Our research has shown that a single layer of graphene is an ideal membrane in which to fabricate high resolution nanopore detectors to sense the presence of single DNA molecules and their nucleobases. Our objective is to develop the tools and procedures needed to realize a scalable nanopore sequencing device which will significantly reduce future de novo sequencing cost by directly identifying the nucleobases on single stranded genomic DNA molecules that are driven sequentially through an array of precisely dimensioned graphene nanopores. The final system is intended to provide a relatively high quality sequence from >6.5-fold coverage of a genome using DNA from fewer than 1 million cells, with no amplification or labeling.
The specific aims are to: a) implement a graphene edge-sputtering process to facilitate high precision fabrication of nanopore arrays;b) optimize discrimination between the four nucleotides of DNA using ionic current blockades or in-plane conductivity change when ssDNA polymers are driven through graphene nanopores;and c) support lipid bilayers across graphene apertures to enhance the feasibility of parallel recordings from arrays of protein pores. Successful completion of these aims will provide the key building blocks of a nanopore sequencing device that can accurately sequence an entire human genome at a cost of less than $1,000. The ability to inexpensively and accurately sequence complete genomes has the potential of remarkably improving many facets of human life and society, including the understanding, diagnosis, treatment and prevention of disease.

Public Health Relevance

We are developing the critical methods and core elements of an instrument that will produce a high-quality sequence of one mammalian genome in ~20 hours at a cost of less than approximately $1,000. Genomic sequencing at these reduced costs has the potential of remarkably improving many facets of human life and society, including the understanding, diagnosis, treatment and prevention of disease;advances in agriculture, environmental science and remediation;and our understanding of evolution and ecological systems.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
2R01HG003703-08
Application #
8359840
Study Section
Special Emphasis Panel (ZHG1-HGR-N (M1))
Program Officer
Schloss, Jeffery
Project Start
2005-08-01
Project End
2015-07-31
Budget Start
2012-09-14
Budget End
2013-07-31
Support Year
8
Fiscal Year
2012
Total Cost
$1,200,000
Indirect Cost
$471,255
Name
Harvard University
Department
None
Type
Schools of Engineering
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
Hoogerheide, David P; Lu, Bo; Golovchenko, Jene A (2014) Pressure-voltage trap for DNA near a solid-state nanopore. ACS Nano 8:7384-91
Nagashima, Gaku; Levine, Edlyn V; Hoogerheide, David P et al. (2014) Superheating and homogeneous single bubble nucleation in a solid-state nanopore. Phys Rev Lett 113:024506
Lu, Bo; Hoogerheide, David P; Zhao, Qing et al. (2013) Pressure-Controlled Motion of Single Polymers through Solid-State Nanopores. Nano Lett :
Garaj, Slaven; Liu, Song; Golovchenko, Jene A et al. (2013) Molecule-hugging graphene nanopores. Proc Natl Acad Sci U S A 110:12192-6
Han, Anpan; Kuan, Aaron; Golovchenko, Jene et al. (2012) Nanopatterning on nonplanar and fragile substrates with ice resists. Nano Lett 12:1018-21
Bell, David C; Russo, Christopher J; Kolmykov, Dmitry V (2012) 40 keV atomic resolution TEM. Ultramicroscopy 114:31-7
Gardener, Jules A; Golovchenko, J A (2012) Ice-assisted electron beam lithography of graphene. Nanotechnology 23:185302
Russo, Christopher J; Golovchenko, J A (2012) Atom-by-atom nucleation and growth of graphene nanopores. Proc Natl Acad Sci U S A 109:5953-7
Lu, Bo; Albertorio, Fernando; Hoogerheide, David P et al. (2011) Origins and consequences of velocity fluctuations during DNA passage through a nanopore. Biophys J 101:70-9
Han, Anpan; Chervinsky, John; Branton, Daniel et al. (2011) An ice lithography instrument. Rev Sci Instrum 82:065110

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