Re: [DIYbio] Ultra-Cheap DNA Printing/Sequencing

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There have been a few papers on alternative reactions for DNA synthesis
that looked pretty promising, but I've never heard of them being
commercialised.

I wonder was that because someone tried them and failed to scale them
up, or because the risk involved is too high?

I can't believe it's the latter, because there's so much money to be
made with an alternative reaction that avoids the chain-branching issue,
but the former would surely have merited a follow-up paper..

Anyways, alternative reactions, if someone wants to try them, are where
the potential is I think. The phosphoramitide system is too prone to
side-branches, which limits the practical length of an oligo to only a
few hundred bases at most; I imagine most people make them only 100bp
long or so. Assembly and quality assurance are what add most of the cost
to the final gene; that's why a few companies offer such cheap 500bp
synth runs.

An alternative reaction without chain-branching, which can be recovered
as pure DNA using PCR, would be great. I've seen at least one paper on
this but lost it, and forgot the keywords! :( - It used a DNA analogue
for the synthesis step, which was compatible enough with DNA Polymerases
that it could be PCR'd into real DNA afterwards.

On 21/02/14 19:18, L wrote:
> Hey there,
>
> We all would love to be able to print DNA as cheaply and easily as we can
> print a copy of a article. This would transcend printing just oglio
> primers. Every day I wish I could print whole genomes, and I'm sure most of
> you do as well.
>
> The issue: printing large DNA fragments costs about $0.35 a base, $0.10 at
> best. (Gen9)
>
> This means that a 1 kb gene would cost $350 to make. Imagine the cost of
> printing 20 variants of that gene and testing the expression product of
> each to figure out exactly which version of your synthetic protein works
> best for you. The cost would be insane. What if compiling a 350-line C++
> program cost even just $50. *Programming would be reserved to graduate
> schools, just as synthetic biology is today. *
>
> Designing and successfully generating synthetic genomes in a garage for
> less than $500 per genome is necessary for the biotech revolution to play
> out even half as well as the computer revolution did. Thus, it's evident to
> all of us that DNA printing needs a massive cost reduction.
>
> While organizations like Cambrian Genomics and Gen9 are doing great work
> quickly, they are still mainly limited to academia even though I know that
> neither wants to be. (Especially Cambrian)
>
> Perhaps it's time that we at DIYBio came up with our own means of DNA
> printing and sequencing. It may be rough and inaccurate at first, but I'm
> certain that the project will take off within a year or so, and eventually
> become industry-standard. It would be like the GNU/Linux of synthetic
> biology. ;)
>
> As a seed idea, we could use carbon nanotubes created using vapor
> deposition around nickle nanoparticles of around 12 nm in diameter. Then,
> in an argon atmosphere, the nanotubes would be doped with gold atoms on one
> side. DNA would be pulled through a stack of these nanotubes as in
> electrophoresis (from a positive charge to a negative one of the other side
> of the chamber) and surface interactions with the DNA bases could be
> monitored through the gold nanoparticles. It wouldn't be easy to pull off,
> but one divide could shotgun sequence DNA incredibly quickly with a high
> degree of accuracy. As for printing, DNA would be produced conventionally,
> but this time with a small laser at the end of the carbon nanotubes. If the
> DNA currently running through any given carbon nanotube did not match the
> desired strand, the laser at the end would activate, destroying the strand.
>
> Production of a device like that would not be something everyone was doing,
> but rather something in the public domain that any company could
> manufacture. We don't make our own CPUs, nor would they be easy to make at
> home (by not easy I mean virtually impossible), but we all know how to use
> them. Just like the modern CPU, however, we can do something that follows
> the same idea, just is much less efficient. From there, increasing purity
> would be all that is required.
>
> I would love to hear your ideas.
>
> -L
>

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