Year 12 Biology

DNA Profiling

Today you are looking at how a tiny DNA sample can be copied, separated into fragments, and compared with other DNA samples to produce a DNA profile.

What to do: Work through the pack in order. Read the explanations, use the diagrams, and complete the checkpoint questions in your notebook or in the spaces provided by your teacher.

DNA profiling problem Big picture PCR STRs Gel electrophoresis Profile interpretation DNA probes Writing task

The problem DNA profiling solves

You already know that DNA contains genetic information. You have also seen that biotechnology can manipulate DNA, for example by cutting DNA with restriction enzymes and joining DNA fragments using DNA ligase.

This lesson asks a different question. Instead of asking how scientists can build recombinant DNA, we are asking how scientists can analyse DNA.

The difficulty is that DNA evidence is usually microscopic. A sample from a cheek swab, blood stain, plant tissue, or crime scene may contain very little DNA. Scientists also need a way to compare samples that is more useful than simply saying, "this sample contains DNA".

Central question: How can scientists turn a tiny DNA sample into a visible pattern that can be compared with other DNA samples?

The overall process: copy, separate, compare

A DNA profile is a pattern of DNA fragments that can be compared between samples. It is sometimes called a DNA fingerprint, but it is not a picture of a whole genome. It is a pattern produced by analysing selected regions of DNA.

The process works because DNA samples can contain fragments of different lengths. When those fragments are separated, they form bands. If two samples have bands in the same positions, those fragments are the same size. If many bands match, the samples are more similar.

1. Copy

PCR makes many copies of selected DNA regions so there is enough DNA to analyse.

2. Separate

Gel electrophoresis separates DNA fragments according to size.

3. Compare

Banding patterns are compared to identify similarities and differences between samples.

Key terms for today

Read these terms now, but do not try to memorise them as isolated definitions. Each one will make more sense as you see how it fits into the profiling process.

Term	Meaning for this lesson
PCR	Polymerase chain reaction. A technique used to amplify, or rapidly copy, selected DNA regions.
Primer	A short single-stranded DNA sequence that binds to the start of the region being copied. DNA polymerase extends from the primer.
Taq polymerase	A heat-stable DNA polymerase used in PCR to build new DNA strands.
STR	Short tandem repeat. A short DNA sequence repeated several times at a specific location in the genome.
Locus	A specific location on a chromosome.
Gel electrophoresis	A technique that separates DNA fragments by size as they move through a gel in an electric field.
DNA ladder	A set of DNA fragments with known sizes, used to estimate the size of fragments in other samples.

Checkpoint 1

Answer this before moving on.

Question: Why would a scientist need to make more copies of DNA before trying to analyse a tiny biological sample?

Why tiny DNA samples need copying

PCR stands for polymerase chain reaction. It is used when scientists need many copies of a selected DNA region. The word amplify means to increase the amount of something. In PCR, the amount of target DNA increases because the same copying cycle is repeated many times.

PCR does not copy every part of the genome. Primers are designed to bind on either side of the DNA region of interest. This means the primers help define which section of DNA will be copied. Once the primers bind, DNA polymerase can extend from them and build new DNA strands.

This matters for DNA profiling because a sample may begin with only a very small amount of DNA. After PCR, there are many copies of the selected regions, making it possible to separate and compare the DNA fragments.

PCR cycle showing denaturation, annealing and extension of DNA strands

Figure 1: PCR uses repeated cycles of heating and cooling. The DNA strands separate, primers bind to the target region, and Taq polymerase builds new DNA strands.

Denaturation separates the DNA strands

The reaction is heated so the two DNA strands separate. This creates single-stranded templates that can be copied.

Annealing lets primers bind

The reaction is cooled so primers can bind to complementary sequences on the DNA template. The primers mark the edges of the region to be copied.

Extension builds new DNA strands

Taq polymerase adds free nucleotides to the primers and builds new DNA strands. New DNA is synthesised in the 5' to 3' direction.

Check your understanding: why use Taq polymerase?

