DIY DNA synthesis?

[Koeng]

Hello all! I was recently thinking about how wonderful it would be to be able to synthesize my own primers (Since I do not use restrictive enzymes in cloning). Has anyone done it? I was thinking about the 3D printer to make reactions and perhaps that could work... although I do not exactly know all the steps in synthesis... Anyone please put your 2 cents!

Koeng

[Avery louie]

It can be done.  There is an open source DNA printer that it stupid expensive called POSAM, and you can buy used machines.

--A

On Mon, Mar 11, 2013 at 10:43 AM, Koeng <koen...@gmail.com> wrote:

Hello all! I was recently thinking about how wonderful it would be to be able to synthesize my own primers (Since I do not use restrictive enzymes in cloning). Has anyone done it? I was thinking about the 3D printer to make reactions and perhaps that could work... although I do not exactly know all the steps in synthesis... Anyone please put your 2 cents!

Koeng

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[J Adams]

A system is offered by Azco Biotech called the OligoArray for making oligos on a chip using electronic deprotection.  Please look into this instrument as well.  We also offer refurbished versions of this instrument.

 

You may want to consider purchasing a couple of oligo pools to make sure it works before either building your own POSAM or purchasing an OligoArray.  Purchasing pools is fairly inexpensive and will provide a good proof of concept test.

 

I hope this too helps.

 

Regards;

 

 

 

J Adams

[Patrik D'haeseleer]

This was one of the applications we looked at for our bioprinter. We decided not to pursue this because IIRC the chemistry is rather toxic.

One important thing to keep in mind that oligo synthesis is really getting commoditized. It's definitely not as cheap as sequencing, but it seems to be growing on a similar exponential trend - just a couple years behind sequencing. So it's highly unlikely you'll be able to throw something together that will be anywhere near competitive with just farming out your oligo synthesis somewhere.

It would definitely be a great learning experience, and you may want to pursue it for that reason alone. But chances are you'll spend orders of magnitude more effort, time and money per oligo than if you just ordered them commercially. And then you'd still have to do sequencing to check that your oligo was synthesized correctly.

Patrik

[Bryan Bishop]

On Mon, Mar 11, 2013 at 5:01 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:
> One important thing to keep in mind that oligo synthesis is really getting
> commoditized. It's definitely not as cheap as sequencing, but it seems to be
> growing on a similar exponential trend - just a couple years behind
> sequencing.

The graphs/trends don't seem to support that. Oligonucleotide
synthesis has been more or less at the same place for a few years now.
Also, assembly time is all over the map (weeks - months) for longer
sequences.

- Bryan
http://heybryan.org/
1 512 203 0507

[Patrik D'haeseleer]

Do you have any current data along these lines? I'm going by some graphs I've seen George Church and others present a while back, but I've seen precious little new data. Even in DNA sequencing, most of the graphs I keep seeing tends to be a couple of years old by now ($1000 genome by end of 2012 - really?)

I'd love to some data that's a little less stale by now - especially for a field that is developing this rapidly.

Patrik

[J Adams]

Oligo synthesis is Very Old technology where there was a big drop in price that corresponded to the end of the Carruthers patent.  Today, the cost and thus price for traditional oligo synthesis is very stable and not likely to change because the raw materials vendors and oligo houses are surviving with very little, if any, profit.

But, there are a couple of new companies such as Cambrian Genomics in San Francisco that are employing new technology to allow them to reduce the costs of oligo synthesis by orders of magnitude.  If companies like Cambrian are successful (co founded by Church) you will likely see a dramatic drop in the cost of synthetic, I've been told dow to a few cents per base pair.

Please check out this company...

J Adams

Azco Biotech, Inc.

3626 Ocean Ranch Blvd.

Oceanside, CA 92056

t. 858-525-2770

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[Koeng]

Thanks everyone, those are some very interesting companies :D

Koeng

On Monday, March 11, 2013 7:43:09 AM UTC-7, Koeng wrote:

[Ashley Heath]

I think it is true as Patrik indicated that this very much depends upon what you want to get out  of it. For example, if you buy primers for PCR from SIGMA the list price starts at 32 cents per base (US pricing of course). So, around $12 for a pair of primers of typical length. In some cases and maybe from other companies you might pay even less. So it would not it seems to me be worth launching a 3D printing project just for that, it would cost way too much. Learning about 3D and oligo synthesis (and maybe launching your own company??) now that's something else!

[Koeng]

That saddens me to see that. I would not see why in the WORLD they would not ship to us DIY people... Wish there was a reagent version of OpenBioTech....

On Monday, March 11, 2013 7:43:09 AM UTC-7, Koeng wrote:

[Avery louie]

You have to shop around, but I think that while being able to print oligos is nice, there is really no reason unless you absolutely cannot get primers, to print your own.  As for reagents, Edvotek sells buffers/agarose on amazon for crying out loud (although, I am not sure if they sold me TAE or TBE...).

A useful thing to print would be DNA/RNA microarrays.  Those are still expensive, I think?

@paul: I would direct you to Carl Sagans quote "If you wish to make an apple pie from scratch, you must first invent the universe.".  The reason we can do cool things (barcoding, for example) is by working within the framework of molecular biology, but without the limitations of a need to publish or make money.  If we wanted to do it ourselves at the level you mentioned, we should at least start growing forests of sea-weed to extract agar from!

