Gene Sculpt Suite

Gene Sculpt Suite provides computational tools to design oligonucleotides and predict microhomology-mediated DNA repair outcomes to improve precision of genome editing with Zinc Finger Nucleases, TALENs, and CRISPR/Cas systems.

Key Features:

• GTagHD: Automates the design and generation of oligonucleotides tailored for the GeneWeld knock-in protocol.
• MEDJED: Employs machine learning to predict the likelihood that a double-stranded DNA break will engage the microhomology-mediated repair (MMR) pathway.
• MENTHU: Identifies genomic loci likely to yield a single predominant microhomology-mediated end joining allele (PreMA) and predicts the specific repair products following DNA breaks.
• Supported nucleases: Provides design and prediction capabilities applicable to Zinc Finger Nucleases, TALENs, and CRISPR/Cas systems.

Scientific Applications:

• Functional genomics: Facilitates targeted perturbations and precise knock-ins to study gene function via predicted repair outcomes and oligonucleotide designs.
• Therapeutic gene editing: Supports design choices that influence repair pathway usage and allele outcomes relevant to therapeutic gene modification strategies.
• Synthetic biology: Enables precise insertion and predictable repair outcomes for engineering genetic constructs and pathways.

Methodology:

Automated oligonucleotide design for the GeneWeld knock-in protocol; machine learning–based prediction of MMR engagement at double-stranded breaks; identification and prediction of PreMA microhomology-mediated end joining outcomes.