While APOBEC3A has a preferred substrate of C-containing ssDNA, it will deaminate 5mC-containing ssDNA with 2-fold less activity in a 30-minute reaction under recommended reaction conditions. In an overnight incubation (16 hours), APOBEC3A can reach complete deamination of 5mC-containing ssDNA and can deaminate 5-hydroxymethylcytosine (5hmC)-containing ssDNA less than 10%. APOBEC3A is not active on ssDNA containing beta-glucosyl-5-hydroxymethylcytosine (5gmC), 5-carboxylcytosine (5caC), or 5-formylcytosine (5fC).
| ssDNA Modification | Activity after 30 min. | Activity after 16 h |
| C to U | 100% | 100% |
| 5mC to T | 50% | 100% |
| 5hmC to 5hmU | 0% | <10% |
| 5fC to 5fU | 0% | 0% |
| 5caC to 5caU | 0% | 0% |
| 5gmC to 5gmU | 0% | 0% |
