Quantitative and multimodal kinetic modulation of DNA strand displacement using side-arm structures

Strand displacement reactions serve as a basis for the operation of DNA-based nanodevices. The precise regulation of strand displacement reaction rates is a critical challenge that must be addressed to advance DNA nanodevices toward practical applications. Existing regulation methods suffer from limitations in achieving fine, quantitative rate control and multimodal signal response, thereby restricting the controllability of reaction kinetics and the versatility of DNA nanodevices. Herein, we propose a rate regulation strategy based on side arm structures, which enables fine-tuning of the strand displacement reaction rate by modulating the number and binding stability of the side arms. Our strategy allows for the regulation of reaction kinetics using diverse inputs, including DNA mutations, small molecules, and proteins. We establish a mathematical model correlating myoglobin concentration with the strand displacement reaction rate and experimentally validate its predictive accuracy. By leveraging the multimodal signal responsiveness of this strategy, we achieve one-pot simultaneous detection of myoglobin, ATP, and DNA mutations. Furthermore, we successfully apply side-arm-mediated rate regulation to a temporally controlled self-amplifying circuit. This strategy provides a novel orthogonal tool for the precise regulation of strand displacement kinetics and holds great promise for widespread application in DNA nanodevices.