This research has one goal, the creation of nanofabricated Si-based arrays to be used as sequencing devices. The research builds on the use of nanofabricated devices to separate and analyze high molecular weight DNA in arrays composed of 1 um posts separated from each other by 2 um and sealed into a two-dimensional geometry with a glass cover-slip. It is proposed to utilize electron beam lithography and surface treatments of various kinds to create sealed arrays with pore sizes on the order of 10-50 nanometers, thought to be the pore size of polyacrylamide gels. The goal is to produce a 1 cm2-two dimensional device in which a conventional 4-color sequencing reaction can be separated very rapidly with little heating and high resolution, while detecting the sequence by laser scanned microscopy. It is anticipated that the sealed arrays will be much faster than conventional sequencing gels, cheap, and easily adaptable to automation for high throughput. The detailed estimates are that the 1 cm2 version will cost less than $1 to manufacture if thousands are fabricated in a single production run. The sequencing run time will be of the order of 100 seconds, approximately 200 times faster than current commercially available machines. Each device will have multilane capability; and the way in which samples are loaded in each lane will lend itself readily to automation.
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