The first step after collecting samples for genetic analyses is to extract the DNA. Lara and I do this for lancewood and five-finger plants (Pseudopanax) by:
- freezing a small piece of leaf tissue in liquid nitrogen (-196 degrees C !) and grinding it as finely as possible.
- adding a detergent to release the DNA from the cells of the leaf tissue.
- adding chloroform. The detergent and chloroform do not mix (like oil and water), but proteins and other things we do not want are drawn into the chloroform while the DNA is left in the detergent.
- the detergent layer is removed, and alcohol is added to it. This precipitates the DNA (i.e., makes it turn into a solid), and we can actually see it. I don’t have any pictures of Pseudopanax DNA, but precipitated DNA all looks much the same – see this link.
It is possible to extract DNA using household items (see this link).
In order to analyse the DNA further we have to make it go back into solution. The alcohol is tipped off, and a small amount of salt solution is added; the DNA ‘dissolves’ in this.
To test the quality and quantity of the extracted DNA, we run a small amount of the DNA solution on an agarose gel in a process called electrophoresis (see link).
In the gel above, each lane corresponds to a separate sample, except the right-most lane which is a ‘ladder’ for sizing the DNA samples. A negative charge was applied at the top and a positive charge at the bottom. DNA is negatively charged, so its moves towards a positive charge.
The bright blobs indicated by the green arrow indicate that we got high quality (the DNA is in big pieces, as it hasn’t moved very far) and quantity (a brighter stain indicates more DNA) for most of these samples, which is great!
The sample labelled 5957 (my collection number) is a bit weak, while we didn’t get anything for sample 5964.
These DNA extractions are all from samples of fierce lancewood (Pseudopanax ferox), except 5966 which is P. macintyrei.
The next step in assessing the relationships of these plants is to genetically ‘fingerprint’ them.