Highly sensitive microRNA detection by a duplex-specific nuclease amplification triggered three-dimensional DNA machine

Abstract

MicroRNAs play important roles in disease diagnosis and therapy. However, current methods for microRNA detection suffer from low sensitivity and cannot directly detect short microRNAs. Herein, we have developed a highly sensitive and selective fluorescent method for direct microRNA detection by combining the duplex-specific nuclease-assisted recycling amplification and the nicking enzyme-powered three-dimensional DNA walker. Target microRNA initiates duplex-specific nuclease-assisted recycling amplification, releasing numerous bipedal walking strands. The released bipedal walking strands hybridize with carboxyfluorescein-labeled track DNA and form nicking recognition site. Driven by the hydrolysis of the nicking enzyme, the bipedal walking strand autonomously moves along the track strand, releasing a large number of carboxyfluorescein-labeled DNA fragments and generating obvious fluorescence signals. This dual-signal amplification method can directly detect microRNA 21 as low as 130 fM and has good selectivity. The proposed method is not only simple for nucleic acid design, but also can be used as a universal method for the highly sensitive detection of all RNAs.