Surface characterization of a silicon-chip-based DNA microarray

The immobilization of DNA (deoxyribonucleic acid) on solid supports is a crucial step for any application in the field of DNA microarrays, It determines the efficacy of the hybridization and influences the signal strength for the detection. We used solid supports made from silicon wafers as an alternative substrate to the commonly used microscope glass slides. The covalent immobilization of thiol-terminated DNA oligonucleotides on self-assembled layers of (3-mercaptopropyl)trimethoxysilane (MPTS) by disulfide bond formation was investigated. Contact angle measurement, variable angle spectral ellipsometry (VASE), X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM) were used to characterize the changing properties of the surface during the DNA array fabrication. During wafer processing the contact angle changed from 3 degrees for the hydroxylated surface to 48.5 degrees after deposition of MPTS. XPS data demonstrated that all sulfur in the MPTS layer was present in the form of reduced SH or S-S groups. VASE measurements indicated a layer thickness of 57.8 Angstrom for the immobilized 16 base oligonucleotides including a 18 carbon atom spacer located between the disulfide bond and the oligomer. AFM was used to characterize the DNA layer before and after hybridization to a complementary target. The data recorded after hybridization revealed a sharp increase in particle size from 89 nm(2) to a mean value of 363 nm(2). Fluorescence microscopy was used to monitor the hybridization of a fluorescently labeled DNA target to the immobilized probe. The heat stable disulfide-linkage formed during the oligonucleotide immobilization allowed the stripping of complementary DNA targets as well as rehybridization, These data show the advantages and applicability of silicon wafers that have been processed with CMOS (complementary metal oxide semiconductor) compatible processes as solid support in DNA technology. This approach offers the possibility of integration with other silicon-based components such as PCR microreactors and capillary electrophoresis units into a "lab-on-a-chip".