Molecular recognition based on non-covalent interactions between two or more molecules plays a crucial role in biological systems. Specific biological molecule recognition has been widely applied in biotechnology, clinical diagnosis, and treatment. The efficiency and affinity of molecular recognition are greatly determined by the spatial conformation of biomolecules. The designability of DNA nanotechnology makes possible the precise programming of the spatial conformation of biomolecules including valency and spacing, further achieving spatial pattern recognition regulation between biomolecules. This review summarizes recent achievements with DNA-based molecular spatial pattern recognition systems, the important factors affecting spatial pattern recognition, and their applications in biosensing, bioimaging, and targeted therapy. The future challenges in and development of this field are discussed and prospected. This review will provide valuable guidance for the creation of new DNA tools to enhance the efficiency and specificity of biomolecular recognition.

DNA origami technology has shown potential across various applications, including the construction of molecular machines. Among these, mimicking the complex structural transitions of natural biomolecules in physiological environments remains a long-standing pursuit. Here, inspired by intrinsically disordered proteins, we propose a strategy for inducing disorder-to-order transitions in DNA origami structures at room temperature using alternative component subsets. In a triangular DNA origami model, we define three subsets of its constitutional DNA staples based on their spatial distributions along the scaffold. Atomic force microscopy and molecular dynamics simulations show that the individual subsets result in metastable assemblies with disordered morphologies and elevated free-energy fluctuations compared with those generated by the complete set of staples. Notably, after the addition of the remaining staples, the irregular structures transform into ordered triangular architectures within 2 h at room temperature, achieving yields of up to ∼60%. These findings suggest that these controlled folding pathways in DNA origami can robustly converge on the global energy minimum at room temperature, thereby providing a promising alternative strategy for engineering biomimetic DNA molecular machines.

A dynamic six‑helix DNA nanomachine enables reversible conformational switching across a broad physiological pH window (5–9), establishing a quantitative performance benchmark for designing dynamic DNA devices in complex biological environments.