A simple, ultrastable, and cost-effective oxygen-scavenging system for long-term DNA-PAINT imaging

DNA-PAINT (Points Accumulation in Nanoscale Topography) is a super-resolution microscopy technique capable of nanoscale imaging through the transient binding of fluorescently labeled imager strands to complementary DNA docking strands. Imager strands can be continuously replenished from an effectively infinite pool, making DNA-PAINT inherently resistant to photobleaching. However, extended DNA-PAINT imaging is limited by the formation of reactive oxygen species (ROS), which damage docking strands and reduce localization sampling over time. Although the state-of-the-art oxygen-scavenging system (OSS) can mitigate this damage, its enzymatic components degrade over time, reducing its performance, robustness and utility. Here, we introduce a simple, enzyme-free oxygen scavenging buffer based on sodium sulfite (Na₂SO₃) that overcomes these challenges. Our optimized formulation, combining Na₂SO₃ with Trolox (SST), effectively preserves docking strand integrity for over 24 hours and enhances long-term imaging performance. SST improves buffer stability tenfold, is easy to prepare and reduces costs by more than 90%, providing a robust, cost-effective, high-performance OSS for extended DNA-PAINT imaging.