New in-Situ Method for On-chip DNA Oligomer Synthesis

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The use of DNA arrays for numerous applications has expanded rapidly in recent years. These arrays are made primarily using photolabile ligands as blocking groups in an array format or by spotting DNA from organisms or a DNA synthesizer. We propose an on-chip, high-density DNA oligomer growth method that will use the standard phosphoramidite chemistry on a proprietary chip design. The key to the technology will be a chip that contains an array of <500um grids regions micromachined directly into a silicon wafer using Si microfabrication techniques. The grid regions are micromeshes fabricated by a wet chemical etching method giving grid mesh element sizes selectable from 10-100um. The growing oligonucleotides are attached to the SiO2 surface of the grid. This array of grids is placed over a second wafer that has <500um holes in registry with, and underneath, the micromesh areas. The ability of a DNA synthesizer to force equilibrium to completion by flowing reagents through the stationary support, and to thoroughly wash each sample, is duplicated on this chip by placing the nucleotide synthesis chemicals on the mesh and then drawing them through the mesh/hole regions of each chip, thereby simulating the flow through geometry of a DNA synthesizer. PROPOSED COMMERCIAL APPLICATION: If feasibility is demonstrated, the economics of silicon microfabrication and mass production will allow the fabrication of custom DNA microarrays by this method to compete very effectively with the current technology. Since only a commercial liquid handling robot and the proposed chips would be necessary to automate this system, the cost reduction could greatly accelerate the use of microarray technology in biology and genetic investigations.