--A

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[SC]

Hello,

Patrick is correct.  Primers are inexpensive to buy, but the companies that make them have purhcased expensive equipment.  Also, the research reagents to make the primers are expensive and perishable.  It really only makes financial sense to make your own if you need a large quantity.  If you are only doing a few experiments, you're much better off buying them premade. 

[Mega]

> A recent thread on the OpenPCR forum was from a guy in the UK who found that the local companies who made PCR supplies, ranging from primers to agarose, would not sell him anything.  As long as we're dependent on   > biotech corporations for materials can we truly be "Do-It-Yourself"?

When you build a house DIY  and you don't burn the bricks from sludge - is it still DIY ?

:D 

[Nathan McCorkle]

if we could amass some info on nanofludiic channels, I have access to
nano milling equipment to make them. I think it would be worth
exploring terminal transferase trapping via a nano sieve and adding
single nucleotide triphosphates to grow the chain. I was reading a
patent on watching the concentration of low molarity nucleotides with
raman spectrosopy recently, it basically needs a gold surface and a
laser and a cutoff filter to detect.

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[Cathal Garvey]

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This issue crops up again and again; is it DIY if you use convenient
higher-level-abstraction-X?

My opinion is that we should aspire to being *capable* of doing
everything from the ground up, firing our own bricks from sludge, as
it were, but that we shouldn't feel *compelled* to when we don't need to.

So, while I avail happily of DNA synthesis services, because doing it
myself would be very difficult/expensive using presently available
methods and equipment, I aspire to being *able* to do DIY DNA
synthesis one way or another, someday. Even so, when I have a DIY DNA
synthesiser on my desk, I'll still probably order from a company
unless my synthesiser is improbably efficient and easy to use, for the
same reason I buy bricks from brick-sellers*.

*Actually I'd avoid buying bricks because their manufacture is so
polluting; were I to build a house today I'd probably use straw-bale
walls for their low cost, high insulation value, ease of construction
and low environmental impact! DIY FTW.

On 04/01/2013 10:12 AM, Mega wrote:
>> A recent thread on the OpenPCR forum

> <http://openpcr.org/forums/index.php?p=/discussion/21/obtaining-chemistry-in-the-uk>

> was from a guy in the UK who found that the local companies who

> made PCR supplies, ranging from primers to /agarose/, would not

> sell him anything. As long as we're dependent on > biotech
> corporations for materials can we truly be "Do-It-Yourself"?
>
>
> When you build a house DIY and you don't burn the bricks from
> sludge - is it still DIY ?
>
>
> :D

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[J Adams]

Hi Cathy;

Very nice response...Even as a DIY'r, when it is cheaper to simply purchase
than do yourself, then purchase. Let your energy be spent doing things that
have not been done before, or if they have that you can do cheaper, faster
or better than existing technologies.

DNA synthesis is sold for almost the cost of the raw materials. You can
never build a system yourself that will compete in a cost effective manner
with IDT, Operon, Sigma and others. These guys have had years of experience
optimizing their processes and they buy raw materials in such bulk
quantities that their costs per unit are almost zero!

So, it's best to spend your time fixing problems that you can...(but, who
knows, maybe there is a way that I've or nobody else has every thought
about, just with this technology, since it's been around 30 or more years
with a lot of very bright people working in the field for a long time) it's
highly improbable!

My 2 cents in support of Cathy's response.






J Adams

-----Original Message-----
From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On Behalf Of

Cathal Garvey
Sent: Tuesday, April 02, 2013 5:21 AM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] Re: DIY DNA synthesis?

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[Cathal Garvey]

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> You can never build a system yourself that will compete in a cost
> effective manner with IDT, Operon, Sigma and others.

Well, we'll see about that! Just, when I have more time to hack. :)
- - Cathal

On 04/02/2013 02:23 PM, J Adams wrote:
> Hi Cathy;
>
> Very nice response...Even as a DIY'r, when it is cheaper to simply
> purchase than do yourself, then purchase. Let your energy be spent
> doing things that have not been done before, or if they have that
> you can do cheaper, faster or better than existing technologies.
>
> DNA synthesis is sold for almost the cost of the raw materials.
> You can never build a system yourself that will compete in a cost
> effective manner with IDT, Operon, Sigma and others. These guys
> have had years of experience optimizing their processes and they
> buy raw materials in such bulk quantities that their costs per unit
> are almost zero!
>
> So, it's best to spend your time fixing problems that you
> can...(but, who knows, maybe there is a way that I've or nobody
> else has every thought about, just with this technology, since it's
> been around 30 or more years with a lot of very bright people
> working in the field for a long time) it's highly improbable!
>
> My 2 cents in support of Cathy's response.
>
>
>
>
>
>
> J Adams
>
> -----Original Message----- From: diy...@googlegroups.com
> [mailto:diy...@googlegroups.com] On Behalf Of Cathal Garvey Sent:
> Tuesday, April 02, 2013 5:21 AM To: diy...@googlegroups.com
> Subject: Re: [DIYbio] Re: DIY DNA synthesis?
>

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