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Invention of DNA "page numbers" opens up possibilities for the bioeconomy

caltech.edu

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Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#31

Post by biophysboy »

codesnik wrote: post #29
biophysboy wrote: post #28

Chemical modifications of DNA are so amazing, and underpin so much DNA related research and engineering. Illumina and Moderna would not exist without DNA mods. It’s very cool that the set of tools is expanding further! “ Guided by the removable DNA page numbers, Sidewinder achieves an incredibly high fidelity in DNA construction with a measured misconnection rate of just one in one million, a four to five magnitude i…

pcr amplifies all sequences, correct or wrong, no? and as I understand it, it works on short snippets the best.

It amplifies sequences that contain the two primer sequences on each end of the target. So if you had synthesized sequence XYZ with some mistakes like YZX, then you could target X and Z and purify.

You're correct that PCR has a limited max length, but it is longer and cheaper than vanilla DNA synthesis.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#32

Post by ssivark »

trebligdivad wrote: post #14

That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article

The early printing press was probably focused on short few page documents (an increasing scale), and it wouldn't be surprising if page numbers were a solution to help printers not mix up pages.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#33

Post by ben_w »

nullbyte808 wrote: post #17

Such a simple concept took this long to discover? Now we just need a way of packing the DNA strings into blank cells reliably.

> Now we just need a way of packing the DNA strings into blank cells reliably.

Huh, I kinda assumed we'd already done that part with Dolly the sheep. But I'm not a biologist, I just saw headlines.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#34

Post by pcrh »

throwaway89201 wrote: post #21
nullbyte808 wrote: post #20

[flagged]

What's the source of the text? It seems to be either a copypasta from a journal article or LLM-generated (and not your own text).

I briefly scanned the paper. The above summary is garbage.

For a biologist, a summary might be like this: pcr fragments are generated with short reverse complementary sequences added to the end of one fragment that match that at the begining of the next to-be-joined fragment.

These will anneal to create a cross-shaped DNA molecule. The short arms of the cross being the complementary sequences. Like so:

  ======∥=====
The short arms can then be processed-off to leave behind the now-longer fragment. The process can be repeated using different reverse complementary sequences between each fragment, the "page numbers" referred to.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#35

Post by oofbey »

biophysboy wrote: post #28

Chemical modifications of DNA are so amazing, and underpin so much DNA related research and engineering. Illumina and Moderna would not exist without DNA mods. It’s very cool that the set of tools is expanding further! “ Guided by the removable DNA page numbers, Sidewinder achieves an incredibly high fidelity in DNA construction with a measured misconnection rate of just one in one million, a four to five magnitude i…

Intuitively I agree some kind of selective amplification should be able to correct for the mistakes. But I think it will be complicated. Because the filtering process needs to be much more complex. It can’t just chemically match to a known subsequence - you won’t know where the mistake might be in a long sequence.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#36

Post by adrian_b »

ssivark wrote: post #32
trebligdivad wrote: post #14

That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article

The early printing press was probably focused on short few page documents (an increasing scale), and it wouldn't be surprising if page numbers were a solution to help printers not mix up pages.

Your hypothesis does not match history, because the early printing was focused on things that had a potentially large market, which at that time meant books like The Bible, with a lot of pages.

The parent article mentions that binding the pages of the first bibles in the correct order, in the absence of page numbers, was an extremely tedious work.

That is why page numbers have invented many years later, exactly as you say, "to help printers not mix up pages".

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#37

Post by oofbey »

nullbyte808 wrote: post #17

Such a simple concept took this long to discover? Now we just need a way of packing the DNA strings into blank cells reliably.

They have a nice simple explanation. But the biochemistry of it I’m guessing is anything but simple. I’ve never heard of three way junctions in DNA before. I wonder how new those are. And designing the molecules to do the matching and splicing must have taken a long time.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#38

Post by oofbey »

pcrh wrote: post #34
throwaway89201 wrote: post #21

Earlier quoted context omitted.

What's the source of the text? It seems to be either a copypasta from a journal article or LLM-generated (and not your own text).

I briefly scanned the paper. The above summary is garbage. For a biologist, a summary might be like this: pcr fragments are generated with short reverse complementary sequences added to the end of one fragment that match that at the begining of the next to-be-joined fragment. These will anneal to create a cross-shaped DNA molecule. The short arms of the cross being the complementary sequences. Like so: ======∥===== T…

So do the complementary sequences naturally bind to their neighbors? So you just mix the “pages” in a soup for a while until they all find their friends. And then the custom enzyme (or what is it) just slices off the three way junctions?

Really clever.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#39

Post by observationist »

trebligdivad wrote: post #14

That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article

Sometime after 685 AD, they invented spaces between words. All text - in Latin to that point, mostly - was written in scriptio continua.

All sorts of ambiguity and hilarity would ensue; to be a good writer, you needed to ensure that words didn't bleed together and form incorrect meanings in unintended combinations. If you lost your place when reading, you'd have to know generally where you were in a scroll, and restart from a place you remembered.

Kinda crazy to think how difficult it would be to cross reference things and do collaborative research with no spaces or pages.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#40

Post by imzadi »

vee-kay wrote: post #11
wartywhoa23 wrote: post #4

Earlier quoted context omitted.

The ease of this "just" is the most concerning thing in the context of humankind's survival.

Then I recommend you don't find out what "Project Molecule" intends to do.

Care to enlighten? Google has nothing meaningful.
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