adding kozak sequence to primer

Peter Ellis via methods%40net.bio.net (by pjie2 from cam.ac.uk)
Wed Oct 28 11:10:54 EST 2009


Cathal Garvey wrote:
> Using the Kozak you have is just fine, I'd say. It's a "Consensus" sequence,
> which means the standard Kozak you find online is the average of hundreds or
> thousands of sequenced Kozaks from natural sequences. Slight deviations from
> the consensus are the norm, and shouldn't have a huge impact. In fact, it
> may be an important part of the gene's natural regulation.
> 
> If you have the time and resources to replace the nucleotide and bring it to
> full consensus, it might be worth it just to have the sequence on hand in
> the future. And it might look better on a paper, though personally I
> wouldn't nitpick such small details if I were reviewing it.


I think it would be a very bad idea to change it.  It's a non-synonymous 
substitution, which means you have a non-zero risk of altering your 
protein's function.  Meanwhile, one presumes that the native gene gets 
translated fine despite not being a perfect match to the consensus.  So 
why change it?

Peter


More information about the Methods mailing list