CRISPR and Repair

Inspect a guide and target, then separate a DNA cut from the repair outcome.

Experimental Cas9 cutaway exposing mint guide RNA, cyan target DNA and the resolved non-target DNA fragment containing the PAM.

Recognition → break → repair

Inspect two recognition requirements, then explore why the same cut can lead to different sequences.

Step 1 / 5Ready to inspect

Schematic molecular shapes and positions; swipe the diagram on a small screen.

Start with a synthetic DNA target and an RNA guide. This example uses SpCas9 with its canonical NGG PAM.

Teaching scope: synthetic sequences and a simplified SpCas9 diagram. These examples do not score guides, predict off-target sites, estimate repair frequencies or establish a knockout. Repair pathways can produce many outcomes; sequence and function need independent validation.

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Quick reference

Recognise a target

SpCas9 uses a guide RNA and a compatible PAM in the DNA to recognise a target. The familiar NGG PAM is adjacent to the targeted sequence. Other CRISPR enzymes can have different requirements.

Cutting is one step

Cleaving DNA creates a substrate for cellular repair. Target recognition, cleavage and repair are distinct events. A guide match by itself does not establish editing efficiency or genome-wide specificity.

Read the result

End joining can restore the original sequence or produce insertions and deletions. Template-directed repair can copy information from a donor. Outcomes vary; the repair choices here are examples, not probabilities or experimental predictions.

Check your understanding Optional

A target was successfully cut. What can you conclude about the final edit?

Every cell now has the intended sequence.The repair outcome must still be checked.The guide RNA becomes a permanent chromosome.

At the bench

Compare the reading frames and translation of original and edited coding sequences.

Open Sequence

Sources and model notes

Structure-based views of resolved experimental coordinates. Cutaways, category colours, camera choices and guided highlights are authored for teaching. Coordinates remain fixed; highlights are not experimental trajectories or simulation outputs.

RCSB PDB · Cas9 target recognition 4UN3

Guide RNA and PAM-containing DNA in a Cas9 structure.

HHMI · CRISPR mechanism and applications

Targeting, cleavage and DNA repair.