A nicking-mediated all-in-one self-consuming molecular beacon bulb lighted by target molecule for point mutation and ultra-sensitive detection of cancer-related gene

We develop a nicking-mediated all-in-one self-consuming molecular beacon bulb lighted by target molecule (the red magic wand) at attomolar level for point mutation and ultra-sensitive detection of cancer-related gene. • The engineered NAS-MB displays an outstanding single-base mismatch discrimination ability and ultra-sensitivity. • The unique self-consuming behavior shortens the detection time and simplifies the operation. • The excellent target detection capacity in human serum emphasizes its potential applications in disease diagnosis. Molecular beacons (MB) are used to explore as a turn-on probe for the detection of biomarkers of great interest. However, most reported MB-based biosensors suffer from limited sensitivity and poor specificity. Herein, a nicking-mediated all-in-one self-consuming molecular beacon bulb (NAS-MB) of new conception was proposed to identify cancer-related gene. Differing from traditional MB, the engineered NAS-MB, composed of a multifunctional fluorescent hairpin probe (MFHP) and a quenching probe (QP), is utilized not only as a signal reporter but also as a primer and self-extending template during the enzymatic polymerization-cleavage processes (EPCPs). Specifically, several functional regions are integrated into NAS-MB, namely, a target recognition region (TRR), a nicking enzyme recognition site, a primer region (PR) and its complementary sequence (CPR), an intramolecular and an intermolecular stem domain, a four-base complementary domain between PR and QP, resulting in a turn-off state. Once lighted by the target gene, QP is displaced and an intramolecular hybridization between PR and CPR occurs to form a new stem-loop structure with a blunt 3′ terminal in MFHP to activate EPCPs. Meanwhile, a steady stream of nicking fragments (NF) and cyclical target gene flow out, which can in turn tandemly trigger EPCPs, leading to the dramatic accumulation of NF and double-inner-circulation-strengthened self-consuming of NAS-MB. In this way, NAS-MB can be turned on by the target gene with a concentration as low as 10 aM and discriminate single-base mismatched sequences through enzyme-mediated self-consuming behavior. The unique analytical properties reveal its potential promise in the diagnosis of genetic diseases.