Accelerating Toehold-Mediated DNA Strand Displacement Reaction using Polyquaternium

Toehold-mediated strand displacement (TMSD) reaction is a widely used programming language in DNA nanotechnology, but its performance is significantly limited by slow kinetics, especially for low-concentration reactants. Herein, we report on polyquaternium-2 (PQ2) as an effective and efficient accelerator of TMSD reaction. We show that PQ2 could drastically increase the reaction constant of 1-nt TMSD by 10⁵-fold. Significant acceleration of TMSD reactions with sub-nanomolar input has been demonstrated in various TMSD-based catalytic DNA amplifiers. By stabilizing DNA reactants and increasing their effective local concentrations, PQ2 enables much faster reaction kinetics in response to picomolar inputs while eliminating the dependence on toehold length, mitigating the inhibitory effect of secondary structures, maintaining single-base discriminating power, and protecting TMSD system in serum. Also, it improves cascaded signal transmission over an 11-layer circuit with 26 rounds of TMSD reactions, with a half-completion time of only 5.3 minutes. The simple-to-use and low-cost PQ2 offers a promising solution for uncovering the full potential of DNA nanotechnology and will facilitate more efficient and versatile TMSD-based applications from sensitive biosensing to high-performance molecular computing.