Exercises: DNA extraction

Explain in your own words what extracting DNA from a eukaryotic cell means, and name two simple materials from which cells can be obtained for the practical (for example, cheek cells or a fruit). Why should the material be thoroughly mashed before starting?

In the DNA extraction practical, washing-up liquid, salt and very cold alcohol are used. Explain the role of each reagent: which cellular structures the detergent dissolves, what the salt is used for, and what happens to the DNA when it comes into contact with the alcohol.

Look at the diagram of the test tube at the end of the DNA extraction practical. Identify what the labels ?1, ?2 and ?3 indicate (the alcohol layer, the aqueous extract with the dissolved DNA, and the DNA strands appearing at the interface), and explain why DNA concentrates precisely in that area.

These steps of the DNA extraction practical are out of order: add the very cold alcohol down the side of the tube without shaking; mash the material; prepare the mixture of water, salt and detergent; filter the mixture; collect the DNA strands with a rod. Put them in order and justify why each step should be in that position.

The alcohol in the practical must be very cold and should be poured carefully so that it forms a layer on top of the extract without mixing with it. Explain the advantage of the alcohol being cold for the solubility of DNA, and why the two layers should not mix.

At the end of the practical, a white cloudy layer formed by strands appears at the interface between the extract and the alcohol. Describe what is observed and explain what this material actually is — it is not a single molecule or the DNA of a single cell — and why it is visible to the naked eye when a single DNA molecule is not.

You want to extract DNA from a strawberry and an onion using the same protocol. Reason what adjustments you might need in mashing or in the amount of detergent depending on the hardness of each tissue, and predict from which one you expect to obtain more visible DNA, knowing that the strawberry is octoploid: its cells have eight sets of chromosomes instead of two.

During a plant DNA extraction practical, three groups obtain failed results:

• Group A: Blended the plant tissue in a blender at maximum power for ten minutes and does not observe strands, only a cloudy liquid without defined filaments.

• Group B: Added 96% alcohol at room temperature ($22\ ^\circ\text{C}$) instead of precooling it to $-20\ ^\circ\text{C}$, and observes hardly any precipitate at the interface.

• Group C: Vigorously stirred the test tube with a glass rod right after pouring the alcohol, and the fibers that were beginning to clump broke apart.

Justify what occurred at a physical or molecular level in each case to explain the failure of the extraction.

In a forensic investigation, a tiny biological sample is collected (a hair with a root containing barely a few dozen cells). A student claims: "We can use the homemade strawberry protocol: we crush it, add dish soap, salt, and alcohol, and then read the genes with a magnifying glass." Refute their claim by identifying three insurmountable limitations of this school method and justify which advanced techniques (such as PCR amplification or enzymatic purification) are essential in a real laboratory to analyze the sample.