What research/field would benefit most from cheaper synthetic DNA?

[Nathan McCorkle]

Just wondering what researchers are limited today other than us DIYers who want to screw around with different DNA combinations. Who else uses long DNA strands?

--
-Nathan

[Omri Drory]

It's not just for long DNA strands. My background is structural biology (protein crystallography) - I can't count the time I spent constructing plasmids to try different combinations of expression tags/expression systems/stability elements/etc/etc. I wish I could spend my time designing and running experiments - but most of my time was wasted in PCR-cloning. 

When I came to Stanford at 2007 the price of DNA was ~$2bp. when I left it was ~$0.39 so my lab moved to just ordering the genes already in the expression plasmids. If DNA was cheaper we would order much more (you never know what would crystalize - need to do tons of experiments) and would also order bigger things (a whole complexes, metabolic pathways, combinatorial libraries, etc). Cheaper DNA is a must in my opinion (and @#%@# those of little imagination that say they doesn't know what they will do with cheap DNA). 

One reason we started Genome Compiler was for seeing that future coming - why else build a software from the ground up that can handle any size sequence?

[Mega]

I assume there would be more start-ups wanting to change the world with their ideas. At least, I hope that ;) 

However, this is quite close to diy-bio, isn't it?

[Jeswin]

It would help us in our PCR assay development. We already order a lot
of different primers to find the one that can give the best qPCR
signals. We deal with highly polymorphic Hep B viral DNA so just
BLASTing won't give us the best primers

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[Nathan McCorkle]

Primers and probes aren't long DNAs though.

[Jeswin]

On Sun, Dec 9, 2012 at 5:11 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> Primers and probes aren't long DNAs though.
>

Is ordering a few long DNA more expensive than ordering many primers?

[Nathan McCorkle]

Yes

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[Patrik D'haeseleer]

Longer stretches of DNA are typically synthesized as shorter oligomers that are then stitched together.

The big differences lie in how much error correction and quality control is needed. When you're making oligos, you typically don't worry about having a small fraction of oligos with a single base error. However, when you're building longer constructs from error-prone oligos, you'll eventually get to the point where it becomes likely that every DNA strand you assembled contains one or more errors.

So you typically need to have much tighter control over how many errors get introduced at the oligo synthesis step, use methods for assembly that will automatically correct against errors, do QC at steps all along the process, and then sequence the resulting construct at the end to verify it is error free. That's a lot of overhead in addition to the oligo synthesis itself.

Patrik