Optimization Strategies for the CRISPR-Cas9 Genome-Editing System

Cold Spring Harb Protoc. 2016 Oct 3;2016(10). doi: 10.1101/pdb.top090894.


The CRISPR-Cas9 system uncovered in bacteria has emerged as a powerful genome-editing technology in eukaryotic cells. It consists of two components-a single guide RNA (sgRNA) that directs the Cas9 endonuclease to a complementary DNA target site. Efficient targeting of individual genes requires highly active sgRNAs. Recent efforts have made significant progress in understanding the sequence features that increase sgRNA activity. In this introduction, we highlight advancements in the field of CRISPR-Cas9 targeting and discuss our web tool CRISPRscan, which predicts the targeting activity of sgRNAs and improves the efficiency of the CRISPR-Cas9 system for in vivo genome engineering.

Publication types

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

MeSH terms

  • CRISPR-Cas Systems*
  • Endonucleases / metabolism
  • Gene Editing / methods*
  • RNA, Guide, Kinetoplastida / metabolism
  • Recombination, Genetic


  • RNA, Guide
  • Endonucleases