CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion

Viktorija Globyte, Seung Hwan Lee, Taegeun Bae, Jin Soo Kim, Chirlmin Joo

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59 Scopus citations


The Streptococcus pyogenes CRISPR/Cas9 (SpCas9) nuclease has been widely applied in genetic engineering. Despite its importance in genome editing, aspects of the precise molecular mechanism of Cas9 activity remain ambiguous. In particular, because of the lack of a method with high spatio-temporal resolution, transient interactions between Cas9 and DNA could not be reliably investigated. It therefore remains controversial how Cas9 searches for protospacer adjacent motif (PAM) sequences. We have developed single-molecule Förster resonance energy transfer (smFRET) assays to monitor transient interactions of Cas9 and DNA in real time. Our study shows that Cas9 interacts with the PAM sequence weakly, yet probing neighboring sequences via facilitated diffusion. This dynamic mode of interactions leads to translocation of Cas9 to another PAM nearby and consequently an on-target sequence. We propose a model in which lateral diffusion competes with three-dimensional diffusion and thus is involved in PAM finding and consequently on-target binding. Our results imply that the neighboring sequences can be very important when choosing a target in genetic engineering applications.

Original languageEnglish
Article numbere99466
JournalEMBO Journal
Issue number4
StatePublished - 15 Feb 2019

Bibliographical note

Funding Information:
We would like to acknowledge Luuk Loeff and Sungchul Kim for their assistance in setting up the experiments. We are grateful to Chun Heung Wong, Iasonas Katechis, and Sabina Colombo for critical reading of the manuscript. C.J. was funded Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) (Netherlands Organisation for Scientific Research) VIDI grant (864.11.005) and the Frontiers of Nanoscience program (NWO). J.-S.K. was supported by grants from the Institute for Basic Science (IBS-R021-D1).

Publisher Copyright:
© 2018 The Authors


  • CRISPR/Cas9
  • lateral diffusion
  • single-molecule FRET
  • target search


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