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Free CRISPR-Cas9 Diagram Generator

Build a labeled SpCas9 schematic with guide RNA, target DNA, a PAM site and distinct DNA repair branches.

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SpCas9 cleavage and repair

Choose a finite scientific preset, edit labels and export the result locally.

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Free CRISPR-Cas9 Diagram Generator— templates & examples

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Crispr cas9 diagram tools

Free CRISPR-Cas9 Diagram Generator

Build a labeled SpCas9 schematic with guide RNA, target DNA, a PAM site and distinct DNA repair branches.

A CRISPR-Cas9 diagram shows guide RNA directing Cas9 to a DNA target beside a PAM sequence. Build a labeled SpCas9 schematic with guide RNA, target DNA, a PAM site and distinct DNA repair branches. Use the diagram to distinguish target recognition from DNA cleavage and the separate repair branches, keeping PAM position and strand direction visible.

Create a crispr cas9 diagram
SpCas9 schematic with guide RNA, target DNA, PAM, a cleavage site and separate NHEJ and HDR repair branches
  • Label guide RNA
  • Retain strand direction
  • Show end joining separately
  • Edit molecular labels

Crispr Cas9 Diagram Features

SciFig’s crispr cas9 diagram brings the inputs, diagram choices and exported result into one focused tool.

Locate guide RNA, target DNA and PAM

Show the guide RNA associated with Cas9 and aligned with the DNA target. The PAM belongs on the DNA rather than on the guide RNA. Keeping those labels separate helps an audience follow target recognition without confusing a sequence feature with the RNA molecule.

  • Label guide RNA
  • Keep PAM on the DNA
  • Identify the Cas9 complex
Locate guide RNA, target DNA and PAM

Show the SpCas9 cutting stage

Use the cutting view to explain the double-strand break near the target-associated PAM. Strand direction and the position of the cut remain part of the schematic. This stage focuses on how the illustrated complex meets the DNA, rather than calculating guide efficiency or searching a genome.

  • Retain strand direction
  • Show the DNA cut
  • Label the SpCas9 stage
Show the SpCas9 cutting stage

Separate NHEJ and HDR outcomes

Display NHEJ and HDR as distinct repair branches after the cut. NHEJ illustrates end joining; HDR introduces the role of a repair template. The branches organize the mechanism explanation without promising that an experiment will produce a particular editing outcome or efficiency.

  • Show end joining separately
  • Identify template-based repair
  • Keep repair routes distinct
Separate NHEJ and HDR outcomes

Prepare a labeled editing schematic

Use SciFig’s CRISPR Cas9 diagram to prepare a labeled editing schematic for a lecture or project introduction. Change the title and molecular labels, then download SVG or PNG. The figure keeps the guide, PAM and repair stages together while leaving actual sequence design to the experimental workflow.

  • Edit molecular labels
  • Set a project title
  • Export SVG or PNG
Prepare a labeled editing schematic

How to Create the Figure

Use the crispr cas9 diagram controls below to prepare the figure from your selected mechanism and labels.

  1. Choose a SpCas9 example

    Open the SpCas9 overview or a focused guide-target example. The preset places guide RNA, target DNA and PAM within the mechanism schematic. Start with the view that fits whether you are explaining recognition, cutting or the repair branches.

  2. Choose guide and repair visibility

    Use the guide-RNA option and choose NHEJ, HDR or both repair branches. The preview retains the SpCas9 mechanism context while the visible repair outcomes change. Keep the route that belongs in the explanation beside the figure.

  3. Edit the title and labels

    Enter a descriptive title and replace the node or structure labels with the terminology used in your document. The preset retains its arrangement while the visible names change. Keep molecular abbreviations consistent with the explanation beside the figure.

  4. Download the labeled figure

    Choose SVG for a scalable vector figure or PNG for a slide, handout or document. The exported diagram retains the selected view and labels. Keep the figure alongside the corresponding explanation so later wording changes can be reflected in another export.

Crispr Cas9 Diagram Uses

Use a labeled crispr cas9 diagram to connect the explanation in your material with a visible figure.

SpCas9 schematic with guide RNA, target DNA, PAM, a cleavage site and separate NHEJ and HDR repair branches

Introduce genome editing in a lecture

Prepare a CRISPR Cas9 diagram that starts with guide-directed recognition and ends with separate repair routes. Students can follow the guide RNA, PAM and cut before discussing editing outcomes. A labeled PNG is convenient for placing the same mechanism beside lecture notes.

Explore this example
Guide RNA and PAM recognition in a SpCas9 schematic displaying the NHEJ repair branch

Explain why a PAM matters

Use a focused guide-target figure to show that the PAM is a DNA sequence feature adjacent to the target. Keep it distinct from the guide RNA label. This supports a mechanism explanation without turning the illustration into a sequence-design calculator.

Explore this example
SpCas9 DNA cleavage near the PAM with the HDR repair branch and a donor-template label

Discuss the DNA cutting stage

Place the cut-site schematic beside a description of the SpCas9 complex. Strand markers and the PAM provide orientation for the audience. Export SVG when the figure will be combined with additional molecular annotations in a presentation or manuscript panel.

Explore this example
SpCas9 cleavage schematic with separate NHEJ and donor-template HDR branches

Compare two repair mechanisms

Show NHEJ and HDR as separate branches emerging from a double-strand break. A teaching handout can use the two routes to introduce end joining and template-based repair. The diagram communicates mechanisms rather than measured editing frequencies.

Explore this example
Labeled SpCas9 guide-target recognition schematic with PAM and both repair branches

Prepare a project overview

A genetics project presentation can begin with a labeled editing schematic before the experimental methods. Change the title and molecular labels to match the project vocabulary. Keep actual sequences, assay measurements and editing outcomes in their respective experimental materials.

Explore this example
SpCas9 schematic with guide RNA, target DNA, PAM, a cleavage site and separate NHEJ and HDR repair branches

Connect editing to DNA structure

Use the editing diagram to introduce guide-target recognition, then show a DNA structure figure when explaining strand complementarity. Each illustration answers a different question. Keep the SpCas9 mechanism panel focused on recognition, cutting and repair rather than expanding it into a replication diagram.

Explore this example

How Researchers Use SciFig

I was preparing a project introduction where the guide RNA and PAM labels had become difficult to distinguish. The CRISPR Cas9 diagram kept the PAM on the DNA and the guide separate. I used the exported SVG to explain recognition before moving to the experiment’s actual sequence and assay details.

Sofia B.

Genome engineering doctoral researcher, University of Zurich

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