Most enzymes lose their shape and stop working at high temperatures. PCR repeatedly heats the reaction mixture during denaturation. Taq polymerase is useful because it is heat-stable, so it can keep working across repeated heating and cooling cycles.

Why different DNA can produce different banding patterns

Human DNA is very similar from person to person, so DNA profiling usually focuses on regions that vary between individuals. One useful type of variable region is called a short tandem repeat, or STR.

An STR is a short DNA sequence repeated several times in a row. For example, a sequence such as ATCG might be repeated three times in one person and six times in another person. The location of that STR on a chromosome is called a locus.

The number of repeats affects the length of the DNA fragment. Fewer repeats create a shorter fragment. More repeats create a longer fragment. When these fragments are separated on a gel, their different lengths can produce different band positions.

Fewer repeats

A shorter repeated region produces a shorter DNA fragment.

ATCG ATCG ATCG

More repeats

A longer repeated region produces a longer DNA fragment.

ATCG ATCG ATCG ATCG ATCG ATCG

Put simply: different numbers of STR repeats can create different fragment lengths. Different fragment lengths can create different band positions on a gel.

Checkpoint 2

Use the STR explanation above to answer the question.

Question: If one person has more repeats at an STR locus than another person, what happens to the length of that DNA fragment?

How a gel separates DNA fragments

After PCR, scientists need a way to sort the copied DNA fragments by size. This is where gel electrophoresis is used. A gel is a thin slab of material with tiny spaces inside it. DNA samples are loaded into wells at one end of the gel.

An electric current is then passed through the gel. DNA has an overall negative charge, so DNA fragments move away from the negative end and towards the positive end. The gel acts a little like a molecular sieve. Smaller DNA fragments can move through the spaces more easily, so they travel further. Larger fragments are slowed down more, so they remain closer to the wells.

Gel electrophoresis setup showing power supply, wells, cathode, anode, buffer and direction of DNA movement

Figure 2: DNA samples are loaded into wells near the negative end. Because DNA is negatively charged, fragments move through the gel towards the positive end.

Short fragments

Short DNA fragments move through the gel more easily. They travel further from the wells.

Long fragments

Long DNA fragments are slowed down more by the gel. They stay closer to the wells.

Common trap: Do not write that larger fragments travel further. In gel electrophoresis, shorter fragments travel further.

How a DNA ladder helps estimate fragment size

A gel gives a visible banding pattern, but scientists also need a way to estimate the sizes of the DNA fragments. A DNA ladder solves this problem. The ladder contains DNA fragments of known lengths.

The ladder is loaded into one lane of the gel. When the gel runs, the ladder fragments separate according to size. Unknown sample bands can then be compared with the ladder bands. If a sample band lines up with a ladder band, it is close to that size. If it sits between two ladder bands, its size is estimated between those values.

Gel electrophoresis result showing DNA ladder and sample bands

Figure 3: The DNA ladder provides known fragment sizes. Sample bands can be compared against the ladder to estimate fragment length.

Check your reasoning: a band between 200 kb and 300 kb

If a sample band is lower than the 300 kb marker but higher than the 200 kb marker, the fragment is between 200 kb and 300 kb. You may not be able to give an exact value, but you can make a reasonable estimate from its position.

How to compare DNA profiles

When you compare DNA profiles, do not judge them by general appearance. Compare the bands by position. A band in the same position in two lanes represents DNA fragments of the same size.

For a simple match, you are looking for bands that line up across samples. For parentage questions, you also need to remember that a child inherits genetic material from both biological parents. A band in the child's profile should be explained by the mother or by the father.

Figure 4: In a paternity-style profile, first identify the child's bands that match the mother. Then check which possible father accounts for the remaining child bands.

Checkpoint 3

Use Figure 4. Write two sentences.

Sentence 1: The most likely father is __________.

Sentence 2: This is supported because __________.

Forensic DNA profiles use the same band-matching logic, but the question is usually different. Instead of asking who a child inherited DNA from, the question might be whether DNA from a sample matches a known reference sample.

A match can support the conclusion that biological material from a person was present in the sample. However, the DNA profile alone does not explain how the DNA arrived there or when it was deposited.

