Click Chemistry-Accelerated DNA Strand Displacement Reaction

The inherent programmability of DNA, dictated by Watson-Crick base-pairing and sequence diversity, renders it a versatile biomolecule for nanoscale engineering. Toehold-mediated strand displacement (TMSD) enhances DNA strand exchange by over 4 orders of magnitude, underpinning applications in molecular circuits, biosensing, and nanodevices. However, its efficiency is constrained by the instability of the toehold duplexes and the reversibility of the initial binding step. Here, we introduce the click chemistry-accelerated toehold exchange (CCATE) reaction, which integrates TMSD with strain-promoted azide-alkyne cycloaddition (SPAAC) to irreversibly stabilize toehold binding and substantially accelerate strand displacement kinetics. By site-specifically conjugating azide and dibenzocyclooctyne (DBCO) near the toehold region, CCATE achieves a ∼1000-fold rate enhancement over conventional TMSD, particularly for short toeholds and mismatched substrates. This catalyst-free, highly orthogonal approach enables the rapid construction of DNA logic gates and amplification circuits, broadening the scope of DNA nanotechnology in biosensing, diagnostics, and molecular computing.