Reading DNA Single-Strand Breaks via Topology Physics in Solid-State Nanopores

ReadSSB addresses a key bottleneck in genome‑stability research by establishing a topology‑aware, label‑free nanopore method to detect DNA single‑strand breaks (SSBs), map their positions, and quantify gap lengths at the single‑molecule level. SSBs are the most frequent DNA lesions and important disease biomarkers, yet existing assays are indirect, slow, and lack single‑molecule resolution. Beyond detection, ReadSSB provides a controlled testbed for non‑equilibrium polymer physics, where SSBs introduce local discontinuities in dsDNA torsional rigidity and mechanical properties.Building on evidence that electro-osmotic flow generates torque and nucleates plectonemes that are suppressed by SSBs, we will: (O1) characterize topology-dependent ionic-current signatures for intact vs SSB-containing DNA; (O2) optimize operating regimes to amplify SSB separability; (O3) characterize SSBs on circular plasmids; and (O4) localize SSB position and gap length along individual molecules via the “molecular ping-pong” method.The methodology integrates DNA nanotechnology for controlled SSB constructs and plasmids, solid-state nanopores with tuned electro-osmotic torque, and data-driven signal processing to extract plectoneme probabilities. Outputs will include a physical model of SSB-governed translocation dynamics, a protocol for SSB mapping and gap-length quantification, and an optimized nanopore platform for high-resolution biomolecule detection.This project goes beyond the state of the art by converting topology-induced dynamics into actionable readouts of DNA damage without labels, enabling rapid and portable assays. Its outcomes directly support Horizon Europe priorities, EU Mission on Cancer and Europe’s Beating Cancer Plan, by underpinning next-generation diagnostics for treatment monitoring and personalized medicine.