--- Log opened Thu Jun 25 00:00:00 2020
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07:35 < lsneff> .t https://www.nature.com/articles/s41563-020-0709-5
07:35 < saxo> De novo nanomaterial crystals from DNA frameworks | Nature Materials
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08:33 < kanzure> https://www.forbes.com/sites/johncumbers/2020/06/23/a-new-way-of-making-dna-is-about-to-revolutionize-the-biotech-industry/#721c44f549ff
08:34 < kanzure> ugh "Businesses like San Diego-based Molecular Assemblies have been adapting polymerase enzymes to create custom DNA molecules. They hold 24 patents on the matter"
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08:34 < kanzure> i hope by polymerase they mean TdT
08:34 < kanzure> i think we technically talked with bill about our techniques
08:34 < kanzure> .title https://youtu.be/0PEOIksxocU
08:34 < saxo> Codexis and Molecular Assemblies Partner to Transform the Field of DNA Synthesis - YouTube
08:35 < kanzure> er, rather, https://youtube.com/watch?v=0PEOIksxocU
10:26 < yashgaroth> they were having real trouble getting TdT to actually do what they wanted when I interviewed there, seems like they're basically just outsourcing the protein engineering to codexis
10:26 < saxo> yashgaroth: <L29Ah> salt licks
10:26 < yashgaroth> oh
10:37 < kanzure> yashgaroth: most likely they are still TdT only right?
10:40 < yashgaroth> oh, for sure; and TdT is technically a polymerase
10:41 < kanzure> do aptamers work because of high entropy sequencs, or can long stretches of low entropy DNA (say on the order of 100 bp) that vary (every few hundred bp they switch to another pattern or nucleotide) would be a functional and useful aptamer?
10:48 < kanzure> did we ever write down what the slowest polymerase is and where to find that?
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11:11 < kanzure> "These nucleotides have a reversible 3' fluorescent blocker so the DNA polymerase can only add one nucleotide at a time onto the DNA fragment. After each round, non-incorporated molecules are washed away. A chemical deblocking step is then used to remove the 3’ fluorescent terminal blocking group."
11:15 < kanzure> "dATPs, dTTPs, dGTPs, and dCTPs are washed over the cell separately so each nucleotide is able to be identified.
11:16 < kanzure> why can this not be used for synthesis? the protocol would be: keep washing over the dNTP you want until you notice that it was incorporated.
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11:18 < kanzure> i guess call this "synthesis by sequencing by synthesis"
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18:18 < fenn> or just single molecule synthesis
18:19 < fenn> polymerase can be slowed down by lowering the temperature
18:19 < fenn> also by lowering reactant concentration
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19:12 < kanzure> probably doesn't work
19:16 < kanzure> some sort of impedance-based nucleotide incorporation sensor https://www.biorxiv.org/content/biorxiv/early/2020/05/30/604553.full.pdf
19:20 < kanzure> oh here we go, is this the same thing? https://www.biorxiv.org/content/biorxiv/early/2019/03/26/561092.full.pdf
19:28 < kanzure> takes 1 hour for a misincorporation event to be observed; i imagine this can be fixed with some polymerase engineering.
19:28 < kanzure> seems a little high. they probably weren't testing for how to shorten that period.
19:29 < kanzure> oh they did look at manganese to increase misincorporation rates. okay.
19:35 < kanzure> were they monitoring for fluorescent events? seems like the 98-99% stepwise yield shouldn't matter too much if you can detect events.
20:15 < kanzure> above is "Rapid and dynamic nucleic acid hybridization enables enzymatic oligonucleotide synthesis by cyclic reversible termination: A novel mechanism for enzymatic DNA synthesis"
20:31 < kanzure> "Enzymatic synthesis of designer DNA using cyclic reversible termination and a universal template" https://pubs.acs.org/doi/abs/10.1021/acssynbio.9b00315
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--- Log closed Fri Jun 26 00:00:01 2020