Detection of CRISPR adaptation

Biochem Soc Trans. 2020 Feb 28;48(1):257-269. doi: 10.1042/BST20190662.


Prokaryotic adaptive immunity is built when short DNA fragments called spacers are acquired into CRISPR (clustered regularly interspaced short palindromic repeats) arrays. CRISPR adaptation is a multistep process which comprises selection, generation, and incorporation of prespacers into arrays. Once adapted, spacers provide immunity through the recognition of complementary nucleic acid sequences, channeling them for destruction. To prevent deleterious autoimmunity, CRISPR adaptation must therefore be a highly regulated and infrequent process, at least in the absence of genetic invaders. Over the years, ingenious methods to study CRISPR adaptation have been developed. In this paper, we discuss and compare methods that detect CRISPR adaptation and its intermediates in vivo and propose suppressing PCR as a simple modification of a popular assay to monitor spacer acquisition with increased sensitivity.

Keywords: CRISPR adaptation; CRISPR arrays; CRISPR-Cas systems; spacers.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Adaptation, Physiological
  • Adaptive Immunity
  • Base Sequence
  • CRISPR-Cas Systems / genetics*
  • Cells, Cultured
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Escherichia coli / genetics*
  • Polymerase Chain Reaction / methods
  • Prokaryotic Cells / immunology