Improving zero-mode waveguide structure for enhancing signal-to-noise ratio of real-time single-molecule fluorescence imaging: a computational study

• Published in: Physical review. E, Statistical, nonlinear, and soft matter physics Vol. 88; no. 1; p. 012727
• Main Authors: Tanii, Takashi, Akahori, Rena, Higano, Shun, Okubo, Kotaro, Yamamoto, Hideaki, Ueno, Taro, Funatsu, Takashi
• Format: Journal Article
• Language: English
• Published: United States 01.07.2013
• Subjects: Computer Simulation; Fluorescence; Models, Theoretical; Molecular Imaging - methods; Signal-To-Noise Ratio
• ISSN: 1550-2376
• DOI: 10.1103/PhysRevE.88.012727

We investigated the signal-to-noise ratio (S/N) of real-time single-molecule fluorescence imaging (SMFI) using zero-mode waveguides (ZMWs). The excitation light and the fluorescence propagating from a molecule in the ZMW were analyzed by computational optics simulation. The dependence of the S/N on the ZMW structure was investigated with the diameter and etching depth as the simulation parameters. We found that the SMFI using a conventional ZMW was near the critical level for detecting binding and dissociation events. We show that etching the glass surface of the ZMW by 60 nm enhances the S/N six times the conventional nonetched ZMWs. The enhanced S/N improves the temporal resolution of the SMFI at physiological concentrations.