Codon optimization, does it matter? - (Nov/04/2006 )

I've created a construct with a 6xHis-tag using CAT CAT CAT CAT CAT CAT. I noticed in some commerical vectors they'll use combinations of CAT with CAC.

I would like to maximize expression, but would codon usage matter in this case? Are these two codons covered by a single tRNA's or two?

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There is a very strong bias for CAC (70%) usage in Class II gene... which are genes strongly expressed during exponential growth. More over the His tRNA that uses the CAC codon is nearly 2 times more abundant then the CAU tRNA.

If anything I would lean more towards a Histag richer in CAC codons for maximal efficiency. With the occasional CAT to break the CAC repeat. Using six consequitive CAC codons might cause problems, as the primer melting temperature would go through the roof and a repeat like that coud cause problems during PCR... base skipping and such..

CODON USAGE

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Thanks.

I should have said I'm expressing in insect cells, not e. coli.

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Ah... thus my suggestion is now in error. Well I guess you should go look up the codon usage of your insert species and see if there is any bias. It probably has, but could be biased toward CAT for all I know.

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