Enzyme-free catalyzed self-assembly of three-dimensional hyperbranched DNA structures for in situ SERS imaging and molecular logic operations

Nonenzymatic isothermal amplification strategy has emerged as a versatile tool for microRNA detection. However, the slow kinetics, limited sensitivity and unsatisfactory efficiency often hinder their further practical applications. Herein, we proposed a DNA tetrahedron-mediated branched catalytic hairpin assembly (DTM-bCHA), achieving the dynamic fabrication of three-dimensional hyperbranched DNA structures. Compared with traditional target-catalyzed hairpin assembly, the reaction kinetics of DTM-bCHA is accelerated by 11.1-fold through tethering the hairpin probes on DNA tetrahedron due to the increased collision probability among the reactants. Moreover, the surface enhanced Raman scattering (SERS) hot spots are generated by assembling Raman reporter DTNB-functionalized gold nanoparticles ([email protected]) with hyperbranched DNAs, leading to the ultrasensitive detection and in situ imaging of microRNA-21 (miR-21) in different living cells. Moreover, a series of two-input molecular logic gates, including AND, OR, NOR and INHIBIT gates, are constructed in response to miR-21 and miR-155, which achieves the multiplexed analysis of biomarkers in a facile way. Overall, the proposed DTM-bCHA based isothermal amplification strategy expands the avenues for the construction of complex DNA nanostructures, which is of great significance for bioanalysis and clinical diagnosis.