Re: [DIYbio] Synthetic promoters

It cost nothing since they could not synthesize it. If I want it I may just PCR it up and clone it the old fashioned way.

On Thursday, August 30, 2012 9:56:22 PM UTC-4, phillyj wrote:

I don't know much about how companies synthesize oligos so what was
the reason for the failure? Too high GC content and other stability
issues?

I know we did some custom synthesis by PCR for a client since they had
trouble getting the synthesis companies to create it. Maybe you have
to go down that road?

By the way, how much did it cost you for this promoter at Operon?

On Thu, Aug 30, 2012 at 4:29 PM, Tom Randall <tara...@gmail.com> wrote:
>
>
> On Thursday, August 30, 2012 3:46:48 PM UTC-4, Dakota wrote:
>>
>> This is pretty neat, if I remember you are the one that payed to get the
>> Neurospora genome sequenced for your own data?
>>
>>
>> How did you go about chosing these 1014 bps for your synthetic promoter?
>> I imagine there are multiple promoter sequences, what about an entirely new
>> one?
>>
>>
>> http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000006085103696
>>
>>
>> http://www.broadinstitute.org/annotation/genome/neurospora/GeneNeighborhoodPage.html?sp=kGene%2F7000006085103696
>>
>> I was just messing around looking at the H1 gene, but I get so lost in
>> genome software and usually quit from frustration.  I just want to see the
>> ssDNA sequence upstream and downstream of that gene but can't figure out
>> how.
>>
>> Out of curiosity, why are those repeat homopolymers needed?  The cytosine
>> run of 11 bp's in the already rich GC area seems to be something they had
>> trouble with.
>>
>> Unfortunately I do not have experience with this to offer any help, but it
>> is a pretty sweet project!
>
>
> I just picked that sequence since somebody else had used it in a construct
> as a promoter and it was sufficient to drive expression, cant remember the
> reference offhand. I dont know why those repeats are needed, or if any
> detailed promoter bashing of this sequence has been done, likely not. Why
> they are there? Either they are needed or an evolutionary accident I
> suppose.
>
> The Broad display of this genome is a bit clunky, but I find it easier to
> use that the version at Ensembl Genomes, and the UCSC Browser people do not
> do much support of micro-organisms.
>
> Funny you should ask about the genome, I just put up the current status of
> that project in a different post, the link is below.
>
> http://www.roningenetics.org/Sequencing.html
>
>
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