# CRISPR-Cas9 Gene Editing Sandbox

Design a guide RNA, scan a target gene for on-target and off-target sites, watch Cas9 cut, and explore NHEJ knockout vs HDR knock-in repair outcomes in an interactive CRISPR-Cas9 molecular model.

> Canonical page: https://elysiatools.com/en/visualizations/crispr-gene-editing-sandbox

- **Category:** Biology

## Overview

Interactive CRISPR-Cas9 molecular biology sandbox covering the full gene-editing pipeline — distinct from existing biology cases (dna-replication shows replication mechanics, waddington shows epigenetic fate, this is the only case on genome editing). Design a 20-nt guide RNA (gRNA), scan a target gene for on-target and off-target sites, watch Cas9 cut, and compare NHEJ knockout vs HDR knock-in repair outcomes. Core model: Cas9 is an RNA-guided endonuclease that base-pairs the gRNA with a complementary DNA protospacer, requiring a neighboring PAM motif (5'-NGG-3' for SpCas9); the HNH and RuvC nuclease domains each cut one strand 3 bp upstream of the PAM, producing a blunt double-strand break (DSB). The scan engine finds every NGG site on both strands, counts mismatches between gRNA and protospacer, and identifies seed-region (PAM-proximal 8–14 nt) mismatches that abolish binding. Activity scoring combines GC content (ideal 40–60%) with position-dependent weighting (seed region weighted highest), and the specificity score = on-target activity / (on-target + Σ off-target risk). Three visualization panels: (1) Target DNA double helix with gRNA alignment — green = matched base, red = mismatch, gold = PAM (NGG), magenta scissors = Cas9 cut site, animated cut flash; (2) Off-Target Map ranking every candidate site by cleavage likelihood with red highlighting for dangerous off-targets within tolerance; (3) Repair Outcome Spectrum — NHEJ mode shows an indel-size histogram (negative = deletion, positive = insertion, multiples-of-3 muted as in-frame) with frameshift-fraction prediction of knockout efficiency; HDR mode shows an integration success-vs-failure donut driven by donor-template efficiency. Includes a standard 64-codon genetic-code table for protein-level effect prediction. Six scenario presets: EMX1 (canonical human target, Cong et al. 2013), GFP knock-in (HDR insertion), Off-target risk (perfect on-target + dangerous 3-mismatch off-target), Sickle-cell correction (HBB β-globin E6V, the Casgevy/CTX001 therapy target), BRCA1 exon (tumor-suppressor knockout), and Perfect match (high-GC synthetic target showing GC-content effect). Adjustable parameters: gRNA sequence (live 20-nt input with GC% display), target DNA, active-site selector, off-target tolerance (0–6 mismatches), seed length (8–14 nt), repair pathway toggle (NHEJ/HDR), NHEJ indel rate (0.1–0.95), HDR donor template + efficiency (0–0.9). Real-time statistics: sites found, on-target mismatches, specificity score, cut position, activity, frameshift/integration fraction. Educational content covers recognition (gRNA-PAM targeting), cleavage (HNH/RuvC blunt DSB), NHEJ (error-prone indels → frameshift knockout), HDR (precise homology-arm repair → knock-in), off-target effects (seed vs distal mismatch tolerance, the main therapeutic safety concern), and applications (Doudna & Charpentier 2012 / 2020 Nobel Chemistry, Casgevy sickle-cell therapy, base editors, prime editors, CRISPRi/a screens, SHERLOCK diagnostics, agricultural engineering). Multi-language support (zh, en, es, fr, de, ru, pt).

## Related content

- [Zero-Order Reaction - Interactive Visualization](https://elysiatools.com/en/visualizations/zero-order-reaction): Interactive visualization of zero-order reaction kinetics and concentration changes over time
- [First-Order Reaction - Interactive Visualization](https://elysiatools.com/en/visualizations/first-order-reaction): Interactive visualization of first-order reaction kinetics and exponential concentration decay
- [Second-Order Reaction - Interactive Visualization](https://elysiatools.com/en/visualizations/second-order-reaction): Interactive visualization of second-order reaction kinetics and bimolecular collision dynamics
- [Arrhenius Equation](https://elysiatools.com/en/visualizations/arrhenius-equation): Interactive visualization of temperature effect on reaction rate - Explore activation energy, pre-exponential factor, and rate constant relationship
- [Reversible Reaction](https://elysiatools.com/en/visualizations/reversible-reaction): Interactive visualization of A ⇌ B reversible reaction kinetics - Explore forward and reverse reaction rates, equilibrium constant, and concentration changes over time
- [Consecutive Reaction](https://elysiatools.com/en/visualizations/consecutive-reaction): Interactive visualization of A → B → C consecutive reaction kinetics - Explore intermediate concentration peaks, rate-determining steps, and complete evolution of all species
- [Chain Reaction](https://elysiatools.com/en/visualizations/chain-reaction): Interactive visualization of free radical chain reaction polymerization - Explore initiation, propagation, termination steps, chain growth animation, and molecular weight distribution
- [Le Chatelier's Principle](https://elysiatools.com/en/visualizations/le-chateliers-principle): Interactive visualization of Le Chatelier's Principle - Explore how changes in concentration, pressure, and temperature affect chemical equilibrium with animated molecular dynamics