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Benjamin L. Oakes

@benjaminloakes.bsky.social

67 followers 78 following 30 posts

CEO @ Scribetx.com | at the interface of molecular and genetic engineering | designing CRISPR to be safe enough for all

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Benjamin L. Oakes @benjaminloakes.bsky.social · 21/03/2025

Why I like it: This study provides a clear playbook for modern molecular engineering. Comparing this work with others in the field, it is clear that comprehensive variant mapping surpasses the effectiveness of targeted mutagenesis and assay-naïve AI engineering approaches. Plus it's just more fun!

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Benjamin L. Oakes @benjaminloakes.bsky.social · 21/03/2025

This meticulous screening reveals specific mutations that greatly enhance TnpB’s nuclease activity. By stacking beneficial single mutations into one optimized variant (“enhanced TnpB”), they achieved up to 50-fold higher activity in plants—a reasonably respectable 🤯 leap in enzyme efficiency.

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Benjamin L. Oakes @benjaminloakes.bsky.social · 21/03/2025

Quick background: TnpB is a compact RNA-guided nuclease and the evolutionary ancestor of Cas12. In this work, the team uses deep mutational scanning with a yeast-based cleavage assay to profile every RNA & protein variation.

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Benjamin L. Oakes @benjaminloakes.bsky.social · 21/03/2025

This week, I’ll highlight two recent CRISPR advances: 1) BEAM’s exciting Phase 1 clinical data for BEAM-302. 2) Impressive work from the labs of Scribe’s co-founders @savagecatsonly.bsky.social & @doudna-lab.bsky.social —providing a textbook example of engineering CRISPR enzymes from zero to hero.

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Benjamin L. Oakes @benjaminloakes.bsky.social · 27/02/2025

When Zheng et al. look more deeply at this question they find the RT domains (fused to Cas or not) cluster at DNA breaks faster than endogenous DNA repair proteins and alter repair outcomes by inserting random nucleotides. This reminds me of how Base Editors can randomly alter DNA R-loops or ssRNA.

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Benjamin L. Oakes @benjaminloakes.bsky.social · 27/02/2025

1. A SC Off-Target (OT) ID From the grahammcvicker.bsky.social lab I always appreciate some good ole method development, and this one is nicely satisfying. They’ve taken a “GUIDE-seq” style off-target ID (oligo drop-in) and upgraded it with a barcoded T7 promoter. It makes so much sense!

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