Probing quenched dye fluorescence of Cy3–DNA–Au-nanoparticle hybrid conjugates using solution and array platforms

[Display omitted] ► Au–DNA–Cy3 prepared using 10-nm AuNPs and ds-DNA with disulfide-modified target and Cy3-labeled probe. ► Quenching of Au–DNA–Cy3 in solution and array platforms assessed using ligand exchange by ME. ► High quenching efficiency observed for the shortest Au-to-Cy3 gap. Tuning the luminescence intensity of fluorophores using nanoparticles has shown great potential for the detection of inorganic metal ions, viruses, and proteins. The enhancement or quenching of a dye’s fluorescence intensity is strongly dependent on the spatial separation of the dye from the nanoparticle surface. To extend luminescence probing from the solution platform to the solid-state platform, we explored and performed dye quenching assessment using an array format in this study. We report the distance-dependent fluorescence behavior of Au–DNA conjugates prepared by equilibrating phosphine-stabilized gold nanoparticles (AuNPs) of 10-nm size with the designed spacer ds-DNA consisting of thiol-modified target and Cy3-labeled complementary probe of different lengths (5–20nm). The Cy3-labeled products were immobilized onto MPTMS (3-mercaptopropyltrimethoxysilane)-modified glass substrates and then excited with a 532-nm laser source. Quenching efficiency of AuNPs with increasing Au-to-dye distance was assessed using ligand exchange of the thiolated oligonucleotide by 2-mercaptoethanol (ME) to obtain free Cy3–DNA probe, thus eliminating nanoparticle effect on the dye’s luminescence intensity. Effective exchange, revealed by UV–vis absorption and fluorescence profiles, was achieved in a few minutes. It was observed that fluorescence quenching of Au–DNA–Cy3 assessed using the array format was consistent with the result in solution phase for the conjugates with up to 10-nm Au-to-Cy3 separation distance.