An atomic force microscopy study of DNA hairpin probes monolabelled with gold nanoparticle: Grafting and hybridization on oxide thin films

First and original results are reported regarding the surface evolution of two kinds of oxide film after covalent grafting and hybridization of hairpin oligonucleotide probes. These hairpin probes were monolabelled with a 1.4 nm gold nanoparticle. One kind of oxide film was rough Sb doped SnO2 oxide film and the other kind was smooth SiO2 film. Same process of covalent grafting, involving a silanization step, was performed on both oxide surfaces. Atomic force microscopy (AFM) was used to study the evolution of each oxide surface after different steps of the process: functionalization, probe grafting and hybridization. In the case of rough SnO2 films, a slight decrease of the roughness was observed after each step whereas in the case of smooth SiO2 films, a maximum of roughness was obtained after probe grafting. Step height measurements of grafted probes could be performed on SiO2 leading to an apparent thickness of around 3.7 ± 1.0 nm. After hybridization, on the granular surface of SnO2, by coupling AFM with SEM FEG analyses, dispersed and well-resolved groups of gold nanoparticles linked to DNA duplexes could be observed. Their density varied from 6.6 ± 0.3 × 1010 to 2.3 ± 0.3 × 1011 dots cm−2. On the contrary, on smooth SiO2 surface, the DNA duplexes behave like a dense carpet of globular structures with a density of 2.9 ± 0.5 × 1011 globular structures cm−2.