The Basics

Polymerase Chain Reaction (PCR) is one method of producing mass quantities of DNA for experimental use.  In this process, a strand of DNA is added to a solution containing   individual nucleotides, DNA polymerase, and synthesized sequences of nucleotides called primers which define what section of the DNA is amplified.  The solution is then heated to nearly 100 degrees Centigrade, at which point the hydrogen bonds between the two DNA strands break.  While cooling, the synthesized primers bind to their complimentary regions on the separated DNA strands.  From there the DNA polymerase recognizes the primers as starting points and begin moving down the DNA strands, adding a complimentary nucleotide for each nucleotide on the template DNA. The end result is two new DNA molecules, each one single stranded before the primer and double stranded after the primer (Samson, 1996).

When the solution is heated again, the new DNA strands melt, allowing primers to attach to the appropriate site, and the process continues until one decides enough DNA has been made.  This shouldn't be very much time, since the amount of  DNA is doubled each time the cycle is enacted.

One problem posed by this method is that most DNA polymerases dissociate, or unfold, well before 100 C.  To solve this, DNA polymerases from a bacterium living in hot springs, which have evolved to function in boiling water, is used. 

Electrophoresis

After a large amount of DNA has been replicated, each sample is run out on an agarose gel.  Because different lengths of DNA move through the gel at different speeds (the smaller the molecule, the more rapid the movement) the length of DNA can be compared.  In our experiment, those who have the mutant CCR-5 allele, which is 32 base-pairs shorter than the wild-type, will have their DNA move more quickly through the gel.  The positions of the DNA in relation to each other and to a reference run of known molecular weights can be compared visually, and recorded by taking a simple picture of the gel after staining the DNA with ethidium bromide.