Evidence map›Paper›PMID 41573840›Full record

ArticlebioRxiv : the preprint server for biology2025

Structure and evolution-guided design of minimal RNA-guided nucleases.

Petr Skopintsev, Isabel Esain-Garcia, Evan C DeTurk, Peter H Yoon, Zehan Zhou, Trevor Weiss, Maris Kamalu, Ajit Chamraj, Kenneth J Loi, Conner J Langeberg and 10 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Petr SkopintsevInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0002-6043-157X
Isabel Esain-GarciaInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0003-1931-4563
Evan C DeTurkInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0009-0004-9613-8625
Peter H YoonInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0002-9156-1393
Zehan ZhouInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0003-1174-2635
Trevor WeissDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.ORCID 0000-0002-2373-0802
Maris KamaluDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.ORCID 0009-0009-8008-7196
Ajit ChamrajInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0009-0005-7114-1753
Kenneth J LoiInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0009-0009-5508-6511
Conner J LangebergInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0002-5609-3758
Ron BogerInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0002-4467-271X
Hunter NisonoffCenter for Computational Biology, University of California Berkeley, Berkeley, CA, USA.ORCID 0000-0003-1357-8111
Hannah M KarpInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0002-1619-5901
LinXing ChenDepartment of Earth and Planetary Science, University of California, Berkeley, CA, USA.ORCID 0000-0003-2774-1952
Honglue ShiInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0003-3847-1652
Kamakshi VohraInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0009-0004-4368-2694
Jillian F BanfieldInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0001-8203-8771
Jamie H D CateInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0001-5965-7902
Steven E JacobsenDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.ORCID 0000-0001-9483-138X
Jennifer A DoudnaInnovative Genomics Institute, University of California, Berkeley; Berkeley, CA, USA.ORCID 0000-0001-9161-999X

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome editing capabilities. However, generating diverse multi-domain proteins with robust enzymatic properties remains challenging. Here we use an artificial intelligence-driven strategy that couples structure-guided inverse protein folding with evolution-informed residue constraints to generate active, divergent variants of TnpB, a minimal CRISPR-Cas12-like nuclease. High-throughput functional screening of AI-generated variants yielded editors that retained or exceeded wild-type activity in bacterial, plant and human cells. Cryo-EM-based structure determination of the most divergent active variant revealed new stabilizing contacts in the RNA/DNA interfaces across conformational states, demonstrating the design potential of this approach. Together these results establish a strategy for creating non-natural RNA-guided nucleases and conformationally active nucleic acid binders, enlarging the designable protein space.

Identifiers

PMID41573840
PMCPMC12822741

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.