Nanotechnology for the Structural Interrogation of DNA

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DESCRIPTION (provided by applicant): We propose a research program to achieve the goal of sequencing of single molecules of polynucleotides using conductance probes within a molecular scale aperture and to demonstrate the technical feasibility of this promising approach. There have recently been intriguing suggestions about how one might rapidly determine the sequence of a single DNA molecule contained in a buffer solution by transporting it through a voltage-biased nanoscale aperture while monitoring the ionic current through that aperture [Kasianowicz, 1996; Deamer, 2000]. Some suggestive proof-of-principle experiments have been demonstrated using lipid bilayer supported protein pores and observing variations in pore axial conductance. We contend that for this strategy to become a realizable technology, robust nanometer scale apertures must be fabricated using a combination of top-down and bottom-up approaches. In addition, interesting variants of this approach such as incorporating laterally opposed nanoelectrodes in a nanochannel for probing monomeric variations in the electrical properties of polynucleotides can only be achieved through nanofabrication. Our specific aims are listed below. Develop fabrication capabilities that combine top-down and bottom-up strategies for forming fluidic channels and electrical probes with length scales approaching 1 nm. Investigate the dependence of the length scale probed on nanopore axial and lateral dimensions. Compare the signal-to-noise ratio for axial and lateral conductance probes of single DNA strands. Determine variation of measurement signal-to-noise ratios as a function of chemical and physical parameters such as aperture size, buffer conditions, interfacial hydrophobicity, and electrode size. Determine impact of polymer dynamics on fundamental limits of DNA structural determinations. Demonstrate proof-of-principle single molecule sequencing of polynucleotides based on achievement of these specific aims.