Note: What are primers?

Primers are small pieces of DNA that bind to specific sequences—in this case, sequences within the 16S rRNA gene. In this lab, the two primers used, 27F and 1525R, bind to opposite ends of the gene, one on each DNA strand. Once the primers bind, DNA polymerase extends the DNA from the 5' end to the 3' end. The primers are selected so that as the two new copies are made, they overlap in the region of interest (see animation for illustration).

These primers are "universal," meaning that they bind to and thus copy the 16S rRNA gene from any bacterial species (except perhaps for the most unusual ones). This is because the sequences to which the primers bind are extremely similar among all bacterial species.

You might ask, If they are similar, how can you use them to identify different bacterial species? Doesn't that require uniquely different signatures? The answer is that some parts of a gene are extremely similar among different species (i.e., highly conserved) while others are highly variable. Universal primers bind to the highly conserved regions of genes so that they can be used to copy DNA from a variety of species of bacteria. The variable regions, which differ between species, are used for identification.