Maximum distance between ATG & SP6 promoter

Nick Theodorakis nicholas_theodorakis at urmc.rochester.edu
Wed Nov 6 18:58:34 EST 2002


On 6 Nov 2002 14:05:14 -0800, rupertyip at msn.com (Studio401) wrote:

>I'd like to express a protein with a cDNA that contains ~180 bases
>upstream of the first ATG.  Will cloning this cDNA into an expression
>vector (with an SP6 promoter) express protein or is the ATG too far
>away from the SP6 promoter?
>
>Does anyone know if there is a maximum distance between the SP6
>promoter and the 1st ATG?  Is there are rule of thumb for such things?

For eukaryotic expression or prokaryotic? In eukaryotes, generally,
the longer  the 5'utr the greater the tendency to be translated
poorly. Generally, though, 180 bp is not too unusual. Upstream AUGs
are also bad for translation, as is too much secondary structure. In
prokaryotes, I don't think there is any length effect as long as there
is an appropriate Shine-Dalgarno sequence available at the right
place.

Nick


-- 
Nick Theodorakis
nicholas_theodorakis at urmc.rochester.edu



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