codon usage optimisation

Mizar molla-remove- at
Fri Mar 30 07:24:40 EST 2001

>I am currently re-designing the coding sequences of viral proteins in an
>expression vector
>in order to have them expressed in mammalian cells. Regarding codon usage
> I am not sure whether I should put the most commonly used codons all over
>(i.e. from a
>"human high" table) or  just change the most unfavorable codons.

I haven't direct experience, but I think that U should change
only unfavorable codons (e.g. don't change all different codons coding
for an amino acid in just the most commonly used one).
I also think that U should focus on the 5'-terminus of the cDNA
because codon bias in that position is more important then in other
part of cDNA (maybe this portion of DNA is also important for
stability of mRNA, but I can't give U clues about it).
Bye Gianluca

University of Insubria @ Varese (Italy)
gianluca.molla at

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