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A web tool for the design of prime-editing guide RNAs
Nature Biomedical Engineering ( IF 28.1 ) Pub Date : 2020-09-28 , DOI: 10.1038/s41551-020-00622-8
Ryan D Chow 1, 2, 3, 4 , Jennifer S Chen 4, 5, 6, 7 , Johanna Shen 1, 2, 3 , Sidi Chen 1, 2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14
Affiliation  

Prime editing enables diverse genomic alterations to be written into target sites without requiring double-strand breaks or donor templates. The design of prime-editing guide RNAs (pegRNAs), which must be customized for each edit, can however be complex and time consuming. Compared with single guide RNAs (sgRNAs), pegRNAs have an additional 3′ extension composed of a primer binding site and a reverse-transcription template. Here we report a web tool, which we named pegFinder (http://pegfinder.sidichenlab.org), for the rapid design of pegRNAs from reference and edited DNA sequences. pegFinder can incorporate sgRNA on-target and off-target scoring predictions into its ranking system, and nominates secondary nicking sgRNAs for increasing editing efficiency. CRISPR-associated protein 9 variants with expanded targeting ranges are also supported. To facilitate downstream experimentation, pegFinder produces a comprehensive table of candidate pegRNAs, along with oligonucleotide sequences for cloning.



中文翻译:

用于设计引物编辑指南 RNA 的网络工具

Prime 编辑可以将不同的基因组改变写入目标位点,而无需双链断裂或供体模板。然而,必须为每次编辑定制的引物编辑引导 RNA (pegRNA) 的设计可能既复杂又耗时。与单向导 RNA (sgRNA) 相比,pegRNA 具有额外的 3' 延伸,由引物结合位点和逆转录模板组成。在这里,我们报告了一个网络工具,我们将其命名为 pegFinder (http://pegfinder.sidichenlab.org),用于从参考和编辑的 DNA 序列中快速设计 pegRNA。pegFinder 可以将 sgRNA 目标和脱靶评分预测纳入其排名系统,并指定二级切口 sgRNA 以提高编辑效率。还支持具有扩展靶向范围的 CRISPR 相关蛋白 9 变体。

更新日期:2020-09-28
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