Stable and programmable formation of DNA nanostructures via inter-strand crosslinking by assembly-triggered oxanine...

DNA's programmable self-assembly makes it a valuable material for nanoscale applications, yet the reversible nature of nucleobase pairing limits the stability of assembled DNA structures, even under physiological conditions. Introducing covalent bonds between DNA strands after assembly offers a promising solution, but these bond-forming reactions must be controlled spatially and temporally. In this study, we explored oxanine (Oxa) as a novel, assembly-dependent crosslinker to address this need. The electrophilic C2 carbonyl of Oxa serves as the reactive site, undergoing a proximity-driven reaction with an amine group, enabling assembly-triggered covalent linkage between Oxa- and amine-bearing DNA strands. The exceptional stability of Oxa in aqueous solutions, combined with its proximity-specific reaction with amines, makes it an ideal approach for stable and programmable formation of strand-crosslinked DNA structures. We demonstrated the linkage of Oxa-modified and amine-modified strands across various DNA motifs, including duplexes, Y-shapes, and T-motif tiles. The assembly-triggered Oxa-amine (At-ON) linkage is compatible with diverse DNA structures, enhancing the stability of assembled DNA nanomaterials and devices.