RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a

Akshay Tambe, Alexandra East-Seletsky, Gavin J. Knott, Jennifer A. Doudna, Mitchell R. O'Connell

Research output: Contribution to journalArticleResearchpeer-review

81 Citations (Scopus)


CRISPR-Cas13a enzymes are RNA-guided, RNA-activated RNases. Their properties have been exploited as powerful tools for RNA detection, RNA imaging, and RNA regulation. However, the relationship between target RNA binding and HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activation is poorly understood. Using sequencing experiments coupled with in vitro biochemistry, we find that Cas13a target RNA binding affinity and HEPN-nuclease activity are differentially affected by the number and the position of mismatches between the guide and the target. We identify a central binding seed for which perfect base pairing is required for target binding and a separate nuclease switch for which imperfect base pairing results in tight binding, but not HEPN-nuclease activation. These results demonstrate that the binding and cleavage activities of Cas13a are decoupled, highlighting a complex specificity landscape. Our findings underscore a need to consider the range of effects off-target recognition has on Cas13a RNA binding and cleavage behavior for RNA-targeting tool development.

Original languageEnglish
Pages (from-to)1025-1036
Number of pages12
JournalCell Reports
Issue number4
Publication statusPublished - 24 Jul 2018
Externally publishedYes


  • C2c2
  • Cas13
  • Cas13a
  • CRISPR-Cas systems
  • RNA biology
  • RNA specificity

Cite this