7OX7 image
Entry Detail
PDB ID:
7OX7
Keywords:
Title:
Target-bound SpCas9 complex with TRAC chimeric RNA-DNA guide
Biological Source:
PDB Version:
Deposition Date:
2021-06-22
Release Date:
2021-09-15
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Description:chimeric RNA-DNA guide
Chain IDs:A
Chain Length:81
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:CRISPR-associated endonuclease Cas9/Csn1
Mutations:D10A, H840A
Chain IDs:B
Chain Length:1372
Number of Molecules:1
Biological Source:Streptococcus pyogenes serotype M1
Polymer Type:polydeoxyribonucleotide
Description:TRAC target DNA strand
Chain IDs:C
Chain Length:28
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:TRAC non-target DNA strand
Chain IDs:D
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell 81 3637 3649.e5 (2021)
PMID: 34478654 DOI: 10.1016/j.molcel.2021.07.035

Abstact

The off-target activity of the CRISPR-associated nuclease Cas9 is a potential concern for therapeutic genome editing applications. Although high-fidelity Cas9 variants have been engineered, they exhibit varying efficiencies and have residual off-target effects, limiting their applicability. Here, we show that CRISPR hybrid RNA-DNA (chRDNA) guides provide an effective approach to increase Cas9 specificity while preserving on-target editing activity. Across multiple genomic targets in primary human T cells, we show that 2'-deoxynucleotide (dnt) positioning affects guide activity and specificity in a target-dependent manner and that this can be used to engineer chRDNA guides with substantially reduced off-target effects. Crystal structures of DNA-bound Cas9-chRDNA complexes reveal distorted guide-target duplex geometry and allosteric modulation of Cas9 conformation. These structural effects increase specificity by perturbing DNA hybridization and modulating Cas9 activation kinetics to disfavor binding and cleavage of off-target substrates. Overall, these results pave the way for utilizing customized chRDNAs in clinical applications.

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Primary Citation of related structures