PINE-CONE

PINE-CONE automates the design of prime editing guide RNAs (pegRNAs) and associated accessory guides and oligonucleotides from specified genomic edit coordinates to support CRISPR-based prime editing experiments.

Key Features:

• Automated PegRNA Design: Automates design of pegRNAs that encode both guide sequences and reverse-transcription edit templates for prime editing.
• High-Throughput Capability: Generates pegRNA designs at scale to enable bulk library creation and large-scale targeting.
• Translation of Edit Coordinates and Sequences: Translates specified genomic edit coordinates and input sequences into comprehensive pegRNA designs, accessory guides, and oligonucleotide sequences.
• Cloning Workflow Support: Provides ready-to-use pegRNA, accessory guide, and oligonucleotide sequences to support cloning for prime editing experiments.

Scientific Applications:

• Synthetic Biology: Enables construction and testing of precise nucleotide changes and engineered genetic variants using prime editing.
• Biomedical Research: Supports studies requiring precise nucleotide substitutions with prime editing, which operates without double-stranded DNA breaks or donor DNA templates.
• Disease Variant Libraries: Enables rapid design of pegRNA libraries targeting disease-relevant genetic variants, exemplified by generation of a pegRNA library for Alzheimer's disease SNPs.

Methodology:

Translates user-defined genomic edit coordinates and sequences into functional pegRNA constructs and generates accessory guides and oligonucleotide sequences through automated computational processing.