--- Log opened Sun Sep 01 00:00:39 2024
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11:57 < hprmbridge> kanzure> "Analysis and control of untemplated DNA polymerase activity for guided synthesis of kilobase-scale DNA sequences" https://www.biorxiv.org/content/10.1101/2024.08.29.610422v1
11:57 < hprmbridge> kanzure> https://x.com/chofski/status/1829795077176053806
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12:17 < hprmbridge> kanzure> "Long Oligos: Direct Chemical Synthesis of Genes with up to 1,728 Nucleotides" https://chemrxiv.org/engage/chemrxiv/article-details/6696cb345101a2ffa88ffc3c
12:21 < hprmbridge> kanzure> "Since 2010, our research team has been making efforts on the development of a new method called catching-by-polymerization (CBP) for synthetic oligo purification
12:21 < hprmbridge> kanzure> (Scheme 1).
12:21 < hprmbridge> kanzure> 14 The method involves tagging the full-length oligo with a polymerizable tagging phosphoramidite (PTP) and incorporating the conjugate into a polyacrylamide gel. Because failure oligos are capped during automated synthesis, they are not tagged with the PTP, and therefore cannot be incorporated into the gel. Oligo purification is then achieved by washing away the failure oligos, followed by
12:21 < hprmbridge> kanzure> cleaving the full-length oligo from the gel. Recognizing the power of the CBP
12:21 < hprmbridge> kanzure> method, we attempted to use it to isolate the extremely low percentage of full-length oligos from the complex mixture generated from thousands of reactions required long oligo synthesis.
12:21 < hprmbridge> kanzure> 15-16 Most recently, using the CBP method, we succeeded in isolation of 400-mers. Sanger sequencing confirmed the sequences.9 Here, with additional innovations involving the use of glass wool and glass beads as solid support for long oligo synthesis, we report the synthesis of the 800-mer green fluorescent protein (GFP) gene and the 1,728-mer Φ29 DNA polymerase gene, and their isolation with CBP
12:21 < hprmbridge> kanzure> and characterization with Sanger sequencing."
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13:11 < hprmbridge> kanzure> "For Catching-by-Polymerization Oligo Purification: Scalable Synthesis of the Precursors to the Polymerizable Tagging Phosphoramidites" https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4790353
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13:45 < cslr> are there people who have EEG-device?
13:45 < cslr> here
14:07 < hprmbridge> kanzure> "Dmoc oligonucleotide synthesis" apparently allows for a more mild reaction environment for de protection, a recent development for oligos
14:07 < hprmbridge> kanzure> er, deprotection
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15:03 < docl> .t https://www.caltech.edu/about/news/programmed-fold-rna-origami-43511
15:03 < saxo> Programmed to Fold: RNA Origami     -         www.caltech.edu
15:40 < hprmbridge> kanzure> "With Dim-Dmoc protection, oligodeoxynucleotide (ODN) deprotection has be achieved with sodium periodate oxidation followed by β-elimination induced by the weak base aniline. Some sensitive groups have been shown to be stable under the deprotection conditions. Besides serving as a base, aniline also serves as a nucleophilic scavenger for the side products of Dim-Dmoc deprotection, which prevents
15:40 < hprmbridge> kanzure> the side products from reacting with the deprotected ODN. For this reason, excess aniline is needed."
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16:26 < hprmbridge> kanzure> some protein design resources in the thread here https://x.com/nootlabs_/status/1830299252523958622
16:36 < hprmbridge> kanzure> "KIBRA anchoring the action of PKMζ maintains the persistence of memory" https://www.science.org/doi/10.1126/sciadv.adl0030
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17:13 < superkuh> re: KIBRA, the "except fear memory" is a big except.
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18:15 < hprmbridge> kanzure> https://chem.sites.mtu.edu/amidities/
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18:49 < hprmbridge> kanzure> "Oligodeoxynucleotide Synthesis Under Non-Nucleophilic Deprotection Conditions" https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.983
18:51 < fenn> re "Long Oligos" it's crazy that nobody tried synthesis on smooth glass beads until now
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19:08 < SOLUTATIONS> Hi there I’m Sol
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--- Log closed Mon Sep 02 00:00:40 2024