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.

Restriction map of a plasmid

Here's more practice for you to use to create a restriction map.  Dr. Bird did another post on this type of exercise.

You can assume the plasmid is circular.  Note that there is more than one solution to this exercise!

 

... and here's the way to find the solutions!

Chromosome inversions and Meiosis

Here's a typical problem involving a chromosome inversion.  Your task is to find out what the end products of meiosis (i.e. haploid cells) will be after a specific crossover during prophase I.

Here's how I solve this:

You can see a full-screen version by clicking on the YouTube link.

Restriction Mapping example

Dr. Bird goes over this restriction mapping example.  Here are the data:

Create a circular restriction map from this.

The answer key is here:

 

You can make it larger by clicking on the YouTube logo in the bottom-right corner and making it full screen from the YouTube site. 

If you want more practice, go to this other blog post!

Sanger Sequencing

My first post in this section will be lazy:  here's a video.  It's good, though!  It's from http://www.dnai.org which is located in Cold Spring Harbor, New York.  They have wonderful lab facilities and are world-leaders in DNA education.

The solution is here:

Click on the YouTube logo at the bottom left of the window above to view a full-screen version.