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TitleStructural basis of Cas9 DNA interrogation with a 5' truncated sgRNA.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 1, Year 2025
Publish dateJan 7, 2025
AuthorsKaitlyn A Kiernan / Jieun Kwon / Bradley J Merrill / Miljan Simonović /
PubMed AbstractThe efficiency and accuracy of CRISPR-Cas9 targeting varies considerably across genomic targets and remains a persistent issue for using this system in cells. Studies have shown that the use of 5' ...The efficiency and accuracy of CRISPR-Cas9 targeting varies considerably across genomic targets and remains a persistent issue for using this system in cells. Studies have shown that the use of 5' truncated single guide RNAs (sgRNAs) can reduce the rate of unwanted off-target recognition while still maintaining on-target specificity. However, it is not well-understood how reducing target complementarity enhances specificity or how truncation past 15 nucleotides (nts) prevents full Cas9 activation without compromising on-target binding. Here, we use biochemistry and cryogenic electron microscopy to investigate Cas9 structure and activity when bound to a 14-nt sgRNA. Our structures reveal that the shortened path of the displaced non-target strand (NTS) sterically occludes docking of the HNH L1 linker and prevents proper positioning of the nuclease domains. We show that cleavage inhibition can be alleviated by either artificially melting the protospacer adjacent motif (PAM)-distal duplex or providing a supercoiled substrate. Even though Cas9 forms a stable complex with its target, we find that plasmid cleavage is ∼1000-fold slower with a 14-nt sgRNA than with a full-length 20-nt sgRNA. Our results provide a structural basis for Cas9 target binding with 5' truncated sgRNAs and underline the importance of PAM-distal NTS availability in promoting Cas9 activation.
External linksNucleic Acids Res / PubMed:39657754 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.1 Å
Structure data

45368

9c9p

EMDB-45368, PDB-9c9p:
Cas9 ternary complex, 14-nt sgRNA, State I (linear)
Method: EM (single particle) / Resolution: 3.1 Å

45586

9cgu

EMDB-45586, PDB-9cgu:
Cas9 ternary complex, 14-nt sgRNA, State II (kinked)
Method: EM (single particle) / Resolution: 3.0 Å

Source
  • streptococcus pyogenes (bacteria)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / Type II-A CRISPR-associated endonuclease RNA-guided DNA targeting Mg2+ dependent / DNA BINDING PROTEIN/DNA/RNA / Type II-A / CRISPR-associated endonuclease / RNA-guided / DNA targeting / Mg2+ dependent / DNA BINDING PROTEIN-DNA-RNA complex

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