--- Log opened Sun Apr 23 00:00:40 2023
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07:38 < docl> yashgaroth: have you seen this APM spiroligomer membrane paper yet? https://onlinelibrary.wiley.com/doi/abs/10.1002/ange.202302809
07:38 < docl> I've only read the supplemental section (non paywalled). good level of detail there
07:43 < yashgaroth> I think you greatly overestimate how much I keep up with spiroligomers. So they're embedding the ligomers into a PES membrane and seeing how it affects filtration? Seems a bit disingenuous, with the title I'd have thought they were membranes made purely of ligomers
07:45 < yashgaroth> this seems like they're coating an existing membrane with a chemical that might retain a bit more of a certain molecule (ethyl vanillin apparently), but I don't want to judge too much based on supplemental info
07:52 < hprmbridge> kanzure> can we put a spiroligomer monomer on to a tRNA? (disregard ribosome compatibility)
07:54 < docl> it looks like the spiroligomers were crosslinked with TMC while trapped between the two PES layers, then these were separated. the crosslinked spiroligomers formed a distinct layer
07:58 < yashgaroth> ah ok that makes more sense
08:01 < yashgaroth> you might be able to conjugate certain monomers onto tRNA, but not with any known method
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10:15 < docl> hmm. might be belaboring the obvious, but if we are about get cheap DNA write, that shifts the equation for what's productive in spiroligomer research such that something that reads [D|R|X]NA as a ticker tape to click the monomers together in a specified order has immense value. because you can amplify DNA. I probably should be deep diving Davie Liu's stuff
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10:28 < alethkit> https://www.nature.com/articles/s41570-022-00456-9
10:52 < docl> Interesting, Liu's lab developed PACE and base editing. PACE is a cheaper way to do directed evolution. https://en.wikipedia.org/wiki/Phage-assisted_continuous_evolution
11:01 < docl> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084352/
11:02 < docl> "During phage-assisted continuous evolution (PACE), evolving genes are transferred from host cell to host cell through a modified bacteriophage life cycle in a manner that is dependent on the activity of interest. Dozens of rounds of evolution can occur in a single day of PACE without human intervention."
11:03 < hprmbridge> msnewgooty> PACE is okay, but there's a reason it hasn't caught on like wildfire
11:04 < hprmbridge> msnewgooty> bit difficult to set up and very particular to the selection conditions
11:04 < hprmbridge> msnewgooty> supposedly they're using it at David's new programmable protease company
11:06 < kanzure> i should email him.
11:10 < hprmbridge> msnewgooty> this would be for which enzyme in particular though? You need to convert the evolution to modifying gIII expression in some way
11:35 < kanzure> msnewgooty: what would you make if genome-scale synthesis (gigabase synthesis) cost only a few dollars at most?
11:40 < hprmbridge> jaisel> yo!
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11:46 < muurkha> first I've heard of 'ligomers'
11:51 < hprmbridge> msnewgooty> I think the highest value is incredibly large scale screening of long enzymes
11:52 < hprmbridge> msnewgooty> basically every application across genome editing, delivery (viral capsids, etc), novel enzymes for chemical production, screening different mRNA constructs for expression
11:53 < hprmbridge> msnewgooty> Not to mention synthesis and screening of transcription factors for cellular rejuvenation
12:03 < kanzure> screening was on my list; anything that might not be tho?
12:03 < kanzure> good point about long enzymes though
12:16 < hprmbridge> an1lam> De Novo genomes for (beneficial) microbes? Novel mammalian cell lines?
12:17 < hprmbridge> an1lam> Hoping PRANCE can help with this: https://www.nature.com/articles/s41592-021-01348-4
12:36 < hprmbridge> msnewgooty> PRANCE helps on the bioreactor front but doesn’t address the fact that your evolution needs to flow through gIII
12:37 < hprmbridge> msnewgooty> I think gigabase style synthesis is most useful for screening; I’m not sure we know enough right now to make use of a synthetic 1Gb fragment
12:38 < hprmbridge> msnewgooty> Like, I don’t really know the obvious utility of a synthetic chromosome, with exact design parameters, that couldn’t be made more easily in a different way
12:38 < hprmbridge> msnewgooty> Oh wait, recoding. Like the Church-lab approaches. So that is. O
12:39 < hprmbridge> msnewgooty> You could make virus resistant mammalian lines
12:40 < hprmbridge> msnewgooty> You could also synthesize genomes to remove mobile elements, from a safety perspective
12:41 < hprmbridge> msnewgooty> Potentially some crazy nucleic acid nanostructure
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12:50 < kanzure> sure, you can remove endogenous retroviruses too
12:50 < kanzure> or xenotransplant entire metabolic pathways
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13:28 < hprmbridge> nmz787> Nothing about how current synthesis (or cloning) is done or their timelines seems vaguely convenient. Eliminating tedium is beneficial for all.
