Zero-mode waveguide detection of DNA translocation through FIB-organised arrays of engineered nanopores

Zero-mode waveguides (ZMWs) are optical nanostructures fabricated in a thin metallic film capable of confining the excitation volume to the zeptoliter range. In this work we describe the batch fabrication of a nanopore-based device, based upon high-resolution arrays of nanopores (of various sizes), which is used to directly measure the passage of DNA. In our method, nanopores are fabricated in ultrathin dielectric films with a deposited gold layer. The gold layer on the device induces a zero mode waveguide illumination at the cis end of the nanopores. The method presented allows for optical detection, in real time, at the level of a single molecule and a single pore. The detection of fluorescently labelled single molecules passing through the pores, measured using an electron multiplying charge coupled device camera, is described. Molecules inside the nanopore were invisible until they reached the volume illuminated by the evanescent field. This fabrication methodology appears to be very promising for the development and batch fabrication of a new generation of nanopore-based sensor devices. (C) 2017 Elsevier B.V. All rights reserved.