DNA Sequencing and Translocation Studies using Electrically Addressable Nanopore Arrays

Overview and Objectives: Determination of the genetic code embedded in DNA molecules is fundamental to molecular biology and medicine. The most successful technique used for DNA sequencing has been the dideoxy termination mechanism developed by Sanger. Some of the main limitations of the traditional Sanger method are its relatively high cost (it heavily relies on multiple costly polymerase chain reactions), slow speed (the technique relies on gel separations), and only relatively short DNA strands can be effectively sequenced in each gel (600-800 bases). Alternative, faster and lower-cost methods for DNA sequencing are thus in high demand. There is a worldwide race towards a DNA sequencing technology that will cost no more than $1k per human genome. Such a personal genome technology promises to revolutionize medicine. Among the various proposed alternative DNA sequencing technologies, nanopore sequencing, especially with solid-state nanopore devices, is an exciting example. The objective of this NIRT program is to develop the necessary science and technology to bring nanopore DNA sequencing to reality. Our research program [1] brings together broad expertise in nanobioscience, both experimental and theoretical, encompassing solid-state physics to biochemistry, to attack a major problem of broad scientific interest and with potentially immense societal impact. The science goals of this project include: (1) to develop low-cost approaches for fabricating addressable nanopore arrays [2] using silicon or other low-cost solid-state materials; (2) to study and to elucidate the translocation processes of biomolecules in nanopores; (3) to exploit the phenomena of electricfield driven transport of DNA molecules through nanopores for DNA sequencing [3] and rapid characterization of biomolecules. This research program offers valuable educational experiences to students at Brown and Harvard in the emerging area of nanobioscience, empowering them with useful skills in nanofabrication, molecular biophysics, biochemistry, and statistical physics. These important skills will prepare our students well for the emerging economy of nanotechnology. Research Findings: In the grant period of 2004, we have engaged in a multi-front effort in attacking the nanopore sequencing problem. Since the future of nanopore DNA sequencing is largely resting on the availability of low-cost nanopore devices, we have spent a significant amount of effort in developing the necessary technology for device fabrication. This effort paid off handsomely. We now have developed a simple low-cost approach for fabricating nanopores in silicon chips, using electrochemical feedback etching. The same technique is also applicable for preparing devices with addressable nanopores.