Toeless and reversible DNA strand displacement based on Hoogsteen-bond triplex

Abstract

Strand displacement reaction is a crucial component in the assembly of diverse DNA-based nanodevices, with the toehold-mediated strand displacement reaction representing the prevailing strategy. However, the single-stranded Watson-Crick sticky region that serves as the trigger for strand displacement can also cause leakage reactions by introducing crosstalk in complex DNA circuits. Here, we proposed the toeless and reversible DNA strand displacement reaction based on the Hoogsteen-bond triplex, which is compatible with most of the existing DNA circuits. We demonstrated that our proposed reaction can occur at pH 5 and can be reversed at pH 9. We also observed an approximately linear relationship between the degree of reaction and pH within the range of pH 5–6, providing the potential for precise regulation of the reaction. Meanwhile, by altering the sequence orientation, we have demonstrated that our proposed reaction can be initiated or regulated through the same toeless mechanism without the requirement for protonation in low pH conditions. Based on the proposed reaction principle, we further constructed a variety of DNA nanodevices, including two types of DNA logic gates that rely on pH 5/pH 9 changes for initiating and reversing: the AND gate and the OR gate. We also successfully constructed a DNA Walker based on our proposed reaction modes, which can move along a given track after the introduction of a programmable DNA sequence and complete a cycle after 4 steps. Our findings suggest that this innovative approach will have broad utility in the development of DNA circuits, molecular sensors, and other complex biological systems.