
DNA is now DIY: OpenPCR ships worldwide - minouye
http://openpcr.org/2011/07/dna-is-now-diy-openpcr-ships-worldwide/
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anateus
I'll summarize how this would be used for those new to biotech:

\- You buy some primers which are basically chunks of nucleic acid that match
whatever gene you want to look at.

\- You put DNA you've extracted together with these primers into the PCR
machine. This makes lots of copies of the gene you're interested in.

\- Then you put the resultant amplified DNA into an electrophoresis gel box
(such as the one sold by <http://www.pearlbiotech.com/> who also provide free
plans. This is also run by Tito Jankowski of the OpenPCR project) which lets
you look at the actual genotype (you compare the striations from your sample
against other samples or a reference).

Primers are cheap and easy to get hold of and as other comments mentioned
there are various software tools for letting you design them (you then place
an order with a company like Invitrogen).

 _Edited to add:_

The reason you need to amplify stuff is because biology is annoying like that.
Let's use a simile:

If particle physics is figuring out how a watch works by smashing it against a
wall and studying the debris

Then biotech is throwing gears and springs into a test tube and carefully
stirring at certain temperatures until you can hear ticking.

~~~
oasisbob
That's a good summary.

To put it another way, this is really just a box that does programmed
temperature cycling. This is a critical part of PCR, but there's nothing too
terribly high-tech here. PCR is a relatively simple process.

PCR is frustrating for the undergrad? Sometimes. Historically dependent on
overpriced equipment? Absolutely. Dependent on small temperature variations?
You bet. Complex overall? No.

~~~
Cixelyn
Yup. Highschool / Undergraduate labs that teach PCR with two water baths and a
stopwatch really kill a lot of the "magic" bestowed on these absurdly
expensive machines.

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pw
Whenever I come across this sort of DIY (or at least low-end) biotech I
wonder, "Is this what computers looked like before the PC revolution?" I'm
sure that's a terrible comparison, but it's easy to make, and there's just
enough substance to it that I wonder if I'm missing out on the next revolution
by not being involved in biotech.

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Geee
What can I exactly do with it? Can I find any gene and how does that really
work? The video introduced some gels which reveal the DNA bits, but without
further info it's not clear how does it find a particular gene. Really awesome
stuff anyway.

~~~
austinc
PCR requires short (typically synthesized) DNA primers to initiate
replication. That is, you must know the DNA sequences at the beginning and end
of the region you want to amplify. Ideally you would know the entire sequence
so you can synthesize primers that have one and only one binding site.

Amplifying DNA is useful/necessary for all sorts of biological procedures.
High concentrations of DNA are needed for efficiently transfecting microbes,
for example.

~~~
rflrob
Fortunately, primers are relatively cheap, typically under $0.30/base, so for
two 20bp primers, you may end up paying as much for shipping as for the
synthesis itself.

These days, it's also pretty rare that you won't know the complete genome of
the species you're working with, and there are free web tools that can help
you design unique primers.

~~~
wvoq

      there are free web tools that can help you design unique primers.
    

True, but if you are going to your own PCR, you might as well do your own
primer design. It's practically the "hello, world!" of bioinformatics, not to
mention that a primer design server might not be able to help you if you're
trying to do something fancy.

~~~
tito
Wow, you all know a surprising amount about PCR! Are any of you regular PCR
users?

Tito OpenPCR

~~~
wvoq
Hey Tito, congrats on shipping! This is Patrick from Baltimore-- we talked for
a bit at iGEM and the FBI DIY-BIO thing last year.

In the dry lab, I'm really more of a regular PCR _consumer_ than a regular PCR
_user_ , but yeah, my attitude towards PCR is more or less my attitude towards
snakes: try to keep a respectful distance :-)

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angdis
Really cool stuff.

Of course, you need to get the sequence after you've got your amplified DNA.
That involves performing electrophoresis or using a more modern DNA sequencer
machine.

Questions:

Do people still work with gels and electrophoresis anymore? That seems like a
barrier for a DIY shop. Not only does it involve a lot of equipment, but the
interpretation of results seems like it would be hard.

Is it possible to send out the amplified DNA and get it sequenced by a
service? I know that sequencing costs have gone down drastically with new
technology, perhaps the DIYer can benefit from that?

~~~
tito
Yes, DNA sequencing is about $5 to $10 a sample. Just send in your DNA!

Electrophoresis is nice and fast relative to sending in your sample, but
currently much more complicated than dropping a tube of DNA in the mail.

Tito

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skeletonjelly
What's your typical use case for one of these? I've read the wiki page on PCR
but I still don't see it.

~~~
tito
Hi, Tito here from OpenPCR. That's a fantastic question! The typical use case
for PCR is "doing stuff with DNA" along the lines of what you read on the wiki
page about PCR. We hope that OpenpCR will enable _new_ uses of PCR, where
perhaps the user doesn't need to know much about DNA. What if PCR could "tell
you whether you have the flu or a cold", or "is this sushi really yellowfin
tuna", or "is this genetically modified corn?". What do you think of those
apps?

Tito

~~~
rflrob
The first two definitely seem like things that one could easily imagine a kit
for: include primers for the species of interest, a bit of positive control,
and perhaps even the Taq and other reagents you'd need. Then, the user could
just collect their sample and run the PCR and a gel.

