Purchasing DNA synthesizer

[Koeng]

Hi all,

I am working on creating an open source chip for oligo synthesis. In order to test it out, I'm in need of an oligo synthesizer (that has a flow cell I can hack to do what I need). Any advice on where to buy a good used one? Or even better, does anyone have an oligo synthesizer on hand they'd be willing to sell?

Thanks,

Keoni

[Abizar Lakdawalla]

How are you doing the oligos synthesis, cyanoethyl protection?

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[jerry maxwell]

Contact Sierra Biosystems (Certified Scientific) at 209-288-2445. They build the new SB “Shasta” as well as several variations of K&A machines for synthesis of oligos. 

Sent from my iPhone

On Aug 8, 2022, at 8:24 AM, Abizar Lakdawalla <abi...@gmail.com> wrote:



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[djwr...@gmail.com]

I have a BECKMAN OLIGO 1000 DNA SYNTHESIZER if you need one.

Dan Wright

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On Aug 8, 2022, at 8:24 AM, Abizar Lakdawalla <abi...@gmail.com> wrote:



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[djwr...@gmail.com]

I would also check with Nathan McCorkle and Bryan Bishop. 

Dan Wright

Sent from my iPhone

On Aug 8, 2022, at 10:03 AM, jerry maxwell <jerrymax...@gmail.com> wrote:

Contact Sierra Biosystems (Certified Scientific) at 209-288-2445. They build the new SB “Shasta” as well as several variations of K&A machines for synthesis of oligos. 

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[Cory J. Geesaman]

This reminds me of a post someone dropped a bit over a decade ago - still on my backlog of projects I don't have the spare time and resources for (I think his name started with a B ["Byron" maybe?] but I can't remember for the life of me, Cathel Garvey might know if he's still around) - but you can control oligonucleotides with microfluidic channels which have really basic capacitor setups printed on the walls and just move them around like charged particles after imparting a charge.  Once you have that you can just connect them to a vat with pure oligonucleotides, binding agents, etc, and set it up like a binary tree to work your way up from 2 oligonucleotides being fused together to millions or billions or trillions - which at the scale of a microfluidic chip is pretty simple to scale out, you'll just need to write a program to map that stuff out geometrically so you don't waste decades doing it by hand.  This of course all requires a sputtering machine, etcher, etc, but it's already proven tech (sorry I don't have the research papers on me, it's been awhile.)

[Cory J. Geesaman]

Bryan Bishop, that was his name - if he's still around I'd love to get a copy of that research repo if he still has it.

[Brian Degger]

https://diyhpl.us/wiki/dna/dna-synthesis.html a the page Bryans on DNA Synth.

Otherwise, search the research papers on microfluidic dna synth. 

Cheers,

Brian

[Bryan Bishop]

Thanks everyone. I am still around (and so is Nathan), and I actually sent an off-list email earlier indicating my interest in funding this project. Onwards and upwards,

- Bryan

https://twitter.com/kanzure

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[Andrew Hessel]

Great that DNA writing is popping up again. It's so foundational yet has received so much less attention than reading DNA. This said, making gene-length fragments is pretty standard and inexpensive these days and is offered by a spectrum of commercial groups. I don't recommend doing it at home/garage/etc if you're planning on working with proteins or short metabolic pathways just because of the economics. Your time and money are better spent on protein/metabolic engineering etc. Also, if you're planning on using older, organic chemistries to make DNA, keep in mind the chemicals required and waste products produced are not great to have around your home or garage. You may want to explore newer enzymatic-based chemistries coming online that are much greener. The idea of a chip-based oligo assembler has been around for a while but to my knowledge no one has been able to get it to work well -- it would be great to have this revisited, but I still would have the oligos pre-synthesized and focus mainly on getting the assembly processes working well. Note that chip-based foundry systems and chip-based test and measurement systems are getting a lot of attention these days. I point people to these two papers to get a sense of where things stand -- Venter's recent review of synbio -- pay particular attention to Figure 4, which describes Avery bio's chip-based DNA synthesis system -- and Roswell's description of their Molecular Electronic chip -- a general purpose, single molecule sensing platform. The problem of making long DNA assemblies necessary for synthetic genomes has not yet been solved. My baseline is E. coli K12 from ATCC, which retails for $400. The genome is about 4.5 megabases. At current synthesis prices, about $0.10 base, K12 would be a $450,000 print job. When it's $450 to print the genome -- and we have base-level control of the entire chromosome -- no one will order the microbe from ATCC again. I look forward to this day.

As Bryan says, onwards and upwards.

Cheers, Andrew

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[Koeng]

@Abizar Yep

@Dan awesome! I'll contact you about that.

@Bryan let's definitely talk!

> making gene-length fragments is pretty standard and inexpensive these days and is offered by a spectrum of commercial groups

Over 200x price difference between genes and oligos. Oligos are about 100-1000x more expensive than they could be with current technology. I am aware of current commercial groups - I used to run the FreeGenes Project and oversaw a few million base pairs of synthesis from Twist.

