PnB Designer

PnB Designer generates prime editing guide RNAs (pegRNAs) and guide RNAs for cytosine and adenine base editors to design and evaluate edits for variant-specific and reference-genome targets, including ClinVar-listed disease-causing mutations.

Key Features:

• Automated pegRNA and gRNA design: Generates prime editing guide RNAs (pegRNAs) for CRISPR prime editors and guide RNAs for base editors, including cytosine base editors (CBEs) and adenine base editors (ABEs).
• Multi-target capability: Designs targeting gRNAs for single or multiple genomic targets using variant-specific sequences or reference genomes.
• Cross-kingdom applicability: Applicable to organisms across multiple biological kingdoms, including animals and plants.
• Disease modeling and mutation correction: Models all known disease-causing mutations listed in ClinVar by designing pegRNAs and identifies optimal base editors by scanning the genome with one CBE and seven different ABE PAM variants.
• CRISPR effector configurations: Supports configurations that fuse deaminases or reverse transcriptases to nCas9 to implement base editing and prime editing.

Scientific Applications:

• Disease modeling and correction: Designing pegRNAs and gRNAs to model and correct ClinVar-listed disease-causing mutations in animal and plant models.
• Functional genomics and therapeutic development: Enabling design of guides for prime editors (PEs) and base editors (BEs) to study gene function, genetic disease mechanisms, and potential therapeutic interventions.

Methodology:

Integrates algorithms that identify optimal guide RNA sequences and performs genome scanning with one CBE and seven different ABE PAM variants to select candidate base editors.