiple VNTR loci is vanishingly small — often quoted as less than one in a billion. This statistical power is what makes genetic fingerprinting so valuable across several fields.

Each application exploits the same underlying principle — that VNTR patterns are heritable and individual-specific — but the question being asked differs. In forensics, the question is identity. In medicine, it may be relatedness or the presence of a disease allele. In breeding programmes, it is genetic diversity and parentage verification.

4. Forensic Science in Detail: Reading the Evidence

In a forensic context, gel electrophoresis results are used to answer one question: does the DNA from a crime scene match the DNA of a known individual? The process begins with extracting DNA from a biological sample — this could be blood, saliva, skin cells, or hair roots — and then amplifying specific VNTR loci using the polymerase chain reaction (PCR) before running the gel.

When interpreting forensic gel results, you must compare band positions precisely. A match requires every band in the crime scene lane to correspond to a band in the suspect lane at the same position. Partial matches — where only some bands align — do not constitute a match and may indicate a mixture of DNA from more than one individual at the scene.

It is also worth noting that genetic fingerprinting provides probabilistic evidence, not absolute proof. Courts consider the statistical probability of a random match alongside other evidence. The technique is highly reliable, but contamination of samples, degradation of DNA, or laboratory error can all affect the validity of results.

5. Medical Diagnosis: Fingerprinting Beyond Identity

In medical contexts, gel electrophoresis is used differently. Rather than comparing whole fingerprint profiles for identity, clinicians may look for the presence or absence of specific bands that correspond to disease-associated alleles. For example, in diagnosing certain inherited conditions, restriction fragment length polymorphisms (RFLPs) — variations in fragment size caused by mutations that create or destroy restriction enzyme cut sites — produce characteristic banding patterns.

Paternity testing is another medical application. Because a child inherits half their DNA from each biological parent, the child's genetic fingerprint should contain bands that can be traced to either the mother or the alleged father. Any band in the child's profile that cannot be accounted for by the mother must come from the biological father. If the alleged father's profile does not contain that band, paternity is excluded.

6. Exam Technique: Scoring Full Marks on Gel Electrophoresis Questions

Gel electrophoresis questions appear in several formats at A Level: data interpretation, extended writing, and evaluate questions. Each demands a slightly different approach, but there are consistent mark-winning habits that apply across all of them.

When asked to describe a gel result, state what you observe in sequence — number of bands, their relative positions, and which lane they appear in. Do not explain at this stage; description means observation only. When asked to explain, add the mechanism: why does that band appear at that position? Link fragment size to migration distance explicitly.

For evaluate questions about genetic fingerprinting as a technique, you need both strengths and limitations before reaching a conclusion. A strong answer acknowledges the statistical power of the method, then considers sources of error such as contamination, degradation, or the possibility of identical twins sharing the same profile.