1. separating & probing DNA
module 2 – biotechnology & gene technologies

2. learning objectives Understand what gel electrophoresis is.
Understand the conditions required for gel electrophoresis to work.
Understand why different lengths of DNA move the way they do through the gel.
Understand why DNA probes are useful.

3. success criteria
State what is required for gel electrophoresis to work properly.
Explain why short sections of DNA move differently to long sections of DNA.
Describe the procedure used in gel electrophoresis.
Describe and explain why DNA probes are useful and where they can be used.

4. what is electrophoresis?
Electrophoresis is used to separate DNA fragments based on their size.
What are the enzymes used to cut DNA into smaller fragments called?
Electrophoresis is accurate enough to separate fragments of DNA that differ by only one base in length.
Restriction Enzymes
Electrophoresis gel showing radioactively labelled fragments of DNA.

5. the principle
The technique relies on the movement of DNA through a gel matrix.
Larger fragments are hindered and tend to move more slowly than small fragments.
But what causes the fragments to move at all?
DNA is negatively charged due to the many phosphate groups in each nucleotide
In an electric field, DNA fragments will move towards the anode (+ve electrode).
Which fragments would get there first?

6. Why is the gel not run indefinitely?
The DNA fragments are placed in ‘wells’ at one end of a gel plate.
The gel is made of agarose or polyacrylamide, which is similar to agar.
Remember that separation occurs because longer strands get caught up in the gel, whereas shorter strands move more quickly through it.
Cathode
(-)
Anode
(+)
Wells
Why is the gel not run indefinitely?

7. the apparatus

8. the procedure
The DNA samples are first treated with restriction enzymes to fragment them.
They are placed into wells at the cathode end of the gel.
The gel is immersed in electrolyte/buffer solution.
A current is passed through the solution for a fixed time.
The fragments of DNA move towards the anode due to the electrical gradient.
Shorter lengths of DNA move faster than longer lengths and so move further in the fixed time.
The position of the fragments can be shown using a dye, or fluorescent/radioactive labelling.

9. the results
If the fragments have been radioactively labelled, placing photographic film over the gel will produce something like this:
Further analysis may be required on the fragments.
They can be lifted from the gel by Southern Blotting.
A nylon sheet is simply placed on the gel and pressed firmly, transferring the fragments.

11. DNA probes

12. investigating a fragment
If one particular fragment that contains a particular gene is being searched for, DNA probes can be used to locate it.
DNA probes are simple, short and single-stranded sections of DNA.
They will bind (anneal) to complementary sections of other DNA strands.
Due to being labelled in some way, they make this ‘other DNA’ easily identifiable.
Labelling with radioactivity
Labelling with fluorescence

13. Page 169
Use this page of the textbook to find out what DNA probes are useful for.
Summarise how DNA probes are used for disease diagnosis.

14. plenary Answer the following questions:
What type of bonding is responsible for annealing?
Why is electrophoresis described as ‘similar to chromatography’?
Why must an electric field be applied over a gel for a fixed period of time?
Why is an electrolyte/buffer mix required to immerse the gel?
Suggest why it is important that DNA probes are relatively short molecules.

15. learning objectives Understand what gel electrophoresis is.
Understand the conditions required for gel electrophoresis to work.
Understand why different lengths of DNA move the way they do through the gel.
Understand why DNA probes are useful.

16. success criteria
State what is required for gel electrophoresis to work properly.
Explain why short sections of DNA move differently to long sections of DNA.
Describe the procedure used in gel electrophoresis.
Describe and explain why DNA probes are useful and where they can be used.