Hybridization of DNA hairpin probes monolabelled with gold nanoparticles grafted on different oxide films: A fluorescence microscopy study

We report results regarding the study of grafting and hybridization of oligonucleotide hairpin probes monolabelled with either a fluorescent dye, a fluorescein, or a 1.4 nm gold nanoparticle. These oligonucleotides were covalently grafted on two different oxide thin films. First, we have deposited a semi-conductor oxide films – Sb doped SnO2 – on glass substrates using the aerosol pyrolysis technique. Second, we have realised insulating SiO2 thin films by thermal oxidization on Si wafers. After this, the same process of functionalization, including hydroxylation and silanization steps, was performed on both oxide surfaces. The grafting of oligonucleotide hairpins on these surfaces was confirmed by fluorescence microscopy. The fluorescence was found to be five-fold less intense on SnO2 than on SiO2. Our study suggests that the semi-conductor SnO2 film has been photosensitized by the fluorescent dye and behaves as a quencher for the dye emission. The hybridization of gold-labelled hairpin probes with complementary DNA targets labelled with Cy3 fluorescent dye was evidenced by fluorescence microscopy. Similar experiments were performed with non-labelled hairpin probes. As expected from Förster Resonance Energy Transfer (FRET) and NanoSurface Energy Transfer (NSET) mechanisms, the gold nanoparticles of probes quenched the Cy3 dye of the complementary target. The fluorescence quenching rate was found to be 86.5 ± 3.8% on SiO2 and 52.6 ± 15.2% on SnO2. The non-complementary hybridization and denaturation experiments led to weak fluorescence intensity values, which confirmed the specificity of complementary hybridization.