In cells co-transfected with a pair of sgRNAs to mediate a genomic (micro)deletion or inversion, indel mutations can be detected either by the SURVEYOR nuclease assay59 or by sequencing (Fig. 5a). Our online CRISPR Design Tool provides recommended primers for both approaches. However, SURVEYOR or sequencing primers can also be designed manually to amplify the region of interest from genomic DNA. Custom primers are chosen using the National Center for Biotechnology Information (NCBI) Primer-BLAST in order to avoid nonspecific amplification. SURVEYOR primers should be designed to amplify 200–400 bp on either side of the Cas9 target (for a total amplicon 400–800 bp long) to allow clear visualization of cleavage bands by gel electrophoresis (Fig. 5b). To prevent excessive primer dimer formation, SURVEYOR primers should be designed to be typically 18 to 25 nt long with melting temperatures of ~60 °C. For SURVEYOR assay or sequencing analysis, we recommend testing that each pair of candidate primers produces a single PCR product, as well as testing for the absence of nonspecific cleavage during the SURVEYOR nuclease digestion process (Fig. 5).
