Enzyme-free simultaneous detection of circular RNA and linear RNA based on DNA-stabilized silver nanoclusters

The circular RNAs (circRNAs) and their homologous linear RNAs are involved in various cellular functions and disease development. The simultaneous detection of them can correctly reflect the changes in the gene transcription process, thereby facilitating the studies of RNA-related mechanisms and biomarker discovery. The high sequence homology between circular RNAs and their linear counterparts has always been a challenge for their specific detection. Herein, a two-type RNA detection platform based on DNA-stabilized silver nanoclusters (DNA-AgNCs) is designed for the simultaneous detection of circRNAs and homologous linear RNAs. The decreased fluorescence induced by the open of the hairpin structure of DNA-AgNCs can indicate the whole amount of the two-type RNAs. When G-rich DNA is present in the system, its bind with the back splice junction site in circRNAs results in a fluorescence redshift and enhancement, which can indicate the presence and amount of the circRNA. The concentrations of the circRNA and the two-type RNAs were quantified by the change in fluorescence intensity, with the limits of detection of 1.10 pM and 3.46 pM, respectively. The homologous linear RNA concentration can be quantified by subtracting the concentration of circRNA from the total concentration of the two-type RNAs. The platform was successfully applied for the detection of circABCB10 and its homologous linear RNA in cells and showed high selectivity and great potential for the detection of disease-related circRNAs and linear RNAs in biomedical research.