Endogenous Enzyme-Driven 3D DNA Nanomachines for Simultaneous Intracellular Imaging of miRNA-155 and miRNA-21

The limitations caused by nonspecific signal interference and single biomarker detection remain the core challenge in achieving highly sensitive and precise identification of cancer cells. To address this, this study innovatively developed endogenous apurinic/apyrimidinic endonuclease 1 (APE1)-driven 3D DNA nanomachines (EAD-DNs), which enabled simultaneous fluorescence detection and intracellular imaging of two target microRNAs (miRNA-155 and miRNA-21 overexpressed in cancer cells). First, all nucleic acids (H1-S1 duplex, hairpins H2, H3, and H4) were assembled on gold nanoparticles (AuNPs) to form 3D DNA nanomachines (DNs) and further delivered into cancer cells. Then, the APE1 protein in tumor cytoplasm recognized and cut the AP sites encoded on H1 and H3, thereby activating DNs. When the target miRNA-155 triggered the catalytic hairpin assembly (CHA) reaction between H3 and H4, the fluorophore FAM labeled on H4 was far from the surface of the AuNPs, thereby restoring the fluorescence signal for miRNA-155 detection. Meanwhile, the other target miRNA-21 hybridized with the remaining locking-chain fragment of H1 after being cleaved by APE1, thereby exposing the reaction sequence of DNAzyme encoded on S1 to sequentially cleave Cy5-labeled H2. The fluorescence signal of Cy5 was restored for miRNA-21 detection. The combination of the inherent specificity of endogenous APE1 in cancer cells with the orthogonal dual-channel detection design targeting two targets, this system minimizes nonspecific interference and significantly improves the diagnostic accuracy of cancer cell recognition.