How do Parkinson's researchers discover new knowledge? Part 1

I will attempt to explain how researchers do their work by describing the tools they use in pursuit of knowledge. These tools include:

1. Polymerase Chain Reaction (PCR) to generate lots of copies of DNA

2. DNA sequencing to read the letters of DNA

3. Expression Plasmids to generate lots of protein from specific genes 

We will see how these tools are used in discovering changes in DNA (i.e. mutations) that cause Parkinson’s.

From the clinic to DNA

A Parkinson’s sufferer is diagnosed and he tells the doctors that some of his relatives also have the disease. This indicates that a mutation causing Parkinson’s might be passed through the generations in this family.

The one thing that is guaranteed to be passed from generation to generation is DNA. DNA is made up of four different subunits (A, T, C, G) and we inherit 3 billion of these subunits. Mutations occur when one subunit is replaced by another. How do we find the one subunit that is mutated in this Parkinson’s family?

DNA mapping

The 3 billion subunits we inherit (collectively called a genome) have distinct landmarks. Imagine you are chasing a criminal and you hear he’s hiding in a house somewhere in London. London has distinctive landmarks and boroughs throughout the city; to find the criminal you split the city into sections and systematically check CCTV and eye witness statements in each section. Lets say there are lots of sightings of the criminal near Big Ben so you narrow your search to houses in that area.

Looking for mutations involves a similar principle but the landmarks in DNA are repeating subunits. For example, at a particular location in the genome there is a repeat that in different individuals will either be AAAAAAAAAA or AAAA. Within the Parkinson’s family sufferers have AAAAAAAAAA while non-sufferers have AAAA. This means that a mutation (e.g. G to T) originally occurred near the repeat in an AAAAAAAAAA individual and both the longer repeat and the mutation causing Parkinson’s are inherited together. Therefore, without knowing the exact location of the criminal we know the area he is in.

But how do we know which repeat is present?