An advanced 3D DNA nanoplatform for spatiotemporally confined enhanced dual-mode biosensing MicroRNA in cancer cell

Dual-mode signal output platforms have demonstrated considerable promise due to their improved anti-interference capability and inherent signal self-correction. Nevertheless, traditional discrete-distributed signal probes often encounter significant drawbacks, including limited mass transfer efficiency, diminished signal strength, and instability in intricate biochemical environments. In response to these challenges, a scalable and hyper-compacted 3D DNA nanoplatform resembling "periodic focusing heliostat" has been developed for synergistically enhanced fluorescence (FL) and surface-enhanced Raman spectroscopy (SERS) biosensing of miRNA in cancer cells. Our approach utilized a distinctive assembly strategy integrating gold nanostars (GNS) as fundamental "heliostat units" linked by palindromic DNA sequences to facilitate each other hand-in-hand cascade alignment and condensed into large scale nanostructures. This configuration was further augmented by the incorporation of gold nanoparticles (GNP) via strong Au-S bonds, resulting in a sturdy framework for improved signal transduction. The initiation of this assembly process was mediated by the hybridization of dsDNA to miRNA-21, which served as a primer for polymerization and nicking reactions, thus generating a multifunctional T2 probe. This probe is intricately designed with three distinct parts: a 3'-palindromic end for structural integrity, a central region for capturing SERS-active probes (Cy3-P2), and a 5'-segment for attaching fluorescence reporters. Upon integration T2 into the GNS-based heliostat unit, it promotes palindromic arm-induced aggregation and plasma exciton coupling between plasma nanoparticles and signal transduction tags. This clustered arrangement creates a high-density "hot spot" array that maximizes the local electromagnetic fields necessary for enhanced SERS and FL response. This superstructure supports enhanced aggregation-induced signal amplification for both SERS and FL, offering exceptional sensitivity with LOD as low as 0.0306 pM and 0.409 pM. The efficacy of this method was demonstrated in the evaluation of miRNA-21 in various cancer cell lines.