To improve DNA sequencing by at least one order of magnitude and to develop practical methods of RNA se- quencing, this Phase I project focuses on using thin solid-state nanopore sensors on low-noise solid-state all- glass chips, operating at 10 MHz bandwidth for DNA sequencing and direct RNA sequencing. The basic concept involves using an applied voltage to drive single-stranded DNA molecules through a narrow nanopore, which separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the nanopore they modify the flow of ions, and structural information can be extracted by analysis of the duration and magnitude of the resulting current reduc- tions. Nanopore in 2D membranes improve the signal-to-noise ratio for molecular detection and analysis because the resistance to the ionic flow through a nanopore increases linearly with the nanopore thickness, so both the magnitudes of the ionic current and the blocked current with a translocating molecule increase with decreasing hanopore height. Specifically, we seek to make solid-state ionic-current based nanopore sequencing possible by combining three important components: two-dimensional solid-state nanopores fabricated with precise di- mensions that achieve signal-to-noise contrast that exceeds biological pores, optimized supporting all-glass chips, and optimally fast measurement of translocation through these pores with recently developed low-noise, high-bandwidth electronics. Our approach eliminates the need for any enzymes and enables DNA molecules to translocate freely through nanopores. Illustration 1: The Economist coverage from 2011 illustrating yet to be real- ized promises of nanopore-based DNA sequencing with two-dimensional na- nopores developed originally at the University of Pennsylvania and forming the scientific bases behind our SBIR R43 project on two-dimensional solid- state nanopores.

Public Health Relevance

This project aims to develop novel technologies that will enable at least one order of magnitude improvement in DNA se- quencing, and practical methods for direct RNA sequencing by developing a nanometer-sized electronic sensor con- structed from a thin layer of a novel two-dimensional material. It will enable major improvements in the understanding, diagnosis, treatment and prevention of disease, by allowing us to determine the underlying genetic causes and symptoms, detect these rapidly and accurately in patients, and treat them appropriately. This project will help improve the quality and efficiency of DNA sequencing and enable direct RNA sequencing (e.g., longer read lengths, faster turn-around time, greater accuracy, and higher-throughput etc.) at reasonable costs with the anticipation that significant advances in any of these and related areas would make significant contributions to the mission of NHGRI and the field of genomics, including to many of NHGRI?s other technology development goals.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
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Special Emphasis Panel (ZRG1)
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Smith, Michael
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Goeppert, LLC
United States
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