Surface characterization of DNA microarray on silicon dioxide and compatible silicon materials in the immobilization process

In this work, the surface properties of a DNA microarray formed on silicon based solid support are studied at different stages during the hybridization process. A modified immobilization process using the covalent immobilization of thiol-terminated DNA oligonucleotides on self-assembled layers of (3-mercaptopropyl) trimethoxysilane (MPTS) by disulfide bond formation is used to selectively attach DNA probes onto the surface of silicon dioxide. Contact angle measurement is used to monitor the bonding of MPTS on the surface. Atomic force microscopy (AFM) shows an increase in particle size before and after the growth of the MPTS layer. Fluorescence microscopy reveals the success of hybridization of complementary oligonucleotides labeled by FAM to the probe. The effects of modified immobilization process on other common material in silicon processing are also studied. As a result of the corrosive chemical used in the process, common metals used in micro-fabrication processes like aluminum are etched away. Silicon nitride is not affected by the immobilization and hybridization process, and thus can be used as a passivation and isolation material to conform the DNA to a specific area for DNA microarray to reduce cross-talk. The fluorescence image from the scanner indicates silicon nitride can effectively be used as an isolation material with linewidth down to 1 mum