Silanization of silica and glass slides for DNA microarrays by impregnation and gas phase protocols: A comparative study

Surface immobilization of oligonucleotide probes (oligoprobes) is a key issue in the development of DNA-chips. The immobilization protocol should guarantee good availability of the probes, low non-specific adsorption and reproducibility. We have previously reported a silanization protocol with tert-butyl-11-(dimethylamino)silylundecanoate performed by impregnation (Impregnation Protocol, IP) of silica substrates from dilute silane solutions, leading to surfaces bearing carboxylic groups. In this paper, the Impregnation protocol is compared with a Gas phase Protocol (GP) which is more suited to industrial requirements such as reliable and robust processing, cost efficiency, etc.… The morphology of the oligoprobe films at the nanoscale (characterized by Atomic Force Microscopy) and the reproducibility of subsequent oligoprobes immobilization steps have been investigated for the two protocols on thermal silica (Si/SiO2) and glass slide substrates. IP leads to smooth surfaces whereas GP induces the formation of islands features suggesting a non-continuous silane layer. The reproducibility of the overall surface layer (18.75 mm²) has been evaluated through the covalent immobilization of a fluorescent oligoprobes. Average fluorescent signals of 6 (a.u.) and 4 (a.u.) were observed for IP and GP, respectively, with a standard deviation of 1 for both protocols. Thus, despite a morphological difference of the silane layer at the nanometer scale, the density of the immobilized probes remained similar.