DNA Synthesizer under development

[Alex Murer [Open Biolab Graz Austria]]

Hey,


Just wanted to invite you to following along the development of our recent project, which is a dna synthesizer named KiloBaser. It's based on microfluidic and magnetic technology, open source and low cost. There are still challenges to overcome, but we are quite convinced to have a basic prototype soon. Our team started at the biohackerspace 'open biolab graz austria', currently working in Ireland for the summer.


FB: https://www.facebook.com/kilobaser.DNA.rapid.prototyping
Twitter: https://twitter.com/DNAPrototyper
Google: https://plus.google.com/109143331381566436146/posts


Best,
Alex Murer

[Bryan Bishop]

On Tue, Jun 17, 2014 at 10:05 AM, Alex Murer [Open Biolab Graz Austria] <alex.m...@gmail.com> wrote:

FB: https://www.facebook.com/kilobaser.DNA.rapid.prototyping
Twitter: https://twitter.com/DNAPrototyper
Google: https://plus.google.com/109143331381566436146/posts

Do you have any files to share that don't involve socila media websites? For example, svg of the layout would be nice.

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

[Alex Murer [Open Biolab Graz Austria]]

I can mail some pictures/videos of the prototyping process later today!

[J Adams]

Hi Alex;

 

I would like to know more!  Do you have a number I can call.  My company specializes in Oligo Synthesizers and is always looking for new options.

 

Regards;

 

 

J Adams

 

J Adams

Azco Biotech, Inc.

3626 Ocean Ranch Blvd

Oceanside, CA 92056

t. +1 858-259-9528

m. +1 858-525-2770

Skype. azcojadams

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[David Ng]

Can you share any details, such as write length, error rate and throughput? Can you do standard wobbles?
-Dave

[Alex Murer [Open Biolab Graz Austria]]

Hi,



Sure, sounds great. I'd suggest we schedule a call.


Phone: 0043 650 4223727

or else Skype: alexander.murer1

Mail: off...@briefcasebiotec.com


Best,
Alex

[Alex Murer [Open Biolab Graz Austria]]

Am Mittwoch, 18. Juni 2014 05:42:54 UTC+1 schrieb David Ng:

Can you share any details, such as write length, error rate and throughput? Can you do standard wobbles?
-Dave

I'd like to give you further details, but it's too early for reliable details, we are still in a early prototyping stage. A single module will have a single column, should provide similar write lenghts and error rates like usual column based synthesizers, but rather low throughput due to the microfluidics. It's rather designed to be a rapid dna prototyper, than for massiv amounts of dna.

Alex
 

[bioscisam]

Hi,

This sounds like a great idea. I'm involved with the London biohacking group and I'm interested in maybe doing some microfluidics stuff for somewhat related projects. Just wondering what kind of fabrication methods you're using and what kind of scales you're achieving?

Cheers,

Sam

[Alex Murer [Open Biolab Graz Austria]]

Hi Sam,


We use uv-cureable polymers and printed masks for the mold, PDMS & SIFEL (fluorinated silicon) for the chip, vakuum pumps to degas the PDMS  and corona treatment to bond the PDMS to glass.

Well, there are more DIY friendly ways to do microfluidics, but we have to deal with strong solvents for dna synthesis and got funds.

Best,
Alex

[Gene Hacker]

Could you provide a basic outline of how you intend to build a DNA synthesizer? What exactly are you using magnetic beads for? And do you really think you'll be able to achieve kilobase write lengths?

We use uv-cureable polymers and printed masks for the mold, PDMS & SIFEL (fluorinated silicon) for the chip, vakuum pumps to degas the PDMS  and corona treatment to bond the PDMS to glass.

Doesn't PDMS experience swelling when used with most solvents?

[kenny kostenbader]

The little fanboy in me thinks it's so freaking cool that the president of Azco Biotech weighted in on this thread. I don't know the terms of your axlr8r funding, but if I were you I'd immediately try to collaborate with Mr J Adams and co.

Anyway, the important stuff: we're all very glad that you guys are taking a public approach to this project, it's clearly been a beautiful execution so far. Now, while we understand that you're under no obligation to share intricate details of your developments, please do not underestimate the delight you would bring this community if you simply uploaded schematics, even coarse and basic ones. Putting in the tiniest bit of effort to open-source the technicalities of your project (that extra mile) would be tremendously worth it. Best case scenario: someone who's worked with deeply related systems (like myself) will get all excited about your work, read your technical specs, and think it over in the shower, on the bus, wherever, and then BOOM there comes an idea that could change the course of your project, bigtime. Happens all the time. Open-source collaboration is beautiful. For now, though, the best we can do is watch and cheer you on through social media.

tl;dr - get a github account, throw some technical specs out there, watch people smile, and enjoy the net positive flow of advice and contributions from this experienced audience.

