Large-scale assembly of geometrically diverse metal nanoparticles-based 3D plasmonic DNA nanostructures for SERS detection of PNK in cancer cells

Abstract

The organization of geometrically diverse metal nanoparticles into a core/satellite structure at a large scale is a promising strategy for improve SERS performance due to hot spots localized enrichment and signal increase. However, due to the lack of extensional frames and strong electrostatic repulsion between plasma NPs, the fabrication of such 3D architectures with a high-density periodic hotspot in the focus volume has proven exceedingly difficult. Herein, we demonstrate a facile large-scale assembly of geometrically diverse metal nanoparticles strategy for constructing spatially extended 3D plasmonic nanostructures resembling "signal towers" based on RCA-mediated periodic organization of gold nanospheres (GNS) surrounding gold nanorods (GNRs). Using cancer cell T4 PNK as a model, a padlock probe with 5'- hydroxyl (P-circle) was designed as the T4 PNK substrate. The center Au nanorod was coated with P₁ and served as a "pedestal" to allow substantial loading of P-circle after target phosphorylation to initiate the rolling ring amplification reaction (RCA). The resultant DNA nanowire serves as an "antenna" to successively lock numerous Raman reporter P₂ (Cy3-P₂-SH) through base pairing at regular intervals. Finally, the 3D plasma DNA nanostructures that resemble "signal towers" could be obtained by placing a large number of GNS with a strong affinity for Au-S. The proposed 3D SERS sensor exhibited a sensitivity of LOD as low as 0.274 mU/mL, which was attributed to a substantial electromagnetic field enhancement at the inter-nanoparticle gaps between the adjacent pedestal and antenna. Moreover, by exploiting the synergistic effect of the periodically extended DNA scaffold generated by RCA amplification and the co-assembly of thiol ligand, the loaded GNS can be extended to three-dimensional space, forming a high-density periodic hotspot in the focal volume, thereby ensuring high enhancement and high reproducibility of Raman signals. In addition, this method can be used to quantify T4 PNK in HeLa cells, demonstrating its applicability in diagnosing and estimating PNK-related diseases in complex fluids.

Keywords: 3D plasmonic DNA nanostructures; Assembly of geometrically diverse metal nanoparticles; Polynucleotide kinase; SERS.