Revisiting the Conformational Flexibility of DNA 3-Arm Junctions for Nanoconstruction

Programmed DNA self-assembly, based on branched DNA structures, provides a general approach for constructing defined nanostructures for drug delivery, biosensing, nanofabrication, and information processing and storage. Three-arm DNA junctions (3aJs), the simplest branched DNA structures, are among the earliest explored DNA motifs for nanoconstruction. However, they have flexible and ill-defined conformations, which greatly limit their use in DNA nanoconstruction. Herein, we report a strategy to address this 40-year quest to reduce the conformational flexibility of individual 3aJs. We further enhance their structural rigidity by geometrically coupling multiple 3aJs into polygon motifs. The resulting 3aJ-containing motifs readily self-assemble into predesigned, higher-order large architectures. This work greatly expands the toolbox for DNA nanoconstruction. In addition, they provide essential structural information for modeling the conformations of natural nucleic acids.