Targeted Genome Editing

CRISPR-Cas9 Diagram Generator

Use the CRISPR-Cas9 Diagram Generator to create clear genome editing mechanism figures. Map target DNA unwinding, single guide RNA (sgRNA) spacer hybridization, Cas9 endonuclease domain cleavage, and double-strand break repair pathways.

sgRNA spacer & scaffoldPAM 5'-NGG recognitionEditable SVG & PPTXJournal quality

CRISPR-Cas9 Diagram Generator

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How it works

How to generate CRISPR-Cas9 diagrams in 3 steps

Design verified genome engineering figures with accurate nuclease lobes, target hybridizations, and downstream DNA repair pathways.

Define your guide RNA, PAM, and target locus

Specify the Cas enzyme variant (SpCas9, SaCas9, Cas12a), 20-nt spacer sequence, PAM motif (5'-NGG), and target genomic locus.

Review nuclease cleavage and repair mechanisms

Verify HNH and RuvC cleavage arrows, R-loop bubble dimensions, and downstream NHEJ knockout or HDR knock-in repair branches.

Export editable vectors for publication

Download layered SVG graphics or native PowerPoint PPTX slides to format nucleotide fonts, protein colors, and panel layouts.

Define your guide RNA, PAM, and target locus

Specify the Cas enzyme variant (SpCas9, SaCas9, Cas12a), 20-nt spacer sequence, PAM motif (5'-NGG), and target genomic locus.

Review nuclease cleavage and repair mechanisms

Verify HNH and RuvC cleavage arrows, R-loop bubble dimensions, and downstream NHEJ knockout or HDR knock-in repair branches.

Export editable vectors for publication

Download layered SVG graphics or native PowerPoint PPTX slides to format nucleotide fonts, protein colors, and panel layouts.

Featured CRISPR-Cas9 diagram examples

Explore editable scientific diagrams detailing Cas9 ribonucleoprotein architecture, PAM recognition, nuclease cleavage, and precision base editing.

Cas9 RNP Complex & Domain Architecture

Bi-lobed Cas9 endonuclease showing the REC recognition lobe, NUC catalytic lobe, bridge helix, and sgRNA scaffold interactions.

Cas9 RNP

PAM Recognition & R-Loop Formation

Protospacer adjacent motif (5'-NGG) binding triggering local DNA unwinding and 20-nucleotide guide spacer hybridization.

5'-NGG-3' PAM

HNH & RuvC Endonuclease Cleavage

Coordinated cleavage of target and non-target DNA strands 3 base pairs upstream of the PAM to produce a blunt double-strand break.

HNH

NHEJ Knockout vs. HDR Knock-in Repair

Cellular DNA repair branches contrasting error-prone indels from NHEJ with high-fidelity template-directed knock-in via HDR.

NHEJ

Base Editing & Prime Editing Systems

Engineered nickase fusions including cytidine/adenine base editors (CBE/ABE) and reverse transcriptase prime editors (PE2/PE3).

Base Editor

In Vivo Delivery & Validation Readouts

Translational delivery modalities comparing AAV vectors and lipid nanoparticles with NGS and GUIDE-seq off-target validation.

AAV

Why SciDraw

Why researchers choose SciDraw for CRISPR diagrams

SciDraw can help draft a scientific visual. Check all labels, relationships, and claims against your source before use.

Workflow Need	SciDraw AI	Generic Image AI
Accurate Bi-Lobed Protein Architecture	Correctly renders the REC recognition lobe, NUC catalytic lobe, and bridge helix aligned with published cryo-EM structures.	Renders amorphous blobs instead of distinct REC/NUC lobes and sgRNA hairpins.
Rigorous PAM & Cleavage Coordinates	Maintains precise 5'-to-3' DNA strand polarity with cleavage markers accurately placed 3 bp upstream of the 5'-NGG motif.	Places cut sites randomly without 5'-NGG-3' PAM alignment or R-loop strand separation.
Full Vector & PowerPoint Presentation Export	Download infinite-resolution SVGs or ungroupable PPTX slides to modify nucleotide letters, colors, and line weights effortlessly.	Produces static pixel images where nucleotide sequences cannot be corrected.
Review Rights Before Use	Paid plans permit commercial use under the SciDraw License, subject to applicable law and third-party rights. Check your publisher’s disclosure requirements.	Ambiguous licensing terms that complicate manuscript and grant disclosures.

Practical guide

Practical guide to designing CRISPR-Cas9 mechanism figures

Follow proven scientific visualization principles to ensure your diagrams are accurate, legible, and aligned with journal requirements.

