How do I show off-target effects?

Add a side panel with a heatmap of cleavage frequency at on-target vs 5 off-target loci. Color cells by frequency.

Life ScienceText → ImageMid creditEN

CRISPR-Cas9 Mechanism Diagram

Guide-RNA-loaded Cas9 binds protospacer, makes a double-strand break, and triggers NHEJ or HDR repair.

When to use this prompt

For molecular biology / gene editing / therapeutics papers and educational explainers.

The prompt

A CRISPR-Cas9 mechanism diagram, three-panel horizontal flow.

Panel 1 — Targeting:
- Cas9 protein (drawn as a rounded multi-domain blob) loaded with a guide RNA (sgRNA, drawn as a curved colored ribbon).
- The complex scans double-stranded DNA and binds the protospacer matching the sgRNA spacer.
- A small PAM sequence (5'-NGG-3') labeled adjacent to the protospacer.

Panel 2 — Cleavage:
- Cas9 induces a blunt double-strand break (DSB) 3 bp upstream of the PAM.
- Show the DNA backbone with the cut clearly indicated by a small zigzag at both strands.

Panel 3 — Repair:
- Two parallel sub-paths from the DSB:
  - Top sub-path: Non-Homologous End Joining (NHEJ), often producing small indels (red bracket showing inserted/deleted bases).
  - Bottom sub-path: Homology-Directed Repair (HDR) using a donor template (drawn as a separate dsDNA snippet) producing precise edits (green check on insertion).

Style: clean biomedical illustration, navy / coral / green palette, white background, sans-serif. Suitable for Molecular Cell / Nature Methods.

Variations

Base editor variant

Replace Cas9 with a Cas9 nickase fused to a deaminase domain (cytidine or adenine base editor). Remove the DSB; show targeted base conversion (C->T or A->G) without strand breakage.

Tips

Show PAM explicitly. Without it, the targeting story is incomplete.
Always contrast NHEJ vs HDR in repair. Single-path diagrams miss the editing-outcome dichotomy.
Label the DSB with the exact distance to PAM (3 bp). Specifics increase reader trust.