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 under 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 successfully demonstrated in various TMSD-based catalytic amplifiers. By stabilizing DNA reactants and increasing their effective local concentrations, PQ2 enables much faster reaction kinetics in response to picomolar-level inputs while eliminating the dependence on toehold length, mitigating the inhibitory effect of secondary structures, maintaining a desired single-base discriminating power, and protecting TMSD system in serum. Also, it improves cascaded signal transmission over an 11-layer TMSD 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.