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Nucleic Acids Res. 2016 Apr 7;44(6):2837-45. doi: 10.1093/nar/gkw138. Epub 2016 Mar 3.

Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3'-terminal segment of guide RNA.

Author information

1
Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA mekler@waksman.rutgers.edu.
2
Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
3
Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia Peter the Great State Polytechnical Institute, St. Petersburg, 195251, Russia severik@waksman.rutgers.edu.

Abstract

CRISPR-Cas9 is widely applied for genome engineering in various organisms. The assembly of single guide RNA (sgRNA) with the Cas9 protein may limit the Cas9/sgRNA effector complex function. We developed a FRET-based assay for detection of CRISPR-Cas9 complex binding to its targets and used this assay to investigate the kinetics of Cas9 assembly with a set of structurally distinct sgRNAs. We find that Cas9 and isolated sgRNAs form the effector complex efficiently and rapidly. Yet, the assembly process is sensitive to the presence of moderate concentrations of non-specific RNA competitors, which considerably delay the Cas9/sgRNA complex formation, while not significantly affecting already formed complexes. This observation suggests that the rate of sgRNA loading into Cas9 in cells can be determined by competition between sgRNA and intracellular RNA molecules for the binding to Cas9. Non-specific RNAs exerted particularly large inhibitory effects on formation of Cas9 complexes with sgRNAs bearing shortened 3'-terminal segments. This result implies that the 3'-terminal segment confers sgRNA the ability to withstand competition from non-specific RNA and at least in part may explain the fact that use of sgRNAs truncated for the 3'-terminal stem loops leads to reduced activity during genomic editing.

PMID:
26945042
PMCID:
PMC4824121
DOI:
10.1093/nar/gkw138
[Indexed for MEDLINE]
Free PMC Article

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