pegFinder

pegFinder designs prime editing guide RNAs (pegRNAs) to enable CRISPR prime editing for precise genomic alterations without double-strand breaks or donor templates.

Key Features:

• Comprehensive pegRNA design: Constructs pegRNAs that include a customizable 3' extension comprising a reverse transcription template and a primer binding site to encode desired edits.
• Candidate generation: Produces candidate pegRNAs for specified genomic target sites to support selection of editing strategies.
• sgRNA-to-pegRNA considerations: Accounts for the additional components and constraints of pegRNAs compared to standard single-guide RNAs (sgRNAs).
• PE2 compatibility: Designs pegRNAs compatible with PE2, the catalytically impaired Cas9 nickase fused to a reverse transcriptase.

Scientific Applications:

• Functional Genomics: Introducing specific mutations to investigate gene function and regulation.
• Therapeutic Development: Designing precise genome edits as potential interventions for genetic disorders.
• Agricultural Biotechnology: Writing targeted genomic changes to modify crop traits.

Methodology:

The approach integrates the PE2 system (catalytically impaired Cas9 nickase fused to a reverse transcriptase) with multifunctional pegRNAs that specify the target and provide a reverse transcription template via a customizable 3' extension encoding the desired edit.