> The idea of a chip-based oligo assembler has been around for a while but to my knowledge no one has been able to get it to work well

Genscript uses it in production. Already have reached out to Drew Hall + some of the Avery folks, since they're jumping on since the patent is expiring from custom array (just like me)

[Abizar Lakdawalla]

DNA writing has been the focus for a few for a while due to DNA based data storage, Twist is one, IDT also, Microsoft (https://www.microsoft.com/en-us/research/project/dna-storage/), Catalog (https://www.catalogdna.com/). There is quite a bit of money funding this, so hopefully some of it will come your way!

The reason I asked about chemical means of synthesis is it might be worthwhile checking enzymatic means of oligo synthesis such as DNAScript.

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[Лангин Сергей]

I think Mr. Koeng plans to make a chip with localized affinity for certain letters with using an autocatalytic reaction

вт, 9 авг. 2022 г., 22:51 Abizar Lakdawalla <abi...@gmail.com>:

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[Лангин Сергей]

Without any polymerase

ср, 10 авг. 2022 г., 12:06 Лангин Сергей <langin...@gmail.com>:

[Dakota Hamill]

Just got this in the mail.  

https://www.ted.com/talks/dan_gibson_how_to_build_synthetic_dna_and_send_it_across_the_internet?language=en

https://codexdna.com/

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[John Griessen]

On 8/9/22 13:13, Koeng wrote:
> @Abizar Yep
>
> @Dan awesome! I'll contact you about that.
>
> @Bryan let's definitely talk!
>
> > making gene-length fragments is pretty standard and inexpensive these days and is offered by a spectrum of commercial groups
>
> Over 200x price difference between genes and oligos. Oligos are about 100-1000x more expensive than they could be with current
> technology. I am aware of current commercial groups - I used to run the FreeGenes Project and oversaw a few million base pairs of
> synthesis from Twist.
>
> > The idea of a chip-based oligo assembler has been around for a while but to my knowledge no one has been able to get it to work
> well
>
> Genscript uses it in production. Already have reached out to Drew Hall + some of the Avery folks, since they're jumping on since
> the patent is expiring from custom array (just like me)

I'm finally getting moved into Albuquerque and would like help with this project since the culture shock electroporator failed to
launch. Culture shock needs plastic housings to be a complete usable system with safety testing, and I've gotten some parts to
begin developing a low pressure slow molding method that will help launch low volume electronics enclosures inexpensively and
certain kinds of low tolerance starting moldings for mechanical systems. Reducing the costs of prototype plastic molded things is
a long, big project though, and won't make money to pay the shop rent for a while... I've been building a side-hustle of trading
junk from national labs to pay that rent, which is working well. Got junk?

The culture shock control circuitry is a compact 7x6cm of pcb area that runs micropython with about 20 I/O lines, 2 USB ports,
A2D, flat flex cables to a 2nd pcb that could be anything. That could be a nice start for an oligo assembler control and it's
freepublished on github. Plus I have silicon chip layout experience that could help plan out how to attack doing a microfluidic
chip, or design parts of it to fab and test. The culture shock push-pull HV power supply might even be useful for generating
volts for parts of an electrowetting charge coupled droplet mover "lab on a" microfluidic chip -- it just wouldn't need to be so
high voltage.

Meanwhile, I'm in Stockholm this week if there's anything I can do to help while there...

--
John Griessen
industromatic.com Albuquerque NM building lab gear for biologists

[Dan Kolis]

Hello to all,

Hopefully somebody can easily poke in a file as an attachment  or float text in a message, perhaps ) regarding this request.

I'm curious what exactly is the machine readbale file 'shape' to make an apparatus asemble a squirt of nuleotide(s).

Or perhaps a URL to a file specification from a real chunk of hardware.

I guess Im curious the entire workflow form for instance FASTQ to a little jar of agar + Protein ! BU the click and go file is a big start.

 

Thanks,

Dan

my ref: nafl, 14 Aug 2022

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[Ravi Ramana]

Any specific reasons why the differentials are so high? other than the long writes between gene & oligos?  

Also, you saying currently we could do 0.001 to 0.01 per bp already and its business model choices its' 100-1000X higher presently? That's tall. 

Enzymatic synthesis offerings even don't get those price points as of today. Curious to look at any pointers. This barrier shd be broken immediately, if so.   

[Koeng]

Oligos have to be stitched together into genes. Enzymatic synthesis is about 5x, last I heard, better than chemical, but also much more expensive and complicated to run.

> This barrier shd be broken immediately, if so.  

It is very difficult, but not impossible.

[Ravi Ramana]

By Enzymatic synthesis about 5X better you mean in  which factor  - speed or efficiency or length ? 

And oligos being 100x-1000x expensive than what current tech could do - is it because of business model choices of the companies 

or 

you mean the current tech base is amenable for that kinda improvement.  Some more light on this will be helpful. 

