G-quadruplex-regulated exonuclease cooperative hydrolysis signal transduction strategy for processing molecular temporal information

Abstract

DNA circuits, as a crucial tool for processing molecular information, achieve precise control of complex molecular reactions within biological systems, demonstrating significant potential in gene expression regulation, molecular computing, and biosensing. Here, we developed a G-quadruplex-regulated (G4-regulated) exonuclease cooperative hydrolysis signal transduction strategy with the advantages of excellent sequence orthogonality, simple modular reaction units, signal amplification capability, and no excess by-products. The reaction principle of this strategy is to use G4 as a switch to regulate signal transduction, and by controlling the conformational change of G4, regulate the cooperative hydrolysis of Exonuclease III (Exo III) and Exonuclease λ (Exo λ), thereby treating the molecular conformation as functional signals for information processing. Based on this strategy, we constructed fan-out and fan-in circuits to perform signal transduction tasks. We also extended them to design a DNA signal network to process temporal information. This work shows the multifunctionality of G4, providing an effective way to regulate enzyme hydrolysis while also offering new ideas and methods for understanding and constructing molecular networks for processing temporal information. This regulation approach and signaling strategy will have future applications in DNA computing, biosensing and nanomachines.