Cas9 ribonucleoprotein complex diagram detailing REC and NUC lobes with sgRNA

1. Structural anatomy of the Cas9 endonuclease and guide RNA

CRISPR-Cas9 (Type II CRISPR system from Streptococcus pyogenes) operates via coordinated ribonucleoprotein (RNP) machinery. When illustrating this system for publication, represent each structural sub-component with fidelity:

Bi-Lobed Organization: The Cas9 polypeptide folds into two prominent lobes separated by a positively charged bridge helix: the alpha-helical Recognition (REC) lobe and the Nuclease (NUC) lobe.
NUC Catalytic Domains: The NUC lobe contains two distinct endonuclease centers: HNH (which cleaves the complementary target DNA strand) and RuvC (which cleaves the non-complementary displaced strand).
Single Guide RNA (sgRNA) Structure: The engineered single guide RNA consists of a 20-nucleotide target-specific spacer sequence linked to an 80+ nucleotide trans-activating crRNA (tracrRNA) scaffold forming three stem-loop hairpins.
PAM Recognition: The C-terminal PAM-interacting domain (PID) binds the 5'-NGG-3' protospacer adjacent motif on the non-target strand, initiating local duplex unwinding.

NHEJ vs HDR repair pathways diagram comparing indel knockout with template knock-in

2. Visualizing DNA double-strand break repair: NHEJ vs. HDR

A complete CRISPR mechanism schematic typically maps the cellular fate of the targeted locus following Cas9-induced double-strand breaks (DSBs):

Non-Homologous End Joining (NHEJ): Dominant in non-dividing and mammalian somatic cells. Recruits Ku70/Ku80 and DNA-PKcs to directly ligate blunt ends, frequently introducing small insertions or deletions (indels) that cause translational frameshifts for gene knockout.
Homology-Directed Repair (HDR): Active predominantly during S and G2 phases of the cell cycle. Utilizes Rad51 to catalyze strand invasion using an exogenous donor template (ssODN or double-stranded plasmid) for precise sequence substitution or tag insertion.
Alternative Technologies: Distinguish standard DSB cleavage from nickase-mediated Base Editing (CBE/ABE deaminations) and Prime Editing (reverse-transcriptase synthesis from pegRNA) where double-strand breaks are deliberately bypassed to minimize indel formation.

PAM recognition and DNA unwinding diagram showing 5-NGG site and R-loop formation

3. Best practices for reporting CRISPR figures in peer-reviewed manuscripts

Academic journals require precise annotation of target genomic sequences, off-target controls, and software generation disclosures:

Sequence Annotation: Always include explicit 5' to 3' orientation markers on both DNA strands and highlight the exact PAM trinucleotide in a distinct contrasting color.
Cleavage Site Indicator: Indicate the predicted cleavage plane between positions -3 and -4 relative to the PAM using clear vertical scissors or dashed lines.
Methods Attribution: State in your manuscript: 'CRISPR-Cas9 mechanism figures and targeting schematics were generated using SciDraw AI (SciDraw, https://scidraw.org) and verified against our target locus sequencing data.'
Reproducibility Checks: Ensure all sgRNA spacer sequences displayed in the figure match the oligonucleotides listed in your Supplementary Methods tables.

Dual nuclease cleavage diagram showing HNH and RuvC domains producing double-strand break

4. Export, layout, and multi-format adaptation for journals and talks

A single pathway or mechanism figure often serves multiple communication needs—from a two-column manuscript panel to a 16:9 conference slide or grant schematic. Plan your visual hierarchy so labels and compartments remain clear across formats:

Export layered SVG or native PPTX slides to adjust font sizes, arrow weights, and color palettes for your target venue.
Maintain consistent color coding across multi-panel figures so upstream triggers, active complexes, and inhibitors are immediately recognizable.
Verify all gene symbols, phosphorylation sites, and causal connectors against primary experimental data before manuscript submission.

Simple Pricing for Scientific Figures

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$19$9/ month

$228$108/year

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Includes

24,000 credits per year (2,000 credits/mo)
Up to 800 figures / year
Up to 80 videos / year
Supports all resolutions, including 1080P, 2K and 4K
Commercial use license included
SVG vector export
Standard member queue
No watermark — high-resolution slide and poster exports
Slide & poster friendly layouts
Run up to 3 generation tasks concurrently
30-day history storage
All illustration styles included

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Best for regular creation

$39$19/ month

$468$228/year

Billed annually · Cancel anytime

Includes

60,000 credits per year (5,000 credits/mo)
Up to 2,000 figures / year
Up to 200 videos / year
Supports all resolutions, including 1080P, 2K and 4K
Commercial use license included
SVG vector export
No watermark — slide/poster review downloads
Everything in Standard, plus:
Run up to 5 generation tasks concurrently
Priority generation queue during busy hours
90-day history + priority support (24h response)
Early access to new features

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Built for high-volume production

$79$39/ month

$948$468/year

Billed annually · Cancel anytime

Includes

144,000 credits per year (12,000 credits/mo)
Up to 4,800 figures / year
Up to 480 videos / year
Supports all resolutions, including 1080P, 2K and 4K
Commercial use license included
SVG vector export
No watermark — slide/poster review downloads
Everything in Pro, plus:
Run up to 10 generation tasks concurrently
Highest priority generation queue
Permanent history + dedicated support (12h response)

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