# CRISPR-Cas9 基因编辑沙盒

设计向导 RNA，扫描靶基因的靶向与脱靶位点，观察 Cas9 切割，并在交互式 CRISPR-Cas9 分子模型中对比 NHEJ 基因敲除与 HDR 基因敲入两种修复结果。

> 标准页面: https://elysiatools.com/zh/visualizations/crispr-gene-editing-sandbox

- **分类:** Biology

## 概述

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).

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