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Kenneth Loi

@kenjmloi.bsky.social
178 followers 26 following 19 posts

Berkeley Biophysics, Doudna Lab kennethloi.com

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Reposted by Kenneth Loi
Luis E. Valentin-Alvarado @luisvalentin.bsky.social · 09/10/2026
Excited to share our work on bacterial immune signaling! Our preprint reveals how RNA-guided Cas13 cleaves host tRNAs to generate small-molecule messengers that activate 2TMβ, linking RNA recognition to membrane damage and phage defense. 1/11
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Reposted by Kenneth Loi
Doudna Lab @doudna-lab.bsky.social · 19/09/2026
Thank you @jpkbravo.bsky.social for the perspective article on our work: www.science.org/doi/10.1126/...
science.org
A viral origin for RNA-guided immunity
Ancient viral warfare could be at the root of modern class 1 CRISPR bacterial defense systems
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Reposted by Kenneth Loi
Doudna Lab @doudna-lab.bsky.social · 19/09/2026
Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
science.org
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
Pretty surreal to see our work in The New York Times. Thank you, Carl Zimmer, for sharing the story of VIPR! www.nytimes.com/2026/09/17/s...
nytimes.com
The Next Gene-Editing Technology May Also Be the Oldest (Gift Article)
Scientists have discovered a powerful gene-targeting system in viruses. Billions of years old, VIPR seems to predate CRISPR and may be even more effective.
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
For the story behind the ultimate anime betrayal, check out the piece by Andy Murdock: innovativegenomics.org/news/vipr-sy...
innovativegenomics.org
VIPR Systems Break the Rules of the Genetic Code to Target and Twist Around DNA
How researchers in the Doudna Lab discovered VIPR, an ancient progenitor of CRISPR found in viruses that snakes around genes
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
Thank you, Jack Bravo, for the accompanying Science Perspective, “A viral origin for RNA-guided immunity.” www.science.org/doi/10.1126/...
science.org
A viral origin for RNA-guided immunity
Ancient viral warfare could be at the root of modern class 1 CRISPR bacterial defense systems
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
Our two papers in Science: Discovery and the noncontiguous targeting code: www.science.org/doi/10.1126/... Structure and geometric triplex formation: www.science.org/doi/10.1126/...
science.org
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
VIPR is now out in Science! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓
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Reposted by Kenneth Loi
Doudna Lab @doudna-lab.bsky.social · 16/07/2026
Our AI-guided design of RNA-guided nucleases is now out in @science.org 💻🧬 We used structure and evolutionary data to generate minimal, active and divergent gene editors! www.science.org/doi/10.1126/... Congrats to @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social & team!
science.org
Structure and evolution-guided design of minimal RNA-guided nucleases
The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic ...
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Kenneth Loi @kenjmloi.bsky.social · 28/04/2026
Yep! The skipped position in the target often aligns with the wobble position of the codon
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Kenneth Loi @kenjmloi.bsky.social · 28/04/2026
Yes! Exactly! This is a recurring theme in some RNA-guided DNA-targeting systems. BridgeRNA recombinases and group II introns also follow similar principles where the guide has discontiguous loops that collectively define a target site! Thereby preventing self targeting!
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Reposted by Kenneth Loi
Michael Baym @baym.lol · 28/04/2026
The wobble-skip mechanism of matching two-of-three bases is wildly cool. Most synonymous mutants can’t escape
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Kenneth Loi @kenjmloi.bsky.social · 28/04/2026
Thanks Martin! Wouldn’t have been possible without FoldSeek
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
I posted the links to the BioRxiv preprints at the end of the thread! Please let me know if you have any issues accessing it
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Reposted by Kenneth Loi
Doudna Lab @doudna-lab.bsky.social · 27/04/2026
We present VIPR, a phage-encoded RNA-guided system that recognizes DNA with a noncontiguous code unlike CRISPR. Tiny, programmable, possibly ancestral to CRISPR immunity; VIPR is built around a striking RNA-DNA-DNA triplex.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
This work was co-led by myself and Peter Yoon. Structure was led by Peter, @terryzzy.bsky.social , and Trevor Docter. Many thanks to our intrepid collaborators and special thanks to Jennifer for supporting us through this project. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
VIPR is tiny: a ~20 kDa protein + <100 nt RNA. Reprogrammed by changing only the NN positions. This makes it one of the most minimal DNA-binding platforms known, and hints that more guide-RNA codes are still hiding in nature.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
CryoEM revealed a striking structure. VIPR wraps around DNA as a protein filament, holding the guide RNA and both DNA strands together in a triplex core.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Adaptive immunity may have begun not as a bacterial invention. Ancient phages likely used VIPR-like systems against rivals. Bacteria acquired one, coupled it to a Cas1-like integrase, and transformed viral conflict into heritable immune memory.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
By reprogramming the NN positions, we demonstrate transcriptional repression of GFP as well as phage defense.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Once we decoded this rule, the natural targets pointed to competing phages. VIPR presents RNA-guided warfare between viruses.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Unlike most guide RNAs—CRISPR, RNAi, Argonaute—VIPR does not read targets as one continuous match. It reads a broken code, leaving much of the would-be RNA-DNA duplex unpaired.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
The surprise was in the RNA. Using Evo2, we found that VIPR RNAs are built from repeated YNNGG units: conserved GGY segments alternating with hypervariable NN bases.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
We went looking for CRISPR’s roots. A structure-guided search uncovered a phage-encoded family of RAMP-like proteins. Phylogeny suggests VIPR predates Cas5-7.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Reposted by Kenneth Loi
Erin Doherty @erinedoherty.bsky.social · 02/10/2025
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity. Check out this work co-led with @benadler.bsky.social here: www.nature.com/articles/s41...
nature.com
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
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Reposted by Kenneth Loi
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 27/04/2025
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...
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Reposted by Kenneth Loi
Erin Doherty @erinedoherty.bsky.social · 31/03/2025
Preprint alert! ✨ In this project that I co-led with @benadler.bsky.social, we show that a miniature CRISPR-Cas10-like enzyme, mCpol, uses a novel inverse signaling mechanism to prevent the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Check it out:
biorxiv.org
A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway
Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems. In these pathways, including CBASS a...
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