DNA Characterization with Ion Beam-Sculpted Silicon Nitride Nanopores

  • Ryan C. Rollings
  • David S. McNabb
  • Jiali LiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 870)


Solid-state nanopores are emerging as robust single molecule electronic measurement devices and as platforms for confining biomolecules for further analysis. The first silicon nitride nanopore to detect individual DNA molecules was fabricated using ion beam sculpting (IBS), a method that uses broad, low-energy ion beams to create nanopores with dimensions ranging from 2 to 20 nm. In this chapter, we discuss the fabrication, characterization, and use of IBS-sculpted nanopores as well as efficient uses of pClamp and MATLAB software suites for data acquisition and analysis. The fabrication section covers the repeatability and the pore size limits. The characterization discussion focuses on the geometric properties as measured by low- and high-resolution transmission electron microscopy (TEM), electron energy loss spectroscopy, and energy-filtered TEM. The section on translocation experiments focuses on how to use tools commonly available to the nanopore experimenter to determine whether a pore will be useful for experimentation or if it should be abandoned. A memory-efficient method of taking data using Clampex’s event-driven mode and dual-channel recording is presented, followed by an easy-to-implement multithreshold event detection and classification method using MATLAB software.

Key words

Ion beam sculpting Silicon nitride nanopore Ionic current blockage DNA size DNA conformation 



This work was supported by the National Human Genome Research Institute (NIH) R21HG004776, and partially supported by NSF/MRSEC 080054, ABI1114, and 1P30RR031154-01 from the National Center for Research Resources (NCRR) of NIH.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of PhysicsUniversity of ArkansasFayettevilleUSA
  2. 2.Department of Biological SciencesUniversity of ArkansasFayettevilleUSA

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