VNTRs
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
An organism’s genome contains many variable number tandem repeats (VNTRs). The probability of two individuals having the same VNTRs is very low.
The genome of most eukaryotic organisms contains many repetitive non-coding sequences of DNA; these are called Variable Number Tandem Repeats (VNTRs).
Individuals have a unique VNTR sequence (except identical twins) and the probability of any two people having the same VNTRs is extremely low. This property makes VNTRs excellent for genetic fingerprinting, where we want to distinguish specific individuals.
For example, the repeated sequence ATTG, I may have 30 copies of this, but my friend might have 1000 copies of this, and the barista at the coffee shop (where I got my coffee while writing this) may have 200 copies of this.
(Note: This can be any repeated sequence, it isn’t just ATTG)
What's the difference between VNTRs and introns?
What's the difference between VNTRs and introns?
- Introns are also non-coding sections within a gene. They are transcribed into pre-mRNA but removed during RNA splicing, so they are not translated into protein.
- VNTRs: Short, repetitive DNA sequences where the number of repeats varies between individuals, so they are useful for DNA profiling.
Note: VNTRs are often found in non-coding regions and can be located within introns or between genes (not always inside introns).
Gel Electrophoresis
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
The technique of genetic fingerprinting in analysing DNA fragments that have been cloned by PCR, and its use in determining genetic relationships and in determining the genetic variability within a population.
After amplifying the DNA through PCR, the results can then be visualised and analysed by using gel electrophoresis.
Gel electrophoresis
Is used to separate DNA fragments according to their size (number of nucleotides).
DNA fragments are pulled through a gel matrix (agarose) by an electric current. This separates DNA fragments according to the size (number of nucleotides) because:
- DNA fragments are negatively charged so move towards the positive electrode
- Smaller fragments move faster and travel further through the gel
We can compare size of the DNA fragments with a reference (DNA ladder) containing fragments of a known size.
Genetic Fingerprinting Method
- Extract the DNA sample (e.g. from a hair strand)
- Increase the amount of DNA with PCR (This ensures there are enough VNTRs to analyse)
- Use restriction endonuclease to cut DNA into fragments, separating the VNTRs
- Separate fragments using gel electrophoresis — smaller fragments move further through the gel, creating a pattern of bands
- DNA Hybridisation. DNA probes are added to fragments. The probes have base sequences that are complementary to VNTRs so they can bind to target DNA sequence. Note: this is the same process as DNA probes
- Identification/development Use an X ray film to reveal the position of the DNA probes and the banding pattern
Using Figure 1, which person has the longest DNA fragment?
Using Figure 1, which person has the longest DNA fragment?
Person 1 (P1), as you can see the line is at 80bp (base pairs in size). This is the highest out of all three people.
Using Figure 2, which suspect is guilty (i.e. their DNA is at the crime scene)?
Using Figure 2, which suspect is guilty (i.e. their DNA is at the crime scene)?
Suspect 2. The pattern of bands from the crime scene matches suspect 2.
Genetic Fingerprinting Applications
What you need to know (from the AQA specification)
What you need to know (from the AQA specification)
The use of genetic fingerprinting in the fields of forensic science, medical diagnosis, animal and plant breeding.
Genetic fingerprinting can have many applications, including:
- Forensic science
- DNA (specifically VNTRs) left at a crime scene can be analysed and compared with the VNTR profiles of suspects.
- A match indicates the DNA likely came from the same individual.
- Medical diagnosis
- Genetic fingerprinting can be used to identify inherited genetic disorders.
- For example, Huntington’s disease, which involves a repeated nucleotide sequence (CAG) on chromosome 4.
- It can also be used to identify carriers of genetic conditions.
- Animal & plant breeding
- Genetic fingerprinting can be used to identify individuals with desirable alleles, such as:
- higher crop yield
- resistance to disease or environmental stress
- These animals or plants can then be selected for breeding to pass on the desirable traits
- Genetic fingerprinting can be used to identify individuals with desirable alleles, such as:
How this topic is tested
This analysis is based on past paper data from 2017 to 2025. It is intended for interest only and is not predictive of what will appear in future papers.
- Tested in 3 of 9 years (2017–2025): 5 question parts worth 9 marks.
- 48th most-examined topic overall by marks, 7th in Unit 8.
Marks by year
Most-tested spec points
- The Technique of Genetic Fingerprinting: tested in 4 parts (8 marks)
Also links to: Producing DNA Fragments, Amino Acid Structure.
Exam Question Practice
EcoRI and PstI are restriction endonucleases. Figure 1 shows where each enzyme cuts a linear DNA molecule that is 12 kb long (1 kb = 1000 base pairs).
Scientists cut many copies of this DNA molecule completely in two experiments, then separated the fragments by gel electrophoresis.
- Experiment 1. The DNA was cut with EcoRI only.
- Experiment 2. The DNA was cut with EcoRI and PstI.
