Controlling\nthe Depth of Hybridization Chain Reaction\nby Extended Dangling Ends and Its Analytical Applications

Hybridization chain reaction (HCR) is a powerful enzyme-free\nnucleic\nacid amplification strategy. Triggered by an initiator strand, it\nyields nicked double helices analogous to alternating copolymers.\nHowever, there is no effective way to regulate the HCR reaction, and\nthe most apparent phenomenon is the uncontrollable polymerization\nof product after introducing an initiator. Here we explore controlling\nthe depth of the HCR reaction by extended dangling ends on hairpin\nmonomers and report that sequence length, nucleotide composition,\nand secondary structure can alter HCR polymerization and can be utilized\nfor the desired regulation. Interaction dynamics between initiator\nand hairpin monomers simulated by oxDNA are in good accordance with\nexperimental results. Such a controlling effect can be utilized for\nnew analytical applications that HCR cannot previously achieve, such\nas analyzing strand-extension enzymes and identifying short-sequence\nstructures. The finding provides a concise but effective way for controlling\nthe depth of HCR reaction and opens the application scope of HCR to\nmore fields.