library_construction_protocol: Genomic DNA was isolated using a Zymo genomic DNA extraction kit. Cells were washed with PBS and permeabilized by incubation in lysis buffer for 10 minutes at room temperature, followed by an additional incubation at 4°C for 5 minutes. After washing once with wash buffer, the cell pellet was resuspended in activation buffer supplemented with purified DddA11-MBP or MGYFPDa829 to achieve a final enzyme concentration of 3-10 µM. The reaction mixture was incubated at 37°C for 2 hours or 3 minutes with shaking at 300 rpm. The reaction was quenched by adding SDS to a final concentration of 0.5%. Proteinase K was then added, and the sample was incubated at 56°C for 10 minutes. Genomic DNA was isolated using a Zymo genomic DNA extraction kit. For naked DNA data, gDNA was extracted from K562 cells using the QIAamp DNA Blood Kit to obtain deproteinized DNA, followed by the DddA reaction.For TDAC-seq, nested PCR was performed using target-specific primers with KOD One PCR Master Mix, and libraries were prepared following the Ligation Sequencing V14 – PCR Barcoding Kit protocol from Oxford Nanopore. For DddA11-Whole genome sequencing, gDNA was fragmented to 10 kbp, and libraries were prepared using the same ligation sequencing kit.