We have discovered that distinct tunneling signals can be generated for all four nucleosides (and 5-methyldeoxycytidine) using one pair of tunneling electrodes functionalized with a simple reagent containing a hydrogen-bond donor and a hydrogen bond acceptor. The goals of this proposal are to extend the measurements to nucleotides in aqueous electrolyte, and then to small oligomers. We will quantify the fraction of single-molecule reads and determine the factors that control this fraction with the goal of eliminating signals that come from more than one nucleotide in the gap at a time. We will explore the factors that control the width of the distribution of current signals for all four bases (and 5-methyl C) with the goal of improving the discrimination of a single read. We will measure the fraction of successful reads and characterize the time required for the complex (that gives rise to the signal) to form in the tunnel gap. From these measurements, we will identify improvements needed to increase the readout efficiency and also develop criteria for design of a nanopore sequencing system equipped with tunneling electrodes. The reagents developed during the course of this research will be made available to other research groups developing nanopore sequencers that use electron tunneling as the readout.

Public Health Relevance

At least seven NIH-supported groups are exploring sequencing methods that propose to use electron tunneling as the readout for a nanopore sequencer, an approach that might greatly reduce the cost of sequencing. We have shown that all four nucleosides and 5-methyl cytidine can be read by functionalized electrodes and we will develop reagents suitable for DNA sequencing in aqueous electrolyte and make these widely available.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21HG005851-03
Application #
8289612
Study Section
Special Emphasis Panel (ZHG1-HGR-N (M1))
Program Officer
Schloss, Jeffery
Project Start
2010-09-01
Project End
2014-06-30
Budget Start
2012-07-01
Budget End
2014-06-30
Support Year
3
Fiscal Year
2012
Total Cost
$287,141
Indirect Cost
$87,141
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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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