A hairpin probe-mediated isothermal amplification method to detect target nucleic acid

Abstract We herein describe Hairpin probe-mediated Isothermal Amplification (HIAmp), a novel isothermal method to detect a target nucleic acid. This method employs a hairpin probe (HP) designed to be opened through binding to the target nucleic acid. Upon opening of the HP, the primer binds to the free stem of the opened HP followed by its extension by DNA polymerase, consequently displacing and recycling the target nucleic acid to open another HP and producing an intermediate product (IP) containing a nicking site. The IP then continuously produces a trigger probe (TP), which subsequently initiates the isothermal amplification cycles in two separate ways by binding to either the intact HP or the overhang region of the IP. Through the following well-designed interconnected pathways, a large amount of final double-stranded DNA products (FPs) is produced and a high fluorescent signal is generated from the duplex-specific fluorescent dye, SYBR Green I. By employing this isothermal strategy, target DNA was very sensitively detected down to 64 zmol with the capability to discriminate the target DNA against non-specific DNAs. This work would provide remarkable insight into the design of a new DNA network enabling isothermal amplification.