A versatile chemistry utilizing the homobifunctional cross-linker 1,4-phenylene diisothiocyanate (PDC) to attach both amine-and thiol-terminated oligonucleotides to aminosilane-coated slides was examined in a microarray format. Three common aminosilanes, 3-aminopropyltriethoxysilane (APS), N-(2-aminoethyl)-3-aminopropyltrimethoxysilane, and m,p-(aminoethyl-aminomethyl) phenethyltrimethoxysilane, were coated onto glass slides and silicon wafers and characterized using contact angle goniometry, ellipsometry, and X-ray photoelectron spectroscopy. Evaluation of the aminosilane-modified surfaces using contact angle measurements, UV-vis spectroscopy, and covalent attachment of a Cy5-conjugated N-hydroxysuccinimide ester reporter molecule suggested that derivatization of the surface with APS + PDC resulted in the best overall coverage. Microarrays printed using APS + PDC chemistry to immobilize both amine-and thiolterminated oligonucleotides resulted in rapid attachment, uniform spot morphology, and minimal background fluorescence. Both amine-and thiol-terminated oligonucleotides showed comparable attachment, although greater attachment and hybridization efficiencies were observed with amine-functionalized molecules at saturating printing densities. The data highlight the influence of surface chemistry on both immobilization and hybridization and, by extrapolation, on microarray data analysis.

We describe reproducible protocols for the chemisorption of self-assembled monolayers (SAMs), useful as imaging layers for nanolithography applications, from p-chloromethylphenyltrichlorosilane (CMPS) and 1-(dimethylchlorosilyl)-2-(p,m-chloromethylphenyl)ethane on native oxide Si wafers. Film chemisorption was monitored and characterized using water contact angle, X-ray photoelectron spectroscopy, and ellipsometry measurements. Atomic force microscopy was used to monitor the onset of multilayer deposition for CMPS films, ultimately allowing film macroscopic properties to be correlated with their surface coverage and nanoscale morphologies. Although our results indicate the deposition of moderate coverage, disordered SAMs under our conditions, their quality is sufficient for the fabrication of sub-100-nm-resolution metal features. The significance of our observations on the design of future imaging layers capable of molecular scale resolution in nanolithography applications is briefly discussed.