Primer Design Exercise

I gave my students a puzzle to work out.  There are three related dog-like creatures:  coyote, wolf, and dog, and not surprisingly they have very similar DNA for a section of their mitochondrial genomes.  The similarity is obvious when you line them up.  Where there is identical DNA, a consensus sequence (below the alignment) shows a capital letter:  mismatches or deletions (-) show a lower case.  The reason a dash is put into a region where nucleotides are deleted is to allow alignment of the regions on either side.

PCR uses short pieces of DNA to initiate replication starting at a very precise region.  You choose your primers based on DNA flanking what you wish to clone.  A good video showing how PCR works is available from McGraw-Hill, as well as another here, although the Internet is full of great videos.  PCR is a staple of laboratories, so you can find what you want fairly easily.  Whatever you do, though, don't go to this site that advertizes thermocyclers!  (If you clicked on that link anyway, I dare you to get the song out of your head).

Here's the question.  Give it a try before looking at the solution video:

The solution is below.