Figure 5: In a forensic-style profile, compare the sample lanes with the known reference lanes. Look for bands that line up at the same height.

Figure 6: In a comparison task, the samples with the most shared band positions are the most genetically similar. The sample with the fewest shared positions is more genetically distinct.

Checkpoint 4

Choose either Figure 5 or Figure 6. Write a short conclusion that includes both an answer and evidence.

Conclusion:

Evidence from band positions:

Sentence frame for profile evidence

The DNA profile from __________ is most similar to __________ because the bands at __________ line up in the same positions. This supports the conclusion that __________.

How DNA probes can identify specific fragments

A DNA probe is a short piece of DNA that is complementary to a specific sequence. Complementary means that the bases can pair with each other: A pairs with T, and C pairs with G.

DNA probes are useful because they can bind to a matching sequence in a sample. If the probe has a fluorescent or radioactive label, the bound probe can be detected. This helps scientists locate particular DNA fragments after the fragments have been separated.

Older DNA profiling workflows can include several steps. DNA is cut into fragments, the fragments are separated by gel electrophoresis, the DNA is transferred to a membrane, and labelled probes are added. The probes bind only where their complementary sequence is present. Detection then reveals the banding pattern.

Workflow showing restriction fragments, gel electrophoresis, Southern blotting, DNA hybridisation and autoradiography

Figure 7: DNA probes bind to complementary DNA sequences. The labelled probes allow particular fragments to be detected and compared between samples.

Fragments are prepared

DNA is cut into fragments so different samples can be separated and compared.

Fragments are separated

Gel electrophoresis separates fragments by size, producing a pattern of positions in the gel.

Fragments are transferred and detected

The DNA is transferred to a membrane and labelled probes bind to complementary sequences. The detected bands can then be compared.

What DNA profiling can and cannot tell us

DNA profiling is powerful because it can compare biological samples using banding evidence. It can support a match, exclude a sample, or show genetic similarity between samples.

But DNA profiling has limits. A DNA match does not automatically prove when the DNA was deposited. It also does not explain the full context of how the DNA got there. In forensic situations, DNA evidence must be considered with other evidence.

Can support

A DNA match, exclusion, biological relationship, or similarity between samples.

Cannot prove alone

The time DNA was deposited, the full context of an event, or guilt without other evidence.

Discussion task: DNA profiling response

This task is the DNA profiling half of your biotechnology discussion work. Choose one of the processes from this lesson and explain it clearly enough that another student could understand it without you speaking over the top of it.

Option A: PCR

Explain how PCR amplifies selected DNA regions and why this is useful before DNA analysis.

Option B: Gel electrophoresis

Explain how DNA fragments move through a gel and why shorter fragments travel further.

Option C: DNA profile interpretation

Explain how banding patterns are compared and what kind of conclusions they can support.

Your response should explain:

what the process is used for
the key molecules, tools, or structures involved
how the process works, in a logical order
one limitation, risk, or common misunderstanding linked to the process

Plan your response here:

Process chosen:

Purpose:

Key tools or structures:

Main steps:

Limitation or common misunderstanding:

Writing support

A clear response might begin like this: The process I have chosen is __________. It is used to __________. It works by __________. This matters because __________. A common misunderstanding is __________.

Keep your explanation specific. For example, instead of writing "the gel sorts DNA", explain that DNA is negatively charged, moves towards the positive end, and shorter fragments travel further through the gel.

Final checkpoint

Answer this in full sentences. This is the main chain of ideas from the whole lesson.

Question: Explain how PCR and gel electrophoresis work together to produce a DNA profile. Your answer should include why PCR is used, how the gel separates fragments, and how the banding pattern is interpreted.

Quick self-check before you finish

I can explain why PCR is used before DNA profiling.
I can describe denaturation, annealing, and extension in PCR.
I can explain why STRs can produce fragments of different lengths.
I can explain why DNA moves towards the positive end of a gel.
I can explain why shorter DNA fragments travel further than longer fragments.
I can use band positions to compare DNA profiles.
I can describe one limitation of DNA profiling evidence.