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产物释放后多轮循环Cas9的可视化。

Visualization of a multi-turnover Cas9 after product release.

作者信息

Kiernan Kaitlyn A, Taylor David W

机构信息

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.

Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.

出版信息

Nat Commun. 2025 Jul 1;16(1):5681. doi: 10.1038/s41467-025-60668-7.


DOI:10.1038/s41467-025-60668-7
PMID:40593576
Abstract

While the most widely used CRISPR-Cas enzyme is the Cas9 endonuclease from Streptococcus pyogenes (Cas9), it exhibits single-turnover enzyme kinetics which leads to long residence times on product DNA. This blocks access to DNA repair machinery and acts as a major bottleneck during CRISPR-Cas9 gene editing. Cas9 can eventually be removed from the product by extrinsic factors, such as translocating polymerases, but the mechanisms contributing to Cas9 dissociation following cleavage remain poorly understood. Here, we employ truncated guide RNAs as a strategy to weaken PAM-distal nucleic acid interactions and promote faster enzyme turnover. Using kinetics-guided cryo-EM, we examine the conformational landscape of a multi-turnover Cas9, including the first detailed snapshots of Cas9 dissociating from product DNA. We discovered that while the PAM-distal product dissociates from Cas9 following cleavage, tight binding of the PAM-proximal product directly inhibits re-binding of new targets. Our work provides direct evidence as to why Cas9 acts as a single-turnover enzyme and will guide future Cas9 engineering efforts.

摘要

虽然使用最广泛的CRISPR-Cas酶是化脓性链球菌的Cas9核酸内切酶(Cas9),但它表现出单轮酶动力学,这导致其在产物DNA上的停留时间较长。这阻碍了DNA修复机制的作用,并且在CRISPR-Cas9基因编辑过程中成为一个主要瓶颈。Cas9最终可以通过外部因素(如易位聚合酶)从产物中去除,但切割后导致Cas9解离的机制仍知之甚少。在这里,我们采用截短的引导RNA作为一种策略,以削弱PAM远端核酸相互作用并促进更快的酶周转。利用动力学引导的冷冻电镜,我们研究了多轮Cas9的构象变化,包括Cas9从产物DNA上解离的首张详细快照。我们发现,虽然PAM远端产物在切割后从Cas9上解离,但PAM近端产物的紧密结合直接抑制了新靶点的重新结合。我们的工作为Cas9为何作为单轮酶提供了直接证据,并将指导未来的Cas9工程研究。

相似文献

[1]
Visualization of a multi-turnover Cas9 after product release.

Nat Commun. 2025-7-1

[2]
Visualization of a multi-turnover Cas9 after product release.

bioRxiv. 2024-11-26

[3]
Structural basis of a dual-function type II-B CRISPR-Cas9.

Nucleic Acids Res. 2025-6-20

[4]
Orthogonal transcriptional modulation and gene editing using multiple CRISPR-Cas systems.

Mol Ther. 2025-1-8

[5]
Structural integrity and side-chain interaction at the loop region of the bridge helix modulate Cas9 substrate discrimination.

Nucleic Acids Res. 2025-6-20

[6]
Spacer-Complementary Single-Stranded DNA Oligonucleotides Can Serve as Target-Specific Inhibitors in CRISPR/Cas9 Systems.

Cell Biochem Funct. 2025-6

[7]
Mechanisms and engineering of a miniature type V-N CRISPR-Cas12 effector enzyme.

Nat Commun. 2025-7-1

[8]
The initiation, propagation and dynamics of CRISPR-SpyCas9 R-loop complex.

Nucleic Acids Res. 2018-1-9

[9]
Harnessing an anti-CRISPR protein for powering CRISPR/Cas9-mediated genome editing in undomesticated Bacillus strains.

Microb Cell Fact. 2025-6-23

[10]
[Improving the Efficiency and Safety of Human CCR5 Gene Editing by Selection of Optimal Guide RNAs for SpCAS9 and CAS12A].

Mol Biol (Mosk). 2025

本文引用的文献

[1]
Structural basis of Cas9 DNA interrogation with a 5' truncated sgRNA.

Nucleic Acids Res. 2025-1-7

[2]
Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles.

Nat Commun. 2024-11-7

[3]
Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor.

Nat Commun. 2024-8-10

[4]
HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing.

Nat Commun. 2024-7-10

[5]
PAM-flexible Engineered FnCas9 variants for robust and ultra-precise genome editing and diagnostics.

Nat Commun. 2024-6-28

[6]
Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9.

Cell. 2024-6-20

[7]
Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9.

Nat Commun. 2024-4-30

[8]
Negative DNA supercoiling induces genome-wide Cas9 off-target activity.

Mol Cell. 2023-10-5

[9]
CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid.

Biochemistry. 2023-9-5

[10]
Efficient high-precision homology-directed repair-dependent genome editing by HDRobust.

Nat Methods. 2023-9

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