We will explore a new approach to DNA """"""""sequencing by recognition"""""""" in nanopores. It is based on a recent report of chemical recognition of the DNA bases via enhanced electron-tunneling when Watson-Crick hydrogen bonded base pairs form between a base-functionalized probe and a base on the DNA to be read. This mechanism is confirmed by preliminary experiments reported in this application. When combined with a nanopore-DNA translocation system that presents each base sequentially to the electronic sensor, it appears that at least 108 bases per day could be read with continuous sequence runs of at least 80,000 bases. The single molecule base-calling accuracy might approach 99%, in which case an array of 10,000 nanopores would yield the required 99.99% accuracy. In order to establish the plausibility of this approach, two key issues need to be resolved. (a) Can flexible 'molecular wires'bridge the gap between sensing electrodes and the target attachment sites on the DNA to be sequenced? These wires must reach from one electrode to a phosphate, and from another electrode to a base, be flexible enough to form bonds at the same time as being highly conductive. (b) Is the conductance of the whole assembly (metal-linker-phosphate-sugar-base-base-linkermetal) large enough to produce an acceptable single-molecule base calling accuracy? We propose to design and synthesize a number of 'molecular wires'as candidate linkers and measure their single-molecule conductance, comparing our data to the results of first-principles simulations. Once suitable linkers are found, we propose to measure the conductance of the entire system, and the statistical distribution of these conductances. We will also develop a multi-scale simulation of the entire system, to help us optimize the design of a real instrument. We will collaborate with the Timp Laboratory (University of Illinois, Urbana- Champaign) in order to tie our designs to the materials constraints of the solid state nanopores being developed there.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Exploratory/Developmental Grants (R21)
Project #
3R21HG004378-03S1
Application #
7913961
Study Section
Special Emphasis Panel (ZHG1-HGR-N (M1))
Program Officer
Schloss, Jeffery
Project Start
2009-09-29
Project End
2011-08-31
Budget Start
2009-09-29
Budget End
2011-08-31
Support Year
3
Fiscal Year
2009
Total Cost
$551,676
Indirect Cost
Name
Arizona State University-Tempe Campus
Department
Physiology
Type
Organized Research Units
DUNS #
943360412
City
Tempe
State
AZ
Country
United States
Zip Code
85287
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Tuchband, Michael; He, Jin; Huang, Shuo et al. (2012) Insulated gold scanning tunneling microscopy probes for recognition tunneling in an aqueous environment. Rev Sci Instrum 83:015102
Chang, Shuai; Sen, Suman; Zhang, Peiming et al. (2012) Palladium electrodes for molecular tunnel junctions. Nanotechnology 23:425202
Chang, Shuai; Huang, Shuo; Liu, Hao et al. (2012) Chemical recognition and binding kinetics in a functionalized tunnel junction. Nanotechnology 23:235101
Lindsay, Stuart (2012) Biochemistry and semiconductor electronics--the next big hit for silicon? J Phys Condens Matter 24:164201
Liang, Feng; Lindsay, Stuart; Zhang, Peiming (2012) 1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling. Org Biomol Chem 10:8654-9
Fuhrmann, Alexander; Getfert, Sebastian; Fu, Qiang et al. (2012) Long lifetime of hydrogen-bonded DNA basepairs by force spectroscopy. Biophys J 102:2381-90
Chang, Shuai; He, Jin; Zhang, Peiming et al. (2011) Gap distance and interactions in a molecular tunnel junction. J Am Chem Soc 133:14267-9
Lindsay, Stuart; He, Jin; Sankey, Otto et al. (2010) Recognition tunneling. Nanotechnology 21:262001
Huang, Shuo; Chang, Shuai; He, Jin et al. (2010) Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers. J Phys Chem C Nanomater Interfaces 114:20443-20448

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