13:40 < hprmbridge> msnewgooty> The way it's currently done is pretty laborious. But my impression of genome-write is that it's more of a technical feat than any specific application
13:42 < hprmbridge> msnewgooty> Also DNA storage, of course
13:43 < hprmbridge> msnewgooty> The mini-symplastome proposal here https://engineeringbiologycenter.org/pilotprojects/ is pretty novel
14:15 < kanzure> DNA data storage doesn't require gene-level precision
14:17 < kanzure> msnewgooty: did you see http://engineeringbiologycenter.org/wp-content/uploads/2017/10/Berry-RMA-Pilot-Project-1.pdf
14:17 < kanzure> or http://engineeringbiologycenter.org/wp-content/uploads/2017/10/Berry-IA-Pilot-Project.pdf
14:18 < kanzure> another writeup of these is located here: https://groups.google.com/g/enzymaticsynthesis/c/41r7D3wHKn8
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14:41 < kanzure> .wik DNA-templated organic synthesis
14:41 < EmmyNoether> "DNA‐templated organic synthesis (DTS) is a way to control the reactivity of synthetic molecules by using nature's molarity‐based approach." - https://en.wikipedia.org/wiki/DNA-templated_organic_synthesis
14:49 < hprmbridge> msnewgooty> Is this a ton different than Gibson assembly though
14:52 < hprmbridge> msnewgooty> I’m not sure how this exactly works—you can only combine 256 8mers, seems like a tricky asssembly
14:55 < kanzure> sequentially
14:58 < hprmbridge> yashgaroth> where's 256 coming from
14:58 < hprmbridge> msnewgooty> 4^4
14:59 < hprmbridge> yashgaroth> ah you only inject one 8mer at a time, then the ligase adds it and you wash out the excess
14:59 < kanzure> sequentially.
14:59 < hprmbridge> msnewgooty> Seems a lil slow
14:59 < hprmbridge> msnewgooty> A batch assembly would scale better
15:00 < hprmbridge> yashgaroth> you could probably flow in a few at a time, as long as there's no sequence incompatibility between them. Regular phosphoramidite synthesis takes several minutes per base, though they do make that up with parallelization
15:02 < hprmbridge> yashgaroth> for the assembly one, the benefit is in decreased risk of mismatches since you're not relying on passive basepairing - the UvsX enzyme performs active homology checking. But yes it is quite similar
15:03 < hprmbridge> yashgaroth> anyway I was young and naive when I came up with it. We're working on a much better synthesis method using a ribosome
15:03 < hprmbridge> msnewgooty> Where you bring in different triplets?
15:04 < hprmbridge> yashgaroth> I don't want to put too many details in a public discord channel, but it's independent of the mRNA sequence
15:05 < hprmbridge> msnewgooty> Maybe this is naive, what if you had two orthogonal protection chemistries
15:05 < hprmbridge> msnewgooty> That allow you to alternate flow to a tdt
15:08 < hprmbridge> yashgaroth> I'll leave TdT to the other DNA synthesis startups, but they prefer conjugating each different nucleotide to the enzyme directly. Still needs another enzyme to deprotect, which seems unscaleable since Twist etc can deprotect electrochemically, but who knows
15:15 < hprmbridge> msnewgooty> Wonder if there’s optical de protection? Haha I am not an organic chemist
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15:16 < hprmbridge> msnewgooty> Also if anybody will beat twist pricing ill be your first customer
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15:22 < kanzure> yes there are optical deprotection methods used in DNA synthesis
15:24 < kanzure> https://diyhpl.us/~bryan/papers2/DNA/A%20flexible%20light-directed%20DNA%20chip%20synthesis%20gated%20by%20deprotection%20using%20solution%20photogenerated%20acids.pdf
15:24 < kanzure> well, this is photogenerated acids i guess
15:24 < hprmbridge> yashgaroth> I am even less of an organic chemist, at least going off Ansa's patent enzymatic is how they deprotect
15:24 < hprmbridge> yashgaroth> aww I got all excited but yeah it's the same mechanism as electrochemical
15:25 < kanzure> here is a more general organic chemistry review:
15:25 < kanzure> https://diyhpl.us/~bryan/papers2/DNA/Photoremovable%20protecting%20groups%20in%20chemistry%20and%20biology%20-%20reaction%20mechanisms%20and%20efficiency.pdf
15:33 < kanzure> photoremovable protecting groups:
15:33 < kanzure> https://diyhpl.us/~bryan/papers2/DNA/nucleosides/Photoremovable%20protecting%20groups%20-%20reaction%20mechanisms%20and%20applications.pdf
15:55 < kanzure> .title https://nitter.nl/WFeanor/status/1650227933259390976
15:55 < EmmyNoether> Wrath of Fëanor (@WFeanor): 'There are many interesting individuals who have carried the torch of futurism - broadly defined - in the wake of the Extropian era...and I can't help but think that it is a shame that people such as Bishop are overshadowed by names like Yudkowsky.We should work to change that.' | nitter.nl
15:57 < kanzure> alethkit: what is your background btw?
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17:35 < docl> yeah it seems cleaving bonds of protecting groups with light is a lot more practical than my naive idea from when I was young and stupid a couple days ago about steering molecules. there's also reversible shape changes with light you can do like azobenzene
17:35 < docl> https://en.wikipedia.org/wiki/Azobenzene
17:36 < docl> I'll read those papers about PPGs kanzure, they looks interesting
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--- Log closed Mon Apr 24 00:00:41 2023