Hybridization Chain Reaction Based on Paranemic Crossover DNA

The classic hybridization chain reaction (HCR) is applied to paranemic crossover (PX) DNA structures, which generates assembled DNA nanostructures instead of linear DNA duplexes. As an analog of the stem-loop structure, PX structures with terminal loops and toeholds are designed as HCR reaction monomers. Isothermal strand displacement reaction on the PX-loop structure is studied, and the following PX-based HCR is carried out with both single-stranded DNA and RNA as the initiator. Furthermore, 2'-OMe modifications of the toehold and PX are used to enhance the binding to RNA, which optimized the kinetics of RNA initiated PX-HCR. In addition, paranemic crossover structures with the minimal paranemic cohesion are designed for microRNA triggered PX-HCR based on the 2'-OMe strategy, with a visible fluorescence response in minutes, suggesting the generality of this strategy. The facile initiation of HCR reaction on PX with both DNA and RNA indicates its potential for biosensing applications as well as assembling complex DNA nanostructures in the future.