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PrimeDesign 软件可快速简化向导 RNA 设计。

PrimeDesign software for rapid and simplified design of prime editing guide RNAs.

机构信息

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.

出版信息

Nat Commun. 2021 Feb 15;12(1):1034. doi: 10.1038/s41467-021-21337-7.

DOI:10.1038/s41467-021-21337-7
PMID:33589617
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7884779/
Abstract

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

摘要

Prime 编辑 (PE) 是一种多功能的基因组编辑技术，但所需的指导 RNA 的设计比标准的基于 CRISPR 的核酸酶或碱基编辑器更为复杂。在这里，我们描述了 PrimeDesign，这是一个用户友好的端到端网络应用程序和命令行工具，用于设计 PE 实验。PrimeDesign 可用于单编辑和组合编辑应用，以及全基因组和饱和诱变筛选。使用 PrimeDesign，我们构建了 PrimeVar，这是一个全面的、可搜索的数据库，其中包括候选的 Prime 编辑引导 RNA (pegRNA) 和切口 sgRNA (ngRNA) 组合，用于安装或纠正来自 ClinVar 数据库的 >68,500 种致病人类遗传变异。最后，我们使用 PrimeDesign 设计 pegRNAs/ngRNAs，以在人类细胞中安装各种人类致病变异。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/55d9747c5cbc/41467_2021_21337_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/a38420e607b3/41467_2021_21337_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/0e2a86caf29a/41467_2021_21337_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/55d9747c5cbc/41467_2021_21337_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/a38420e607b3/41467_2021_21337_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/0e2a86caf29a/41467_2021_21337_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/7884779/55d9747c5cbc/41467_2021_21337_Fig3_HTML.jpg

相似文献

[1]
PrimeDesign software for rapid and simplified design of prime editing guide RNAs.

Nat Commun. 2021-2-15

[2]
Sequential Activation of Guide RNAs to Enable Successive CRISPR-Cas9 Activities.

Mol Cell. 2021-1-21

[3]
Screening of CRISPR/Cas base editors to target the AMD high-risk Y402H complement factor H variant.

Mol Vis. 2019-3-16

[4]
Prime Editing Guide RNA Design Automation Using PINE-CONE.

ACS Synth Biol. 2021-2-19

[5]
A web tool for the design of prime-editing guide RNAs.

Nat Biomed Eng. 2021-2

[6]
[CRISPR/CAS9, the King of Genome Editing Tools].

Mol Biol (Mosk). 2017

[7]
Shooting the messenger: RNA-targetting CRISPR-Cas systems.

Biosci Rep. 2018-6-21

[8]
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Insect Biochem Mol Biol. 2018-8-26

[9]
In Vivo Genome Editing Restores Dystrophin Expression and Cardiac Function in Dystrophic Mice.

Circ Res. 2017-9-29

[10]
Correction of Three Prominent Mutations in Mouse and Human Models of Duchenne Muscular Dystrophy by Single-Cut Genome Editing.

Mol Ther. 2020-9-2

引用本文的文献

[1]
Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.

Nat Methods. 2025-9-1

[2]
Precise correction of G6PD Viangchan mutation in iPSCs by prime editing strategy.

Sci Rep. 2025-8-18

[3]
Simvastatin overcomes the pPCK1-pLDHA-SPRINGlac axis-mediated ferroptosis and chemo-immunotherapy resistance in AKT-hyperactivated intrahepatic cholangiocarcinoma.

Cancer Commun (Lond). 2025-8

[4]
New hope and promise with CRISPR-Cas9 technology for the treatment of HIV.

Funct Integr Genomics. 2025-5-24

[5]
Make-or-break prime editing for genome engineering in Streptococcus pneumoniae.

Nat Commun. 2025-4-23

[6]
Rewriting regulatory DNA to dissect and reprogram gene expression.

Cell. 2025-4-14

[7]
Prime Editing of Mouse Primary Neurons.

Methods Mol Biol. 2025

[8]
Current trends in gene therapy to treat inherited disorders of the brain.

Mol Ther. 2025-5-7

[9]
Recent advances in therapeutic gene-editing technologies.

Mol Ther. 2025-6-4

[10]
In vivo prime editing rescues photoreceptor degeneration in nonsense mutant retinitis pigmentosa.

Nat Commun. 2025-3-10

本文引用的文献

[1]
Predicting the efficiency of prime editing guide RNAs in human cells.

Nat Biotechnol. 2021-2

[2]
Prime genome editing in rice and wheat.

Nat Biotechnol. 2020-3-16

[3]
Efficient generation of mouse models with the prime editing system.

Cell Discov. 2020-4-28

[4]
Search-and-replace genome editing without double-strand breaks or donor DNA.

Nature. 2019-10-21

[5]
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage.

Nature. 2017-11-23

[6]
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage.

Nature. 2016-5-19

[7]
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.

Nat Biotechnol. 2016-2

[8]
ClinVar: public archive of interpretations of clinically relevant variants.

Nucleic Acids Res. 2016-1-4

[9]
Efficient genome editing in zebrafish using a CRISPR-Cas system.

Nat Biotechnol. 2013-1-29

[10]
RNA-guided human genome engineering via Cas9.

Science. 2013-1-3

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