Oligo-seq protocol for mapping DNA motifs targeted by base editors.

Determining which DNA sequences are preferentially targeted by base editors is critical for understanding how APOBECs, AID, and other CRISPR-Cas9 base editors edit DNA in cells or improve their editing efficiency. We have developed Oligo-seq, an in vitro sequencing-based method to identify the preferred sequence motifs targeted by these enzymes. This assay monitors DNA deaminase activity on DNA oligonucleotides containing random nucleotides and/or DNA structures and determines by sequencing which sequences are preferentially deaminated. For complete details on the use and execution of this protocol, please refer to Sanchez et al.1.