Complete Figure 2 to show the relative positions of the bands in experiments 1 and 2.
(2 marks)
Hint
How many cuts are there in each experiment, and how many fragments does that give for a linear molecule? Which fragment is not cut by PstI? Which fragments travel furthest?
Mark Scheme
Experiment 1 with 3 bands and experiment 2 with 5 bands, all in the correct relative positions = 2 marks
Experiment 1 with 3 bands and experiment 2 with 5 bands, but not in the correct positions = 1 mark
For 2 marks, the 4 kb band must be at the same height in both lanes.
Explanation (not marked): EcoRI cuts at 3 kb and 7 kb, giving fragments of 3, 4 and 5 kb. PstI also cuts the 3 kb fragment into 1 and 2 kb, and the 5 kb fragment into 3.5 and 1.5 kb. The 4 kb fragment isn’t cut by PstI, so it is in both lanes. Shorter fragments travel further through the gel.
Tips
- Count the cuts. A linear molecule gives one more fragment than the number of cuts, so experiment 1 gives 3 bands and experiment 2 gives 5
- Draw horizontal bands, with the shortest fragments furthest from the wells
- A fragment that isn’t cut by the second enzyme must be at the same height in both lanes
Scientists cut a DNA molecule with restriction enzymes and separated the fragments by gel electrophoresis.
Suggest how they could find the size of each DNA fragment.
(2 marks)
Hint
How could you tell the size of a band if you had something to compare it with on the same gel?
Mark Scheme
- Run DNA fragments of known sizes (a DNA ladder) on the same gel (1 mark)
- Compare the positions of their bands with the bands of the unknown fragments (1 mark)
Tips
- Answer the question. Run fragments of known sizes (a ladder) alongside the samples, then compare the band positions
- Describing how electrophoresis separates fragments doesn’t answer it
Two restriction enzymes cut a linear DNA molecule at four sites in total.
How many fragments would be produced if the DNA molecule was a plasmid with the same four sites?
(1 marks)
Hint
What shape is a plasmid? How many pieces do you get if you cut a ring in four places?
Mark Scheme
4 (1 mark)
Explanation (not marked): A plasmid is a circle of DNA, so four cuts give four fragments. A linear molecule gives one more fragment than the number of cuts.
Tips
- A plasmid is circular, so the number of fragments equals the number of cuts. A linear molecule gives one more
Short tandem repeats (STRs) are short base sequences, usually 2 to 7 base pairs long, that are repeated one after another. For example, the STR called TH01 is the sequence TCAT, repeated between 3 and 14 times. People differ in the number of repeats, so STRs are used in genetic fingerprinting.
Describe how a section of DNA containing an STR could be cut out of a sample of DNA.
(2 marks)
Hint
Which enzymes cut DNA? Where exactly do they cut?
Mark Scheme
- Use restriction endonucleases (restriction enzymes) (1 mark)
- They cut the DNA at specific base sequences (recognition sites) on either side of the STR (1 mark)
Also accepted / rejected
Tips
- Name restriction endonucleases (restriction enzymes), not ligase, helicase, reverse transcriptase or DNA polymerase
- They cut at specific base sequences (recognition sites). “At a specific site” isn’t enough
In families where many people have had cancer, relatives can be tested for harmful mutations in the TP53 gene, using DNA from a cheek swab.
Describe how the DNA could be screened for known harmful mutations in the TP53 gene.
(4 marks)
Hint
How do you get enough DNA? How is it cut and separated? What binds to a mutated sequence, and how would you see it?
Mark Scheme
Max 4 marks
- Amplify the DNA using PCR (1 mark)
- Cut it with restriction endonucleases (1 mark)
- Separate the fragments by gel electrophoresis (1 mark)
- Add labelled DNA probes, which bind (hybridise) to the mutated sequences (1 mark)
- Find the bound probes by fluorescence (or radioactivity), or compare the bands with DNA known to have the mutations (1 mark)
Explanation (not marked): Each technique has a different function. PCR makes enough copies of the DNA. Restriction endonucleases cut it into fragments, and electrophoresis separates the fragments by size. Electrophoresis can’t show a mutation on its own, because it only sorts fragments by length. The labelled probe finds the mutation, because it only binds to the complementary mutated sequence, so it shows which fragment carries the mutation. You see it by its label, for example fluorescence under UV light. Some methods skip the cutting and electrophoresis, but for 4 marks give every step.
Also accepted / rejected
Also accepted
- Using a microarray (point 3)
- Instead of points 2 to 5, sequencing the amplified DNA and comparing it with the known mutation sequences (max 3 marks altogether)
Tips
- Amplify the DNA by PCR, cut it with restriction endonucleases, and separate the fragments by electrophoresis
- Add labelled DNA probes, which bind to the mutations. Say “bind”, not just “complementary”
- Find the bound probes by fluorescence or radioactivity
- Don’t mix up probes with primers
Also accepted