Much love for this excellent pursuit of science,
Kenny

[Alex Murer [Open Biolab Graz Austria]]

Hey,

Sorry for the late answer, we ve been very busy in the last days.

The chemistry is mainly based on phosphoramidite synthesis. Our approach is to guide MCPG in a magnetic field to the reagents, instead of a static solid support. Liquid delivery us carried out by syringe pumps.
We are expecting similar write lenghts as classic column based synthesizers. In a second step we are planning to fully automate OE-PCR and link it to the synthesizer or integrate it into the chip.


PDMS does slightly swell, that's why we are also working with SIFEL which doesn't.  Silicone tubing might be replaced by PTFE or Fluran F-5500-A tubing.

[Bryan Bishop]

On Wed, Jun 25, 2014 at 1:32 AM, kenny kostenbader <kenst...@gmail.com> wrote:

tl;dr - get a github account, throw some technical specs out there, watch people smile, and enjoy the net positive flow of advice and contributions from this experienced audience.

To clarify, git repos means smiles, fuzzy facebook pics means frowns and resentment.

[Alex Murer [Open Biolab Graz Austria]]

Heya,


I totally understand your view, but please understand, that we don't feel like giving out detailed information of a half finished prototype, for several reasons. (especially because those 'details' rapidly change). It's wouldn't consider it good practice or sincere either to burst out data in the general public which isn't yet reliable at all; open source or not.
Once the project is finished, the consturction plans will be available for non commercial use, patience please.

[Bryan Bishop]

On Sat, Jul 5, 2014 at 3:43 PM, Alex Murer [Open Biolab Graz Austria] <alex.m...@gmail.com> wrote:

Once the project is finished, the consturction plans will be available for non commercial use, patience please.

Hm, well that's interesting, but the non-commercial restriction means that it's not actually "open source". Thanks for playing.

[Alex Murer [Open Biolab Graz Austria]]

I'd consider e.g.  http://creativecommons.org/licenses/by-nc/4.0/  an open source licence. But feel free to call it what you want.

[Cathal Garvey]

Actually, freedom to use something for commercial purposes is part of
the generally accepted definition of open source:
http://opensource.org/faq#commercial

--
T: @onetruecathal, @IndieBBDNA
P: +353876363185
W: http://indiebiotech.com

[Alex Murer [Open Biolab Graz Austria]]

Following the as at least you believe "generally accepted" definition, the Kilobaser software itself will indeed also be available for commercial purposes.

[Alex Murer [Open Biolab Graz Austria]]

Hi everyone,

I'm happy to show you pictures of the latest milestone we accomplished. We finished the liquid handling mechanics, magnetic actuator and general builtup of the prototype a couple of days ago! Next steps are writing the software, finishing the electronics, getting reliable synthesis done and sequencing.

[kenny k]

Very cool, very cool.

I think this is exetreeeeemely cool work, clearly must be deeply fun. We're breathing hard thinking about the specs and all, but we can definitely wait, must be a storm of development going on, early stages and all.

If you run into trouble you can always turn to your favorite synbio mailing list, we'll be keeping an eager eye on the progress till you're ready to call it a finished product.

Keep up the awesome, awesome work.
Signed,
Fanboy

[jarlemag]

Sounds great! Approximately how much in material costs are we looking at here?

[Cathal Garvey]

From what I've seen first-hand, I suspect the materials will cost very
little, but the process will cost a fair bit more! :)

[Alex Murer [Open Biolab Graz Austria]]

Hopefully we will one day be able to call it a finished product, there are still many challenges to overcome!

Thank you for your kind words Kenny, I appreciate that!

Best,
Alex

[Alex Murer [Open Biolab Graz Austria]]

Hard to tell, because we needed some fabrication devices and larger quantities of materials. Material price of ~1000$ should be in reach for those who want to DIY it, at least that's our aim.  The readily fabricated device with guarantee, support and everything will of course cost a lot more.

Best, Alex

[Alex Murer [Open Biolab Graz Austria]]

Am Dienstag, 24. Juni 2014 06:57:23 UTC+1 schrieb Gene Hacker:

Doesn't PDMS experience swelling when used with most solvents?

You could also take a look into the paper: A microfluidic oligonucleotide synthesizer (Cheng-Chung Lee1,2, Thomas M. Snyder2,3 and Stephen R. Quake 2,3,)
Dichloromethan mainly causes the swelling, so they changed the deprotection reagent to 10% trifluoroacetic acid in acetonitrile.

[Alex Murer [Open Biolab Graz Austria]]

Our programmer Bernhard has written two articles about Beaglebone Blacks GPIOs and device-tree overlay generator he coded, for those of you who are interested in programming.



http://kilobaser.com/blog/2014-07-28-beaglebone-black-devicetreeoverlay-generator
&
http://kilobaser.com/blog/2014-07-15-beaglebone-black-gpios