bioRxiv Biochemistry
bioRxiv Biochemistry
5 years ago

The effect of sequence mismatches on binding affinity and endonuclease activity are decoupled throughout the Cas9 binding site

Bussemaker, M. A., Pufall, H. J., Rube, H. T., L., Zhang
The CRISPR-Cas9 system is a powerful genomic tool. Although targeted to complementary genomic sequences by a guide RNA (gRNA), Cas9 tolerates gRNA:DNA mismatches and cleaves off-target sites. How mismatches quantitatively affect Cas9 binding and cutting is not understood. Using SelexGLM to construct a comprehensive model for DNA-binding specificity, we observed that 13-bp of complementarity in the PAM-proximal DNA contributes to affinity. We then adapted Spec-seq and developed SEAM-seq to systematically compare the impact of gRNA:DNA mismatches on affinity and endonuclease activity, respectively. Though most often coupled, these simple and accessible experiments identified sometimes opposing effects for mismatches on DNA-binding and cutting. In the PAM-distal region mismatches decreased activity but not affinity, whereas in the PAM-proximal region some reduced-affinity mismatches enhanced activity. This mismatch-activation was particularly evident where the gRNA:DNA duplex bends. We developed integrative models from these measurements that estimate catalytic efficiency and can be used to predict off-target cleavage.

Publisher URL: http://biorxiv.org/cgi/content/short/176255v1

DOI: 10.1101/176255

You might also like
Discover & Discuss Important Research

Keeping up-to-date with research can feel impossible, with papers being published faster than you'll ever be able to read them. That's where Researcher comes in: we're simplifying discovery and making important discussions happen. With over 19,000 sources, including peer-reviewed journals, preprints, blogs, universities, podcasts and Live events across 10 research areas, you'll never miss what's important to you. It's like social media, but better. Oh, and we should mention - it's free.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.