Isothermal, enzyme-free amplification techniques, such
as the hybridization
chain reaction (HCR) and catalytic hairpin assembly (CHA), have gained
increasing attention for miRNA analysis. However, current methodological
challenges, including slow kinetics, low amplification efficiency,
difficulties in efficient cellular internalization of DNA probes,
and concerns regarding the intracellular stability of nucleic acids,
need to be addressed. To this end, we propose a novel strategy for
sensitive miRNA detection based on a three-dimensional (3D) CHA-HCR
system. This system comprises two DNA nanospheres, named DS-13 and
DS-24, which are functionalized with CHA and HCR hairpins. Target
miR-21 initiates CHA between the two nanospheres, thereby activating
downstream HCR and bringing cyanine 3 (Cy3) and cyanine 5 (Cy5) into
proximity. The 3D CHA-HCR process leads to the formation of large
DNA aggregates and the generation of fluorescence resonance energy
transfer signals. In this strategy, the employment of a cascaded reaction
and spatial confinement effect improve sensitivity and kinetics, while
the use of DNA nanocarriers facilitates cellular delivery and protects
nucleic acid probes. The experimental results in vitro, in living
cells, and in clinical tissue samples demonstrated the desirable sensing
performance. Collectively, this approach holds promise as a valuable
tool for cancer diagnosis and biomedical research.