There is strong demand for third-generation DNA sequencing systems to be single-molecule, massively- parallel, and real-time. For single-molecule optical techniques, however, the signal from a single fluorophore is typically <2500 photons/sec (equivalent to electrical current levels on the order of 50 fA). This leads to complex optics to try to collect every photon emitted and makes scaling of the platforms difficult. Additionally, synthesis reactions must be intentionally slowed to 1 Hz (or slower) to allow sufficient imaging times for these weak, noisy optical signals. The limitations of single-molecule optical techniques highlight key advantages of electrochemical detection approaches, which have significantly higher signal levels (typically three orders of magnitude higher), allowing for the possibility for high-bandwidth detection with the appropriate co-design of transducer, detector, and amplifier. Significant effort has been directed toward the development of nanopore technology as one potential bioelectronic transduction mechanism. Nanopores, however, have proved to be extremely limited by the relatively short time biomolecules spend in the charge-sensitive region of the pore. Restricted by the use of off- the-shelf electronics, the noise-limite bandwidth of nanopore measurements is typically less than 100 kHz, limiting the available sensing and actuation strategies and defying multiplexed integration which would be required for any sequencing application. In this four-year effort, we focus on improving significantly the noise-limited bandwidth of the detection electronics for nanopores allowing their full potential to be realized through close integration of the electronics and the pore while simultaneously supporting high levels of parallelism with multiple nanopores on the same detection substrate. We consider techniques for integrating both solid-state (Specific Aim 1) and biological pores (Specific Aim 3) onto these measurement substrates in a massively parallel manner (Specific Aim 2). The techniques we propose for leveraging commodity CMOS technology and co-integrating detection electronics are completely general and have significance to all other single-molecule bioelectronic transduction approaches. These high-bandwidth integrated electronics will also enable "closed-loop" sensing and actuation (Specific Aim 4), allowing dynamic manipulation of capture and translocation dynamics at microsecond (or better) timescales.

Public Health Relevance

The integration of CMOS electronics with nanopores will address key obstacles that must be overcome to achieve nanopore-based low-cost high-speed sequencing of chromosomal length DNA molecules. Fast and low cost full genome DNA sequencing will allow, for example, major improvements in the understanding, diagnosis, treatment and prevention of disease, and significant advances in evolutionary research and the understanding of cellular operation.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Special Emphasis Panel (ZHG1-HGR-N (M1))
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Schloss, Jeffery
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Columbia University (N.Y.)
Engineering (All Types)
Schools of Engineering
New York
United States
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Rosenstein, Jacob K; Lemay, Serge G; Shepard, Kenneth L (2015) Single-molecule bioelectronics. Wiley Interdiscip Rev Nanomed Nanobiotechnol 7:475-93
Bellin, Daniel L; Sakhtah, Hassan; Rosenstein, Jacob K et al. (2014) Integrated circuit-based electrochemical sensor for spatially resolved detection of redox-active metabolites in biofilms. Nat Commun 5:3256
Rosenstein, Jacob K; Ramakrishnan, Siddharth; Roseman, Jared et al. (2013) Single ion channel recordings with CMOS-anchored lipid membranes. Nano Lett 13:2682-6
Venta, Kimberly; Shemer, Gabriel; Puster, Matthew et al. (2013) Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. ACS Nano 7:4629-36