Efficient and Reliable MicroRNA Imaging in Living Cells via a FRET-Based Localized Hairpin-DNA Cascade Amplifier

MicroRNAs (miRNAs) play critical roles in many biological processes and are vital biomarkers for disease diagnostics. Hence, it is of significance to develop miRNA biosensors with fast responses, high sensitivity, and excellent reliability in living cells. As one kind of DNA molecular machine, DNA amplifiers are very promising for intracellular miRNA imaging due to their nonenzymatic, isothermal working principle and excellent signal-amplification ability. However, the practical application of current DNA amplifiers is still an issue because of their slow kinetics, unsatisfactory efficiency, and false-positive signals. Herein, taking advantage of the spatial-confinement effect on a three-dimensional (3D) finite DNA nanostructure, a FRET-based localized hairpin-DNA cascade amplifier (termed as localized-HDCA) is developed for the rapid, efficient, and reliable imaging of intracellular tumor-related miRNA. The localized-HDCA system consists of two metastable hairpin DNAs (H1 and H2) localized on a DNA nanocube. Benefiting from the spatial-confinement effect in the confined space of DNA nanocubes, not only was the speed of the miRNA-triggered HDCA reaction significantly accelerated (7 times faster), but also the reaction efficiency was greatly improved (2.6 times higher). In addition, the FRET-based 3D finite DNA nanocubes provide this localized-HDCA with improved cell permeability and better nuclease resistance as well as the ability to avoid false-positive signals, which guarantee reliable miRNA imaging in living cells. With these advantages, this strategy is expected to be widely applied to the development of more efficient and robust DNA molecular machines for biomedical research and clinical diagnosis.