Author Topic: Does anyone know about writing DNA?  (Read 1822 times)

bwall

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Does anyone know about writing DNA?
« on: May 09, 2019, 12:57:51 PM »
I found this video (like below) this week and it piqued my interest.

It's about a company that writes DNA, as a form of computer code. Apparently DNA has significant advantages over binary code. There are some cool examples of what companies are doing as far as business ideas--creating rhino horn to sell to asia, creating silk on an industrial scale, etc. Apparently the opportunities are endless.

My question: has anyone here heard of this before or have any experience (at any level) with it?

To me it's all brand new but the video is from 2016 so it's anything BUT cutting edge by now.

https://www.youtube.com/watch?v=YXkK-QuBU7s

Watchmaker

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Re: Does anyone know about writing DNA?
« Reply #1 on: May 09, 2019, 02:39:04 PM »
In school I helped build a system for reading DNA electronically by passing the strands through a narrow opening and measuring the changing capacitance*.

I'm moderately familiar with the ideas in the attached video, is there something specific you're wondering?

It's not exactly what you're talking about, but I've been fascinated by the work on DNA origami (making structures out of DNA). Here's a video on that:
https://www.youtube.com/watch?v=Trg2__Lgnc0
 

*Ours didn't work so good.

sol

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Re: Does anyone know about writing DNA?
« Reply #2 on: May 09, 2019, 02:51:42 PM »
I can't be bothered to watch an 18 minute youtube video, sorry.  Can you summarize for us?

It's been about a decade since we developed the technology to construct DNA one base pair at a time.  The problem is that it would take hundreds of years to write an entire organism this way, so what it was usually used for was short segments like primers tagged with fluorescent dyes, so that you can identify specific sequences in a cell optically.

Alternately, you can rewrite a short segment of DNA and then insert into another organism.  This accomplishes the same goal as earlier technologies, letting you put vitamin A into golden rice, or making mice glow in the dark.  Anything where a particular protein sequence will be replicated by a host organism.  I think it's mostly e. coli they put stuff into, because you can grow it rapidly to enormous volumes and then extract the protein you've inserted.  Good for things like making insulin.

The other, and I think more exciting technology on this front, is all of the work around crispr and cas9.  These are technologies that make it easy to cut and paste different pieces of DNA into specific places, so for example you could cut out a defecting gene (or more often, a tiny part of gene) that causes a genetic abnormality like SMA or cystic fibrosis, and replace it with the fully functioning version.  As long as you do it with an embryo, you can basically prevent that person from ever getting the disease.  To my knowlege, this is all still very illegal.

Then there are a variety of nefarious purposes, too.  Synthetic biology is a terrifying field, IMO.  There are literally thousands of biochem graduate students around the world who know how to end all life on earth with about a week's worth of lab work.

bwall

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Re: Does anyone know about writing DNA?
« Reply #3 on: May 09, 2019, 07:32:40 PM »
I can't be bothered to watch an 18 minute youtube video, sorry.  Can you summarize for us?

Fair enough. i didn't consider that when posting the link. The good stuff starts about 2 or 3 minutes in.

TL; DR This is how everything will be made in the future. I don't understand how. Please help!

The thing is, I don't really understand it well enough to summarize. I know that they are creating ("writing") DNA on silicon chips according to their customer's code/specifications. And then somehow that company can then take the code and create . . . . damn near anything? (this is where it gets hazy for me- how do they create? like 3D printing? ) with that DNA code.

Examples provided in the video: synthetic DNA-grown rhino horn that . . . is basically real rhino horn in every way. Just grown in the lab, not on the upper lip of a rhino. Right now rhino horn goes for $30,000 per pound in Asia. The only thing more expensive per pound in the world is heroin. A company (their client?) wants to flood the market with lab grown rhino horn that is exactly the same in every way as wild grown rhino horn and therefore save the rhino from extinction.

Another example similar to above but with shark fins, IIRC.

Another example of growing (?) industrial quantity silk that, again, has the same quality as spider grown silk, but with DNA.

Yeast products (fermentation) to replace anti-malaria drug creation, as well as vanillin (?). Shortened production cycles and vastly lower costs. How does DNA on a silicon chip interact with yeast?

One thing I do (kinda) grasp is how they use DNA to fight cancer. Just cut and paste with CRISPR-cas9 gene editing tool and voila! you now have a smart-bomb that only hunts cancer cells.

And another tidbit that blew my mind; all the information found on the internet, all across the world, cloud, server farms, etc. if stored on DNA on silicon chips, would fit in a single shoe box. 

My background isn't in computers, software or biology, so I'm just trying to wrap my head around this. I always thought that DNA was the 'building blocks of life' and that therefore, I guess, it was made up of organic material. So how can organic material be put on a silicon chip?

How can DNA (an organic material?) be stored (forever and with no degradation or loss, apparently, also in the video), on a silicon chip? Or is DNA referring to an alternative to the binary (1's and 0's) computer code that we've had until now. If this is the case, how does that work (ok; not an easy question to answer, I know.)

The video also explained how writing DNA can serve as a replacement for oil; maybe not replace the internal combustion engine, but everything else petroleum is used for; (think: fertilizer, plastics, tires, shores, etc). Major reduction in greenhouse gases, etc. (again, IIRC and if I understood correctly). How can you create a yeast-based bio-factory (her term) with DNA on a silicon chip?

Someone told me that this is like the discovery of oil . .. in the 1920's. I guess I'm like the simpleton from 100 years ago who didn't understand how oil could replace the tried and true work horse, the only thing he'd known up till then.

Watchmaker

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Re: Does anyone know about writing DNA?
« Reply #4 on: May 10, 2019, 07:35:49 AM »
TL; DR This is how everything will be made in the future. I don't understand how. Please help!

