Single-Molecule Insight Into Target Recognition by CRISPR–Cas Complexes

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Ribonucleoprotein (RNP) complexes from CRISPR–Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR–Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule. Specifically, we demonstrate how magnetic tweezers are applied to measure the local DNA unwinding at the target in real time. To this end we introduce the technique and the measurement principle. By studying modifications of the consensus target sequence, we show how different sequence elements contribute to the target recognition mechanism. From these data, a unified target recognition mechanism can be concluded for the RNPs Cascade and Cas9 from types I and II CRISPR–Cas systems. R-loop formation is hereby initiated on the target at an upstream element, called protospacer adjacent motif (PAM), from which the R-loop structure zips directionally toward the PAM-distal end of the target. At mismatch positions, the R-loop propagation stalls and further propagation competes with collapse of the structure. Upon full R-loop zipping conformational changes within the RNPs trigger degradation of the DNA target. This represents a shared labor mechanism in which zipping between nucleic acid strands is the actual target recognition mechanism while sensing of the R-loop arrival at the PAM-distal end just verifies the success of the full zipping.
Original languageEnglish
Pages (from-to)239-273
Number of pages35
JournalMethods in Enzymology
Early online date5 Dec 2016
Publication statusPublished - Jan 2017

Bibliographical note

Issue: Single-Molecule Enzymology: Nanomechanical Manipulation and Hybrid Methods


  • Magnetic tweezers
  • Single molecule
  • DNA supercoiling
  • DNA unwinding
  • CRISPR–Cas
  • R-loop
  • Cascade
  • Cas9
  • Targeting


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