A target-triggered mimic nucleic acid enzyme enables versatile and sequence-independent biosensing

Abstract

Simultaneous quantification of multiple microRNAs (miRNAs) is very important because lots of pathologies are associated with abnormal expressions of several miRNAs. In this work, we proposed an enzyme-assisted cleavage of nucleic acids signal amplification (TMNAE enzyme sensing) based method enable simple, highly sensitive and selective multiple miRNAs detection. Two unmodified probes and analyte were assembled into a Y-shaped structure that contains a nicking endonuclease recognition site in the complementary region of the unmodified probe and two side arms complementary to reporter probe. Thus, it enables the loading of a Nicking endonuclease (NEase) on the complementary region of the unmodified probe, localization to a specific locus through hybridization of the side arms with reporter probe, and cleavage thereof. NEase is employed to recycle the process of Y-shaped structure assisted digestion of reporter probe, thus, resulting in a significant fluorescence signal amplification through which one analyte molecule cleaves thousands of reporter probe molecules. We demonstrate the efficiency of this TMNAE enzyme sensing strategy for rapid direct quantification of multiple sequence specific miRNAs in homogeneous solution with the detection limit in the femtomolar range, nearly 4 orders of magnitude lower than that of conventional hybridization assay methods. This assay also has the ability to discriminate the target from other miRNAs or even single-base mismatched sequences. Moreover, the TMNAE enzyme sensing strategy can be used to detect other molecules apart from nucleic acids. The detection of thrombin in biological samples showed a LOD of as low as 1 nM. Overall, our proposed TMNAE enzyme sensing strategy provides a versatile, reliable, simple, highly sensitive, and selective detection method and shows promising application in molecular disease diagnosis and biomedicine.