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DNA Sequencing by Nanopore-Induced Photon Emission

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Nanopore-Based Technology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 870))

Abstract

Nanopore-based DNA analysis is an extremely attractive area of research due to the simplicity of the method, and the ability to not only probe individual molecules, but also to detect very small amounts of genomic material. Here, we describe the materials and methods of a novel, nanopore-based, single-molecule DNA sequencing system that utilizes optical detection. We convert target DNA according to a binary code, which is recognized by molecular beacons with two types of fluorophores. Solid-state nanopores are then used to sequentially strip off the beacons, leading to a series of photon bursts that can be detected with a custom-made microscope. We do not use any enzymes in the readout stage; thus, our system is not limited by the highly variable processivity, lifetime, and inaccuracy of individual enzymes that can hinder throughput and reliability. Furthermore, because our system uses purely optical readout, we can take advantage of high-end, wide-field imaging devices to record from multiple nanopores simultaneously. This allows an extremely straightforward parallelization of our system to nanopore arrays.

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Acknowledgments

We acknowledge financial support from NIH awards HG-004128 and HG-005871, and support from Harvard University’s Center for Nanoscale Systems.

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Authors and Affiliations

  1. Department of Biomedical Engineering, Boston University, Boston, MA, USA

    Alon Singer, Ben McNally, Ruby Dela Torre & Amit Meller

Authors
  1. Alon Singer
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  2. Ben McNally
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  3. Ruby Dela Torre
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  4. Amit Meller
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Corresponding author

Correspondence to Amit Meller .

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Editors and Affiliations

  1. , Department of Physics, Clarkson University, Clarkson Ave. 8, Potsdam, 13699, New York, USA

    Maria E. Gracheva

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Singer, A., McNally, B., Torre, R.D., Meller, A. (2012). DNA Sequencing by Nanopore-Induced Photon Emission. In: Gracheva, M. (eds) Nanopore-Based Technology. Methods in Molecular Biology, vol 870. Humana Press. https://doi.org/10.1007/978-1-61779-773-6_6

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  • DOI: https://doi.org/10.1007/978-1-61779-773-6_6

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-772-9

  • Online ISBN: 978-1-61779-773-6

  • eBook Packages: Springer Protocols

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