Methods for detecting site-specific and spurious genomic deamination induced by base editing technologies

A method of detecting deaminated sites in substrate DNA, the method comprising:

• providing a sample comprising substrate DNA;
• deaminating the substrate DNA using a base editing fusion protein comprising a deaminase domain and a DNA binding domain;
• contacting the deaminated substrate with Endonuclease MS from Thermococcus kodakarensis (TkoEndoMS) to induce double strand breaks (DSBs) at deamination sites in the substrate DNA to produce DNA fragments with single-stranded, five-base pair overhanging ends;
• treating the DNA fragments with uracil DNA glycosylase and endonuclease VIII;
• end-repairing and/or A-tailing the ends of the DNA fragments;
• ligating an adapter oligonucleotide to the ends;
• and
• sequencing the DNA fragments.