Shield strike shatter in DNA topology and nuclease interactions.

DNA degradation by nucleases is central to genome maintenance, immune defense, and the clearance of extracellular DNA, yet its execution at the single-molecule level remains poorly defined. Here, we use high-speed atomic force microscopy (HS-AFM) to directly visualize the real-time dynamics of DNA digestion by DNase I at nanometer resolution. DNase I repeatedly revisits structurally strained DNA regions before cleavage initiation, revealing a topology-sensitive mode of interaction that is inaccessible to ensemble biochemical approaches. Time-resolved imaging further uncovers a multistep degradation trajectory involving DNA scanning, localized engagement, strand rupture, and progressive filament disassembly, which we term STORM (Scan, Target, Occupy, Rupture, Mobilize) framework. In parallel, we show that protamine-induced DNA condensation into rod- and toroid-like architectures markedly suppresses enzymatic accessibility and stabilizes DNA against nuclease attack. Together, these findings establish a nanoscale structural and kinetic framework for how DNA is either degraded or protected under enzymatic stress, with implications for chromatin biology, innate immunity, autoimmune disease, and the design of nuclease-resistant gene delivery systems.