The third might be a bit harder to make a commercial kit for while steering
clear of patents. It's also not clear to me what kinds of samples you'd be
able to test. An ear of fresh corn would probably work, but what about
(un-)popped popcorn, or cornflakes, or corn starch? It would definitely take
some experimentation.

To make these kits really user friendly, ideally you could figure out some
quick, easy way to determine the result of the PCR without running a gel,
which require a relatively high voltage DC power supply and usually use
Ethidium Bromide (a chemical that, depending on who you believe, is either
nasty or really, _really_ nasty) and UV light. I'm thinking maybe some kind of
spectrophotometer-like setup, which are used in things like a NanoDrop, but I
don't know how easy/economical it would be to build a DIY-level work-alike.

~~~
tito
GMO testing: there's a kit available for high schoolers (and we've used it
too)
[http://www.carolina.com/category/teacher+resources/classroom...](http://www.carolina.com/category/teacher+resources/classroom+activities/detecting+transgenes+in+genetically+modified+foods.do)

Pretty sweet!

Tito

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minouye
Looks like the site might be down--here's a repost of most of the content on
Make Magazine's blog:

[http://blog.makezine.com/archive/2011/07/dna-is-now-diy-
open...](http://blog.makezine.com/archive/2011/07/dna-is-now-diy-openpcr-
ships-worldwide.html)

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brettevans
I just built our KickStarter ordered OpenPCR today. The directions were easy
to follow. And the assembled version is strong. Waiting on our order for a
dremelfuge (a centrifuge attachment for a dremel) and our electrophoresis box.
Can't wait to try it out!

~~~
tito
You rock, Brett! Tito

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JunkDNA
I have been out of the lab for a while, but as I recall the consumables were
an expensive part of PCR. Taq polymerase used to be pretty costly. Perhaps
scale has caused that to come down recently? I see a lot of comments from
hackers here questioning why this would be useful. In general, you can't get
anything done in molecular biology without PCR. It's a critical tool for
manipulating DNA. If you're going to do even the most basic biological
manipulation (inserting genes into E. coli, comparing dan samples, amplifying
small quantities of DNA for further work, etc...) you _need_ PCR.

~~~
tito
Yes, the cost of the reagents (taq++) is now cheap, about ~$1 per run, and DNA
sequencing is cheap ($5 to $10 a run).

Tito

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d136o
That's disruptive tech. Very impressive guys.

Could you talk about the most difficult technical challenge you came across?
The temperature regulation (i.e. the heart of the pcr machine) seems to me
like the toughest part to get right.

I had the luck of working in a couple of well funded research labs, and I
wonder if some of the tall prices we see for this type of lab equipment is due
to "using someone else's" money for research.

In any case, I'm sure there'll be plenty of cash strapped labs around the
world who'll make some science with it.

~~~
tito
Thanks, we hope to get the word out to a lot of cash strapped labs.
Suggestions where find them?

Re: Challenges -- Sounds like a good title for a future blog post: "The
Toughest Challenge of OpenPCR". Off the top of my head, 2 challenging areas
were the mechanical design of the heated lid and super-hacking Arduino for our
USB control. For instance with the heated lid, we knew we had to have a flat
hot surface come down on top of the PCR tubes. We went through several
mechanical prototypes, and learned that the high tolerance of the heated lid
meant that the tolerance for the rest of the device needed to match. Not
giving you enough details at this point, but look out for that "challenges"
blog post in the future :)

Tito

~~~
d136o
I'll keep an eye out for that, it'll be an interesting read.

As to where to find cash strapped labs, definitely not the elite institutions
that we always hear of, but perhaps more local or state universities.

This might be a tool that international labs in less well funded countries
could appreciate, have you reached out internationally?

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viggity
Awesome! Are you guys going to make an open dna microarray next? ;)

<http://en.wikipedia.org/wiki/DNA_microarray>

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bh42222
This is fantastic!

Imagine you want to do something with DNA, perhaps you'd like to sequence
something, or stick some in on orange, or beer yeast.

So you have this bit of DNA, but it's so incredibly tiny and fragile, it's
almost not real, it's more like the idea of a thing then a thing.

So you use one of these PCR machines to make your idea real. You put your
tiny, fragile sequence in and out comes a robust bucket full of DNA!

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minikomi
As a former biotech grad now starting to finding my feet at contributing on
github, this just put a massive smile on my face.

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bhickey
Congrats on shipping, Tito. Glad to see you carrying the iGEM(-inspired) torch
onward.

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toisanji
so if I'm new to this, how can I use this machine to test out for diseases?
That seems like a good first practical use.

~~~
Cixelyn
Here's one way of doing it with a PCR machine:

1\. First find a risk gene of interest. You can find a gene name via flipping
through scientific articles about the disease, and then finding the exact
sequence of the gene on NCBI
([http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/inde...](http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml)).

2\. Design primers that amplify around the region of interest. ($15 maybe
tops?)

3\. Toss everything into a PCR machine and amplify it up. ($3 or so for per-
run reagents?)

4\. Take your amplified product and send it off for sequencing (another like
$10 or so?). When you get the sequence back, compare your sequence to the
published sequence and see how it looks!

There are a few caveats in primer design, and there are some other ways of
detecting disease markers, but this is one easy relatively low-cost approach.

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hackermom
Me and a friend helped out with a smaller sum each in the early phase of their
Kickstarter campaign - we're really glad to see the project was finalized!

~~~
tito
Thanks hackermom, we <3 u Tito

