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 #
5R01HG003703-10
Application #
8706936
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
2014-08-01
Budget End
2015-07-31
Support Year
10
Fiscal Year
2014
Total Cost
$1,175,999
Indirect Cost
$461,829
Name
Harvard University
Department
Type
Schools of Engineering
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
Levine, Edlyn V; Burns, Michael M; Golovchenko, Jene A (2016) Nanoscale dynamics of Joule heating and bubble nucleation in a solid-state nanopore. Phys Rev E 93:013124
Rollings, Ryan C; Kuan, Aaron T; Golovchenko, Jene A (2016) Ion selectivity of graphene nanopores. Nat Commun 7:11408
Lu, Bo; Fleming, Stephen; Szalay, Tamas et al. (2015) Thermal Motion of DNA in an MspA Pore. Biophys J 109:1439-45
Szalay, Tamas; Golovchenko, Jene A (2015) De novo sequencing and variant calling with nanopores using PoreSeq. Nat Biotechnol 33:1087-91
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
Hoogerheide, David P; Albertorio, Fernando; Golovchenko, Jene A (2013) Escape of DNA from a weakly biased thin nanopore: experimental evidence for a universal diffusive behavior. Phys Rev Lett 111:248301
Lu, Bo; Hoogerheide, David P; Zhao, Qing et al. (2013) Pressure-controlled motion of single polymers through solid-state nanopores. Nano Lett 13:3048-52
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

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