Linkers were assembled on a glass surface based on the hydrolysis and condensation of 3-glycidoxy￣propyltrimethoxysilane (GPS). After the assembly of GPS, four approaches were tried to open the ending epoxide group of GPS or to further elongate the linkers. The effect of these approaches on DNA in situ synthesis and hybridization was investigated. For the spacing of the synthesis initiation sites, the wettability of the support and the length of the linking group that attaches the initiation site to the surface have direct influences on the yield of coupling reactions and the subsequent hybridization events. X-ray photoelectron spectroscopy (XPS) and mean contact angles of deionized water of the above slides were measured to assess the linker's characteristics in each procedure. It was proved that the glass slides were successfully modified and became excellent supports for the oligonucleotides synthesis. In addition, it proved best for the in situ oligonucleotides synthesis that a glass slide was in turn treated with ethylenediamine, glutaradehyde, ethanolamine and sodium borohydride solution at ambient temperature after silanized with GPS.
To quantitatively detect hypermethylation and to analyze methylation pattern, a methylation-specific oligonucleotide microarray for quantitative analysis was developed. The method used bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. The amplified product, therefore, may contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status. A test sample was hybridized to a set of oligonucleotide arrays that discriminate methylated and unmethylated cytosine at specific nucleotide positions,and quantitative differences in hybridization were determined by fluorescence analysis. Four clinical samples of gastric cancer were quantitatively detected and methylation pattern of five methylated clones were analyzed with the methylation-specific oligonucleotide microarray. The results of microarray hybridization were in agreement with bisulfite genomic DNA sequencing. It showed that methylation-specific oligonucleotide microarray for quantitative analysis is a promising technique for mapping methylation changes in multiple CpG island loci and for generating epigenetic profiles in cancer.
