Module 4 Assignment

In the paper by Scholz, Haring, Wittmann-Liebold, Ashman, Bagdasarian, and Scherzinger; Gene. 1989 Feb 20;75(2):271-88; they describe the sequence for a plasmid.

A.   Retrieve the abstract for this paper.

B.   Import the sequence into vectorNTI. Draw a plasmid map with only the following features:

1. Display all unique (i.e. cutting only once), 6-mer, blunt cutting restriction sites.
2. Display all CDS with the name of the coding sequence underneath the CDS arrow.
   If the molecule is a circle, place the CDS names inside the circle
3. Make all CDS arrows blue.

Because we are using the demo version, you can not email me the camera view. Tell me that you have done it!

C.   Design primers to amplify the ampicillin resistance encoding open reading frame from the plasmid pUC19. The PCR product should have a minimum annealing temperature of 70C

1. Which open reading frame is amplified from the primers?
2. How long is the PCR product?
3. What is the Tm of the PCR product and each of the two primers?
4. Do the two oligos that you designed have any hairpin loops, if so where and how long?
5. Do the two oligos hybridize to each other?

Paste the abstract, graphic, and other results into a microsoft word file and email it to Rob