Site-Directed Mutagenesis

Rafael Maldonado rafael at
Mon Mar 17 14:05:17 EST 1997

On Fri, 14 Mar 1997, Rani Geha wrote:
> My question is: Is there a preference as to which codon to chose 
> for a particular amino acid change, or can I chose any of the 
> codons that code for an amino acid?

You should choose codons used at the same rate than the one you are 
replacing, or very common codons so your protein is not affected with 
some rare codon. You will need a codon usage table for yeast. There are 
many around, and since the genome is completed already, probably they have 
got absolute numbers. Check:

> I am also constructing a C-terminally truncated form of the gene 
> by introding a stop codon near the C-terminus. Again, is there a 
> preference as to which stop codon to use, i.e. TAA, TAG, or TGA?

There are also preference for termination codons, and it looks like some 
are more effective than others. In yeast, the favorite codon is UAAG. 
Yes, it is a four bases codon, but in termination codons the fouth base 
is very important also. Check:

Brown et al (1990), NAR 18, 6339


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