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.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG002647-02
Application #
6953014
Study Section
Special Emphasis Panel (ZRG1-GNM (90))
Program Officer
Schloss, Jeffery
Project Start
2004-09-30
Project End
2006-09-25
Budget Start
2005-09-01
Budget End
2006-09-25
Support Year
2
Fiscal Year
2005
Total Cost
$958,049
Indirect Cost
Name
University of North Carolina Chapel Hill
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
Pedersen, Jonas Nyvold; Boynton, Paul; Ventra, Massimiliano Di et al. (2017) Classification of DNA nucleotides with transverse tunneling currents. Nanotechnology 28:015502
Menard, Laurent D; Ramsey, J Michael (2013) Electrokinetically-driven transport of DNA through focused ion beam milled nanofluidic channels. Anal Chem 85:1146-53
Iancu, Violeta; Zhang, X-G; Kim, Tae-Hwan et al. (2013) Polaronic transport and current blockades in epitaxial silicide nanowires and nanowire arrays. Nano Lett 13:3684-9
Krems, Matt; Di Ventra, Massimiliano (2013) Ionic Coulomb blockade in nanopores. J Phys Condens Matter 25:065101
Wilson, James; Di Ventra, M (2013) Single-base DNA discrimination via transverse ionic transport. Nanotechnology 24:415101
Iancu, V; Kent, P R C; Hus, S et al. (2013) Structure and growth of quasi-one-dimensional YSi2 nanophases on Si(100). J Phys Condens Matter 25:014011
Menard, Laurent D; Mair, Chad E; Woodson, Michael E et al. (2012) A device for performing lateral conductance measurements on individual double-stranded DNA molecules. ACS Nano 6:9087-94
Menard, Laurent D; Ramsey, J Michael (2011) Fabrication of sub-5 nm nanochannels in insulating substrates using focused ion beam milling. Nano Lett 11:512-7
Cui, Shengting (2011) Dynamics of ion migration in nanopores and the effect of DNA-ion interaction. J Phys Chem B 115:10699-706
Zwolak, Michael; Wilson, James; Di Ventra, Massimiliano (2010) Dehydration and ionic conductance quantization in nanopores. J Phys Condens Matter 22:454126

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