Surface Characterization of DNA Microarray on Silicon Dioxide and Compatible Silicon Materials in the Immobilization Pro
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Surface Characterization of DNA Microarray on Silicon Dioxide and Compatible Silicon Materials in the Immobilization Process Wen Xu1, Jiong Li4, Mei Xue1, Maria Carles3, Dieter Wilhelm Trau3, Ralf Lenigk3, Nikolaus J.Sucher2, Nancy Y. Ip3, and Mansun Chan1 1 Department of Electrical and Electronic Engineering, 2 Department of Biology, 3Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 4 National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, China ABSTRACT 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 µm. INTRODUCTION In recent years, DNA microarray technology has become a focus of attention in the field of life science. DNA microarray, as a high-throughput technology, is a powerful tool to analyze a vast amount of genetic information in gene activity or expression. It is composed of a solid surface with arrays of DNA fragments at discrete locations ready for hybridization with the targeted DNA sample. Various solid supports such as glass-slides, nitrocellulose-coated microscope slides, and silicon-based DNA microarrays have been investigated in different applications. Glass microarrays with optical fluorescence detection, pioneered by Patrick Brown’s laboratory at Stanford [1], are now the most popular method because an external CCD camera can be used as the detection system. To facilitate the fabrication of the so-called “lab-on-a-chip” devices, there has been a surge in the study of silicon-based DNA arrays [2-4]. Compared to the commonly used microscope slides, silicon materials have lower surface roughness that allows more uniform DNA deposition with higher density and smaller spot size. In addition, it al
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