Designing Primers

Today you will formulate a hypothesis about the organization of the Mozy genome. You will also design primers that you can use in PCR reactions to test your hypothesis.

These links may be useful to you:

Use BLAST, restrictionmapper.org, the restriction maps that you have already done, and the following image to formulate a hypotheiss about where our contigs fit into the complete Mozy genome.

Please turn in your answers to the following questions.

  1. What do you consider to be the most likely order of the Mozy contigs in the finished genome?
  2. Is the DNA that was purified from Mozy capsids more likely to be linear or circular? Why?
  3. How can PCR be used to test your prediction?
  4. How big do you expect the PCR products to be?
  5. What are the sequences of the primers that you would like to order? (Remember that all DNA sequences should be written 5'->3', but keep in mind the strand of DNA to which they will anneal.)