DNA Sequencing by Nanopore-Induced Photon Emission

  • Alon Singer
  • Ben McNally
  • Ruby Dela Torre
  • Amit MellerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 870)


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.

Key words

Solid-state nanopore Nanopore array Circular DNA Conversion DNA sequencing 



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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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Alon Singer
    • 1
  • Ben McNally
    • 1
  • Ruby Dela Torre
    • 1
  • Amit Meller
    • 1
    Email author
  1. 1.Department of Biomedical EngineeringBoston UniversityBostonUSA

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