Palladium Zero-Mode Waveguides for Optical Single Molecule Detection with Nanopores

TL;DR

This paper introduces palladium-based zero-mode waveguides (ZMWs) for optical detection of single molecules, enabling high-resolution, background-suppressed fluorescence detection of DNA, proteins, and fluorophores.

Contribution

It presents a novel use of palladium as a metal film in ZMWs, enhancing single-molecule detection capabilities over traditional materials.

Findings

Successful detection of multiple fluorophore colors

High signal-to-noise ratio in single-molecule detection

Detection of DNA and proteins at high bandwidth

Abstract

Holes in metal films block any transmitting light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called Zero Mode Waveguides (ZMWs). Molecules on the other hand, can still passage through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW and thereby traverse from the dark region to the illuminated side, upon which they emit fluorescent light. This is beneficial both for background suppression and to prevent premature bleaching. We use palladium as a novel metal-film material for ZMWs, which is advantageous compared to conventionally used metals. We demonstrate that it is possible to simultaneously detect translocations of individual free fluorophores of different colors. Labeled DNA and protein biomolecules can be detected as well at the single-molecule level with a high signal-to-noise ratio and at high bandwidth, which opens the door to a variety of single-molecule biophysics studies.