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

On Mon, Feb 24, 2014 at 7:54 PM, L <lakopa.palumbo@gmail.com> wrote:
>
> I completely agree, and that is exactly the kind of technology we want to
> build this chip on. That's why I bring this up now after staying quiet for
> so long. I realized this idea of a read/write chip for DNA was getting no
> where within the University I'm at because of how small and perhaps
> over-academic the pool of people is, so I'm opening it up. Let people try to
> patent it; we'll slap an open-source license on it faster than they can say
> "patent pending." The only way for a community to get things done is through
> trust, and I trust all of you.

I'm literally saying I want to do this to pay off my school loans, and
that I wouldn't want to release my plans, secrets, or sell devices.
I'd sell DNA as a service to begin, not at cost but likely
orders-of-magnitude cheaper than current market prices. I'm also
concerned with specific legal matters like ITAR (because I'm in the
U.S.) and, practical matters like nefarious powers whipping up
bioweapons.

The verbiage as-is is still a bit unclear when it comes to
nucleotides, as they are 'parts' of DNA.
"1. "Genetic elements"include, inter alia, chromosomes,
genomes, plasmids, transposons, and vectors, whether
genetically modified or unmodified, or chemically synthesized
in whole or in part."

Section XIV subsection (m) of ITAR doesn't look to promising
('Technical data') for DNA synthesizers, since polynucleotides are
mentioned in XIV subsection (g).
http://www.pmddtc.state.gov/regulations_laws/documents/consolidated_itar/ITAR_Part121.pdf

>
> So, back to the true issue at hand: The actual read and write mechanisms.
> Let's try building a small list of options first, and then go through each
> and pick a top two in each category.

Most of that is on wikipedia.

>
> I'm partial to using carbon nanotubes as reaction centers because, as I said
> before, their size is easy to control, they are easy to make, and their
> properties are fairly well known at this point. We can use a static field to
> control their position on a chip down to nanometers, which is exactly what
> we need. The experimental setup wont be cheap, but we can wrangle something
> up and it's not like anything will be, that's the problem. A nanopore has no
> length,

That's completely wrong, there is generally some depth associated with them.

> so it wouldn't be all too useful as the actual reaction center of

Sure it would be, the whole point is to know where your reactions are
happening and decrease diffusion times.

> either read or write, though I like the idea of a layered microfluidic
> system. The challenge there would be to have DNA held in known locations,
> but that's something we can surmount.

The whole point of down-scaling in the first place is to beat your
'challenge', stuff is smaller so your statistics of where it can be
decreases significantly.

> Raman spectroscopy and gold nanoparticles are both up for the read "head,"
> but neither would be easy to do. Other ideas?

Actually not really, you need a good interference notch filter though
($100-$300). http://www.youtube.com/watch?v=tRrOdKW06sk


--
-Nathan

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