My understanding is synthesis needs to get way more cheaper as per the "data storage" drivers. Wondering if it's just hype or realistically possible. 

[Koeng]

Length, which is a function of reliability

> is it because of business model choices of the companies

Absolutely.

> Some more light on this will be helpful.

I wrote a couple essays on this topic here - https://keonigandall.com/posts/affordable_dna_2.html

> My understanding is synthesis needs to get way more cheaper as per the "data storage" drivers. Wondering if it's just hype or realistically possible.

The reason DNA is expensive right now, IMO, is that companies spend a lot of money on development of technology and the cloning process, and don't have enough users to aggregate the development costs against. You can always just solve the first bit with shittier/older technology, but reduce the requirement of cost aggregation, and therefore get a much more affordable end product.

[Лангин Сергей]

Sorry for interrupting the conversation.

YES, they need technology like de novo DNA synthesis just for seconds. For example, DNA synthesis by dNTPs on virtual matrix (maybe "optical trap") and filling gaps by polymerase-free autocatalysis.

> companies spend a lot of money on development of technology

пт, 19 авг. 2022 г. в 23:13, Koeng <koen...@gmail.com>:

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Sergei Langin

[Dan Kolis]

Human nature foments to invariably underestimate cost and time, this is no exception. I saw a recipe for a mRNA experiment and the reagents and one-of juices, slides, trays and whatnot was many dense pages. All sorts of different vendors. How many new accounts to open can a P.A. do in a workday ? Maybe 12 ? Some stuff over borders, safety paperwork, on and on it goes.

Like the standard notion: "You see the top poking out, the volume of the glacier below the waterline is 90% of what you see".

But if Synthetic biology wants to take off, these easy no brainer issues could be addressed. But, It's no fun. Nobody gets a Nobel prize for standardising ordering chemicals. Stuff like emulating retail generally and using barcodes, precise minimums and maximums for cell sizes, is possible. There is some chance standardization like this is still now premature.

Imagine the laughter at NIH to read you want to write a machine learning program ( OH ! Its A.I. ! ) to get the right jars of goop in at the lowest price quickly.... To preprint a foot of stickers for experiments instead of hand write them, etc.

All the constraints like temperature, 'best before'. I know a cancer researcher who spends maybe 1/2 her workday in a BSL-3 lab trying to keep some stupid fussy cells alive.

The details ! 

[Лангин Сергей]

After enzymatic (or chemically) DNA synthesis, you need to correct your strand to avoid errors.

пт, 19 авг. 2022 г. в 18:00, Koeng <koen...@gmail.com>:

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[suha.almohammadi]

+2. I'd like a copy as well. Pls

Sent from my Galaxy

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[Sean Sullivan]

Been thinking about part of @AndrewHessel's response earlier in the thread where he said:

"I don't recommend doing it at home/garage/etc if you're planning on working with proteins or short metabolic pathways just because of the economics. Your time and money are better spent on protein/metabolic engineering etc."

Do y'all think he was talking more about the importance of improving/developing automation around constructing and testing different sequences or simply that enough brainpower is going towards the DNA synthesis problem and more should be spent on what we are going to make with cheap DNA (any why)?

@Dank in terms of hiding a lot of the complexity that goes into running a given experiment, many vendors now sell kits that contain all the reagents + consumables + instructions needed to do things like isolate plasmids, generate cDNA libraries, prepare DNA for next-gen sequencing, etc. Even since the start of my PhD, I feel that is has become easier to find 'off-the-shelf' kits for well-established methods.

[Dan Kolis]

Question to Sean Sullivan, possibly but really a general question

Anytime the question is asked ? "How often does this succeed ?" The usual answer starts with a long observation; ex: "It depends ...". Ok

Recall from a strict numerical method approach, if success or failure criterea can be decided upon per act, and acts batched into some kind, there is always a number in the noise, and an important one. What is the line item success rate, as usually composed ? 

 Sure some if;s in the question ! Situation:

*) Gene BP count is 3K NT, promotor tails, introns if any etc well known to work.
*) Expression system known, like locally managed Yeast or 'whatever'
*) Selection itself is reliable, UV florescence or some other property

 Q1) How many labor hours is typical, no paperwork time, just wet lab including end game verification ?
 Q2) Whats the success rate of a new germ line in percent ?
 Q3) How often is a success rate wrong ultimately. not that the Gene did do what is expected, but some 'other' flaw made it not really get expressed ?
 Q4) Is sequencing the believed usable final modified colony invariably reliable enough to make Q3 irrelevant ?

Thanks in advance of anyone who answers. As people like me want to make this technology, not science, this is a big thing hugely.

is Q2) Closer to what ? 30% 80 %

For Q1) I mean hands on time with endless revisits to the plates and so on, not includng incubation times, centerfuge, etc.

Thanks! 

Daniel B Kolis

my ref: nafl, 30 Aug 2022, diybio