...How can you create a yeast-based bio-factory (her term) with DNA on a silicon chip?

Someone told me that this is like the discovery of oil . .. in the 1920's. I guess I'm like the simpleton from 100 years ago who didn't understand how oil could replace the tried and true work horse, the only thing he'd known up till then.

You're misunderstanding them slightly. They write the DNA on a silicon chip-- but then put the DNA into yeast, bacteria, a cancer patient, etc. They aren't using the DNA outside of biological systems-they are simply creating custom DNA for use in biological systems

BTDretire

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Re: Does anyone know about writing DNA?
« Reply #5 on: May 12, 2019, 10:37:44 AM »

Another example of growing (?) industrial quantity silk that, again, has the same quality as spider grown silk, but with DNA.


 Just one quick fix, silk comes from the silk worm. :-)

bwall

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Re: Does anyone know about writing DNA?
« Reply #6 on: May 13, 2019, 11:16:40 AM »

Another example of growing (?) industrial quantity silk that, again, has the same quality as spider grown silk, but with DNA.


 Just one quick fix, silk comes from the silk worm. :-)

I know, right?!? SOOOOOO many questions that have to be answered still!

Here is the website of the company that's using DNA to ferment sugar into protein which is then harvested and spun into fibers and woven into silk. They say spiders, not silk worms.....

https://boltthreads.com/technology/microsilk/

Crazy stuff!



EvenSteven

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Re: Does anyone know about writing DNA?
« Reply #7 on: May 13, 2019, 11:30:15 AM »

Another example of growing (?) industrial quantity silk that, again, has the same quality as spider grown silk, but with DNA.


 Just one quick fix, silk comes from the silk worm. :-)

I know, right?!? SOOOOOO many questions that have to be answered still!

Here is the website of the company that's using DNA to ferment sugar into protein which is then harvested and spun into fibers and woven into silk. They say spiders, not silk worms.....

https://boltthreads.com/technology/microsilk/

Crazy stuff!

Especially crazy because DNA does not catalyze a fermentation reaction, and the fermentation reaction does not produce protein form sugar. Something is getting confused somewhere along the lines of science to marketing.

bwall

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Re: Does anyone know about writing DNA?
« Reply #8 on: May 13, 2019, 11:49:14 AM »
hmmm... quite likely that my interpretation is off.

Is your critique of my interpretation or of the information on the website? Not trying to nit-pick; just would genuinely like to know if they have it wrong on their website or if I misunderstand it.

I always thought that fermented sugars would result in alcohol and carbon dioxide, not proteins. I'd just like to understand it a bit better.


EvenSteven

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Re: Does anyone know about writing DNA?
« Reply #9 on: May 13, 2019, 12:31:48 PM »
hmmm... quite likely that my interpretation is off.

Is your critique of my interpretation or of the information on the website? Not trying to nit-pick; just would genuinely like to know if they have it wrong on their website or if I misunderstand it.

I always thought that fermented sugars would result in alcohol and carbon dioxide, not proteins. I'd just like to understand it a bit better.

The website is light on details, to say the least.

Some quick biology 101:

What is called "the central dogma of biology" is DNA -> RNA -> Protein. If they are wanting to produce a lot of a particular protein, it looks like they are putting DNA into yeast that will be transcribed into an mRNA that will be translated into the protein that they want to harvest. They then grow big vats of this yeast to produce the protein at scale.

This technology has been used for decades, to produce anything from medicine to improved crops. It is an interesting and useful technology, but not new.

bwall

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Re: Does anyone know about writing DNA?
« Reply #10 on: May 15, 2019, 05:51:45 AM »
Thank you for the biology info. I did not know that.

It appears then that if the big breakthrough isn't in technology, then it's in the cost of that technology. The new company (original video) has found a way to bring the cost of writing DNA down substantially and significantly.

maizefolk

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Re: Does anyone know about writing DNA?
« Reply #11 on: May 15, 2019, 06:25:54 AM »
There has been several companies seeking to, or marketing breakthroughs in bringing down the cost of DNA synthesis. As sol mentioned, we've had technology for "writing" short stretches of DNA since the 1970s. The problems were 1) early tech didn't scale to long sequences 2) it was quite expensive.

Both problems have gotten better, but if I want to create a 1 kilobase gene from scratch today (1,000 As, Cs, Ts, or Gs), I'll probably still pay at less $0.20/base pair (so $200 for the full thousand nucleotides). And if I wanted to resynthesize the human genome, we're talking >$100M and it would come in lots of relatively short pieces that I'd then spend years and years trying to lego those pieces together in the right order.*

*Plus once they get up into the 100,000s-1,000,000s of base pairs range the DNA molecules will break if you look at them funny.

For the rhino horn, getting one copy of the rhinoceros gene for keratin and sticking it in yeast or something similar is easy, you don't even need to synthesize the gene, you just need a bit of DNA from a rhinoceros and some PCR primers. If the folks you are talking about are the company called Pembient, I think the reason DNA synthesis is mentions is that they want to "dope" their synthetic rhino horns with synthetic rhino DNA (lots of copies of almost all the DNA in a rhinoceros, not just a single gene) so that even people doing DNA tests won't be able to distinguish a synthetic horn from one poached from an actual animal.

geekette

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Re: Does anyone know about writing DNA?
« Reply #12 on: May 16, 2019, 08:06:49 AM »

Another example of growing (?) industrial quantity silk that, again, has the same quality as spider grown silk, but with DNA.


 Just one quick fix, silk comes from the silk worm. :-)

Mostly.  However, spiders produce their own version of silk to spin webs, and this can be used for cloth (2009 Wired article about a spider silk textile).  Modified silkworms are producing spider silk (which is stronger than silkworm silk) to produce fabric for the military, per this 2017 Marketplace article.