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利用工程化嵌合 Cas9 进行 PAM-flexible 基因组编辑

PAM-flexible genome editing with an engineered chimeric Cas9.

机构信息

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.

出版信息

Nat Commun. 2023 Oct 4;14(1):6175. doi: 10.1038/s41467-023-41829-y.


DOI:10.1038/s41467-023-41829-y
PMID:37794046
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10550912/
Abstract

CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.

摘要

CRISPR 酶需要一个定义明确的邻近基序 (PAM) 侧翼的指导 RNA 编程的靶位点,这限制了它们在强大的基因组编辑应用中的序列可及性。在这项研究中,我们重组了 SpRY 的 PAM 相互作用域,SpRY 是一种具有广泛靶向的 Cas9,具有 NRN>NYN(R=A 或 G,Y=C 或 T)PAM 偏好,与 Sc++的 N 端相结合,Sc++是一种同时具有广泛、高效和准确的 NNG 编辑能力的 Cas9,生成一种具有高度灵活 PAM 偏好的嵌合酶:SpRYc。我们证明 SpRYc 利用两种酶的特性来特异性编辑不同的 PAMs 和与疾病相关的基因座,用于潜在的治疗应用。总之,生成 SpRYc 的方法,加上其强大的灵活性,突出了 Cas9 工程中整合蛋白设计的力量,并为需要精确基因组定位的下游编辑应用提供了动力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/4e90f1f82167/41467_2023_41829_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/bef1167c4623/41467_2023_41829_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/fccd93c435b2/41467_2023_41829_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/4e90f1f82167/41467_2023_41829_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/bef1167c4623/41467_2023_41829_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/fccd93c435b2/41467_2023_41829_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfb/10550912/4e90f1f82167/41467_2023_41829_Fig3_HTML.jpg

相似文献

[1]
PAM-flexible genome editing with an engineered chimeric Cas9.

Nat Commun. 2023-10-4

[2]
PAM-Flexible Genome Editing with an Engineered Chimeric Cas9.

Res Sq. 2023-3-7

[3]
SpRY Cas9 Can Utilize a Variety of Protospacer Adjacent Motif Site Sequences To Edit the Candida albicans Genome.

mSphere. 2021-5-19

[4]
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants.

Science. 2020-3-26

[5]
An engineered ScCas9 with broad PAM range and high specificity and activity.

Nat Biotechnol. 2020-5-11

[6]
Expanding the Genome-Editing Toolbox with Cas9 Using a Unique Protospacer Adjacent Motif Sequence.

CRISPR J. 2024-8

[7]
Minimal PAM specificity of a highly similar SpCas9 ortholog.

Sci Adv. 2018-10-24

[8]
Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9.

Nat Commun. 2024-4-30

[9]
PAM-less plant genome editing using a CRISPR-SpRY toolbox.

Nat Plants. 2021-1

[10]
PAM-Less CRISPR-SpRY Genome Editing in Plants.

Methods Mol Biol. 2023

引用本文的文献

[1]
PAM-interacting domain turn-helix 51 motifs can improve Cas9-SpRY activity.

Nucleic Acids Res. 2025-8-11

[2]
Synthetic and Functional Engineering of Bacteriophages: Approaches for Tailored Bactericidal, Diagnostic, and Delivery Platforms.

Molecules. 2025-7-25

[3]
Off-target effects in CRISPR-Cas genome editing for human therapeutics: Progress and challenges.

Mol Ther Nucleic Acids. 2025-7-17

[4]
Recent applications, future perspectives, and limitations of the CRISPR-Cas system.

Mol Ther Nucleic Acids. 2025-7-17

[5]
Design of highly functional genome editors by modelling CRISPR-Cas sequences.

Nature. 2025-7-30

[6]
Structural basis of a dual-function type II-B CRISPR-Cas9.

Nucleic Acids Res. 2025-6-20

[7]
Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing.

Mol Cell. 2025-5-1

[8]
Make-or-break prime editing for genome engineering in Streptococcus pneumoniae.

Nat Commun. 2025-4-23

[9]
Custom CRISPR-Cas9 PAM variants via scalable engineering and machine learning.

Nature. 2025-4-22

[10]
CRISPR/Cas9: a sustainable technology to enhance climate resilience in major Staple Crops.

Front Genome Ed. 2025-3-18

本文引用的文献

[1]
Inference of CRISPR Edits from Sanger Trace Data.

CRISPR J. 2022-2

[2]
Genome-wide detection and analysis of CRISPR-Cas off-targets.

Prog Mol Biol Transl Sci. 2021

[3]
Scalable characterization of the PAM requirements of CRISPR-Cas enzymes using HT-PAMDA.

Nat Protoc. 2021-3

[4]
A catalogue of biochemically diverse CRISPR-Cas9 orthologs.

Nat Commun. 2020-11-2

[5]
DNA capture by a CRISPR-Cas9-guided adenine base editor.

Science. 2020-7-31

[6]
PAM-less is more.

Nat Methods. 2020-6

[7]
Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity.

Nat Biotechnol. 2020-3-16

[8]
A Cas9 with PAM recognition for adenine dinucleotides.

Nat Commun. 2020-5-18

[9]
An engineered ScCas9 with broad PAM range and high specificity and activity.

Nat Biotechnol. 2020-5-11

[10]
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants.

Science. 2020-3-26

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