DNA microarray is an important technology for DNA analysis in various applications. The adoption of mature electronic micro-fabrication to realize fully integrated and portable DNA analyzer is of great importance to meet the ever-growing demand for on-site clinical diagnosis, high speed and throughput DNA analysis. In this work, silicon materials compatible with the biochemical process were studied to realize high density DNA microarray. Covalent immobilization DNA oligonucleotides is used to selectively attach DNA probes onto the surface of silicon dioxide. Different surface cleaning methods and concentrations of DNA oligonucleotides for immobilization and hybridization were tested so as to increase the sensitivity of the microarray. Fluorescence microscopy revealed the success of hy...[ Read more ]

DNA microarray is an important technology for DNA analysis in various applications. The adoption of mature electronic micro-fabrication to realize fully integrated and portable DNA analyzer is of great importance to meet the ever-growing demand for on-site clinical diagnosis, high speed and throughput DNA analysis. In this work, silicon materials compatible with the biochemical process were studied to realize high density DNA microarray. Covalent immobilization DNA oligonucleotides is used to selectively attach DNA probes onto the surface of silicon dioxide. Different surface cleaning methods and concentrations of DNA oligonucleotides for immobilization and hybridization were tested so as to increase the sensitivity of the microarray. Fluorescence microscopy revealed the success of hybridising of complementary oligonucleotides labeled by FAM to the probe. Contact angle measurement and atomic force microscopy (AFM)) were used to monitor the process.

The Compatibility of silicon materials in regard to the immobilization procedures on silicon dioxide was studied. As a result of the corrosive chemical used in the process, common metals used in micro-fabrication process like aluminum were etched away. Silicon nitride, polysilicon, gold and platinum withstood the process of immobilization and no DNA was hybridized on these materials. Fluorescence intensity analysis showed that using a combination of silicon dioxide (where immobilization takes place) and silicon nitride or polysilicon (where no immobilization takes place), immobilization was confined to the desired area and thus reduce cross talk between different array elements. The fluorescence image from the scanner indicated silicon nitride with line width down to 1 μm can be used as an effective isolation material.

The compatibility of DNA microarray and electro-optic system in regard to the integration was also studied. Fluorescence detection is now the most commonly used detection method. When using this detection method, it is necessary to use on-chip color filter. Red dyed polyimide was the suitable on-chip color filter material. As color filter is used, the covalent immobilization method cannot be used. Avidin-biotin complexation was selected as the immobilization method instead. Thus the fabrication process of DNA microarray on agarose film, which can facilitate the integration, was developed.