CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

Variable activity across different single guide RNAs (sgRNAs) remains a significant limitation of the CRISPR/Cas9 system. We have identified molecular features that influence sgRNA stability, activity and loading into Cas9 in vivo by analyzing 1280 sgRNAs targeting 128 genes in zebrafish embryos. Based on these results, we created a predictive sgRNA scoring algorithm (CRISPRscan.org) that effectively captures the sequence biases affecting Cas9/sgRNA activity.