Tailored Molecular Scissor Unlocks the Autocatalytic Potential of Hybridization Chain Reaction for Tunable Signal Amplification.

Conventional hybridization chain reaction (HCR) offers only limited signal amplification because newly generated target replicates (T-reps) are irreversibly sequestered within polymeric products. Here, we introduce a single hairpin, H3, that establishes a recycling feedback loop to HCR to create a dynamically tunable recycling chain reaction (RCR) that unlocks the autocatalytic potential of HCR. H3 hybridizes to H1 and displaces confined T-reps from HCR polymers, which then reinitiate amplification as autocatalytic drivers. Simple stoichiometric tuning of H3 enables dynamic control over both signal amplification efficiency and the degree of polymerization, redefining conventional HCR as the most constrained state of the RCR system. This compact design enables programmable dynamic DNA assembly and ultrasensitive biomolecular analysis in vitro and in living cells, holding broad potential in biomolecular engineering and cancer diagnostics.