DNA Framework Nanoruler-Directed Surface Fluorescence Enhancement as a Sensing Platform for MicroRNA Detection

Surface-enhanced fluorescence can occur when fluorophores approach a rough or nanoscopic metallic surface, owing to the enhanced local electric field. However, revealing the surface fluorescence enhancement mechanism remains an important concern, primarily due to the lack of a nanoruler for precisely tuning the distance between the fluorophores and the substrate. Importantly, the precise distance is also critical as the heterogeneous size of spacers can lead to differentiated enhancement, resulting in low reproducibility. Herein, we propose a tetrahedral DNA framework (TDF) nanoruler strategy. Three vertexes of TDFs are thiolated for their immobilization on the Au matrix, while the fourth vertex is labeled with fluorophores. Therefore, the distance between the fluorophores and the Au substrate is governed by the size of TDFs. Various TDFs are combined as the nanoruler, and thus, we reveal the distance-dependent emission efficiency. We clearly observed the gradually enhanced and subsequently decreased emission along with the increased distance with the nanoruler. The maximum fluorescence enhancement was achieved at a critical distance of 5-7 nm with a narrow range for the labeled fluorophores on the Au substrate. Moreover, their rigid structure also realizes the uniform size of TDFs for homogeneous signal enhancement. Thus, sensitive detection of microRNA biomarkers of prostate cancer (PCa) was realized with a detection limit of 1 aM and used for early diagnosis of PCa. Furthermore, the TDF nanoruler strategy can be easily extended to other distance-dependent systems, enabling the optimization of their performance.