BNFO 491 
Molecular Biology Through Discovery
Crick et al (1961) simulation - Documentation
Description of the MUTAGENIZE function
Fall 2012 



This function (see A) enables you to mutegenize a derivative of bacteriophage T4 (or the phage itself) with acridine yellow. The mutagenized phage may be used to infect either E. coli B or K12. You'll want to use this function to generate suppressor mutations of T4 strain FC0, for example.

The number box should contain the number of phage to be mutagenized. How to choose that number is discussed later.

To select the phage strain to be mutagenized, click the strain entry box (the box will turn white and become highlighted with red dots; see B), and select a strain from the VARIABLES menu (the strains you see may differ from those in the figure shown at the right).

To select the E.coli strain to be infected, mouse over the green arrow Option icon, select either strain, and then click Apply (see C).

When both boxes have been filled in and an E.coli strain has been selected, then execute the function by double clicking MUTAGENIZE

Output
If no plaques are produced by the infection, you'll see a message at the bottom of the screen (see D). Otherwise a popup window will appear listing the phenotypes of all the plaques (see E).

Screenshot A
MUTAGENIZE function
Screenshot B MUTAGENIZE strain selection
Screenshot C
MUTAGENIZE options

Screenshot D           and           Screenshot E
MUTAGENIZE no output   MUTAGENIZE output

Warning!
You should expect that mutations in a specific gene are quite rare. If they weren't, then many other genes in the phage would also be mutated and the phage would be unlikely to survive. Therefore, you will need to examine a large number of wild-type plaques before you find a mutant plaque. By default, BioBIKE limits you to 500 lines of output. If you want to raise this number, mouse over the black SESSIONS button and click Preferences. Then change the current value of *OUTPUT-LINES-LIMIT* to whatever number you want and click Set These.

You might well profit from a visit to the page How many phages to use in experiments.