File:CRISPR Cas9 interaction with target DNA.jpg

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CRISPR Cas9 interaction with target DNA

The CRISPR/Cas9 complex of Streptococcus pyogenes consists of the Cas9 protein (in gray) and a guide RNA that is a chimera of natural crRNA and tracRNA (in orange).

The targeting sequence at the 5′end of the guide RNA base-pairs with complementary sequences on the target DNA (in blue); the targeting sequence is 20 nucleotides long, but may be shortened to increase specificity (the addition of 1 to 2 unpaired nucleotides at the 5′ end is also tolerated).

The presence of a PAM (protospacer adjacent motif, NGG for Streptococcus pyogenes), located immediately downstream of the 20-nucleotide sequence targeted by the guide RNA, is also essential for target recognition and cleavage.

The PAM sequence does not have a counterpart on the guide RNA. Following recognition of the PAM and base-pairing between the guide RNA and the target,

Cas9 cleaves each of the target DNA strands a few nucleotides upstream of the PAM (red arrowheads). Each strand is cleaved by a different nuclease domain present in Cas9 (HNH and RuvC domains). These domains have been mutated independently to generate Cas9 nickases.

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Gilles AF & Averof M. (2014). Functional genetics for all: engineered nucleases, CRISPR and the gene editing revolution. Evodevo , 5, 43. PMID: 25699168 DOI.


© 2014 Gilles and Averof; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

Gilles and Averof EvoDevo 2014 5:43 doi:10.1186/2041-9139-5-43 Text above from original figure legend.


Cite this page: Hill, M.A. (2024, April 19) Embryology CRISPR Cas9 interaction with target DNA.jpg. Retrieved from

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© Dr Mark Hill 2024, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G

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