9. Single Stranded Conformational Polymorphism (SSCP)
Sometimes we only want to find out if there is any difference between the sequence of bases in different animals. To find out if two animals have different versions of the same gene, we could either determine the entire sequence of the gene or we can screen using a technique called Single Stranded Conformational Polymorphism (SSCP), which is much cheaper and simpler than sequencing.
Although it sounds like a mouthful, the procedure is straight forward. When double stranded DNA - which is its 'natural' state - is made single stranded (a process called denaturation) it forms different structures and shapes (conformations) as it ties itself in a knot. The shape of this 'knot' is determined precisely by its sequence. If we run this on a gel (or through the automated sequencer) it will move at a rate that is determined by its shape. If different samples move at different rates we can be almost certain that it is because their DNA is different. This is called a polymorphism, and tells us a lot about the genetic structure of the group of animals that we are looking at.
If we want to look at the sequence of a gene for a large number of animals, we can screen first using SSCP so as to determine which animals have the same version. Once we know which ones are the same and which are different, we can choose one copy of each version for sequencing. This saves sequencing many copies of the same form of the gene.
We are using this technique in projects like:
- Genetic criteria for reserve selection
- Species diversity and genetic diversity of invertebrates in an agricultural woodland/landscape
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