Dephosphorylation-regulated MNAzyme-PER cascade as a programmable converter for multi-task molecular actuation

Nucleic acid conformational regulation and enzymatic dynamic modulation play a pivotal role in creating collaborative amplification systems with programmable responses. However, the coordination of sophisticated molecular functions within synergistic cascade networks remains constrained by limited progress in leakage mitigation and modular functionality expansion. Here, we report a dephosphorylation-regulated MNAzyme-primer exchange reaction (PER)-based (Dp-PER) strategy, with its core mechanism centered on cyclic phosphate-locked conformation to suppress signal leakage. This design specifically incorporates upstream primer formulation and an enzyme-orchestrated cascade, seamlessly connecting upstream molecular network to PER circuit through dephosphorylation-induced conformational release. Within the sequential reaction mechanism, the transduction module exhibits intrinsic reactivity confinement and strategic activation in actuation of the amplification module distinct from traditional downstream primer. Importantly, the highly programmable MNAzyme sensing arm enables the Dp-PER to respond flexibly to diverse molecular cues. This capability underpins various tasks, including logical operations (YES, NOT, OR, AND, INHIBIT), multifunctional biosensing (nucleic acid, enzyme), and nanostructure cascading with tetrahedral DNA. The MNAzyme-PER enzymatic cascade is a scalable, compatible system that acts as a universal converter in hierarchical DNA networks. It provides a versatile foundation to transform molecular information into actionable outputs, demonstrating the potential of DNA nanotechnology in programmable biosensing and molecular computation.