PT  - JOURNAL ARTICLE
AU  - Ryan D. Chow
AU  - Jennifer S. Chen
AU  - Johanna Shen
AU  - Sidi Chen
TI  - pegFinder: A pegRNA designer for CRISPR prime editing
AID  - 10.1101/2020.05.06.081612
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.06.081612
4099  - http://biorxiv.org/content/early/2020/05/08/2020.05.06.081612.short
4100  - http://biorxiv.org/content/early/2020/05/08/2020.05.06.081612.full
AB  - CRISPR technologies have been widely adopted as powerful tools for targeted genomic manipulation 1. Recently, a new CRISPR-based strategy for precision genome editing was developed that enables diverse genomic alterations to be directly written into target sites without requiring double-strand breaks (DSBs) or donor templates 2. Termed prime editing, this approach involves two key components: 1) a catalytically impaired Cas9 nickase fused to a reverse transcriptase (PE2), and 2) a multifunctional prime editing guide RNA (pegRNA) that specifies the target site and further acts as a template for reverse transcription (RT). pegRNAs are similar to standard single-guide RNAs (sgRNAs), but additionally have a customizable extension on the 3’ end. The 3’ extension is composed of a RT template that encodes the desired edit and a primer binding site (PBS) that anneals to the target genomic site to prime the RT reaction 2. These additional components considerably increase the complexity of pegRNA design compared to standard sgRNAs. While many tools have been developed for identifying candidate sgRNAs in a target DNA sequence 3–8, no user-friendly web application currently exists for designing pegRNAs. We therefore developed pegFinder, a streamlined web tool that rapidly designs candidate pegRNAs (Figure 1). The pegFinder web portal is freely available at http://pegfinder.sidichenlab.org/ (Supplementary Figure 1).Competing Interest StatementThe authors have declared no competing interest.