Cubic DNA nanocage-based three-dimensional molecular beacon for accurate detection of exosomal miRNAs in confined spaces

In situ nondestructive bioanalysis of targets in nanoscale confined space, e.g. exosomes, poses a high challenge to analytical technologies, especially to molecular fluorescent probes, because it is required to enter the confined space to recognize the target, and maintain independent and stable signal output. The unexpected fluorescence quenching and fluorescence resonance energy transfer (FRET) caused by high-frequency Brownian motion and collision in confined space are the main limiting factors. Herein, we constructed a well-defined and programmable cubic DNA nanocage-based three-dimensional molecular beacon (ncMB), which successfully broke through the above dilemma, and realized the detection of miRNA in exosomes. Specifically, steric hindrance and electrostatic repulsion derived from the unique three-dimensional structure of ncMB result in a barrier between fluorescent probes, thus eliminating unexpected fluorescence quenching during single exosomal miRNA detection and unexpected FRET during dual exosomal miRNA detection. Benefiting from the excellent anti-fluorescence and anti-FRET performance of ncMB, compared with traditional molecular beacons (MB), the detected fluorescence signal in exosomes can be improved by an order of magnitude. Moreover, ncMB is proven to have powerful programmability and anti-interference capability. Overall, it is believed that the ncMB can eliminate the signal distortion that was usually associated with commonly used MB, especially in the confined space. The ncMB is considered as a powerful and versatile tool for accurate in situ signal output in exosomes and maybe other confined spaces. [Display omitted] •Cubic DNA nanocage-based three-dimensional molecular beacon (ncMB) is fabricated.•Fluorescence quenching and fluorescence resonance energy transfer can be eliminated.•ncMB is a powerful and versatile tool for in situ signal output in confined spaces.