1. The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes.
- Author
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Steen PR, Unterauer EM, Masullo LA, Kwon J, Perovic A, Jevdokimenko K, Opazo F, Fornasiero EF, and Jungmann R
- Subjects
- Animals, Humans, Nucleic Acid Hybridization, Nuclear Pore Complex Proteins chemistry, Nuclear Pore Complex Proteins metabolism, Neurons metabolism, Nanostructures chemistry, Single Molecule Imaging methods, Fluorescent Dyes chemistry, DNA chemistry, Microscopy, Fluorescence methods
- Abstract
DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a super-resolution fluorescence microscopy technique that achieves single-molecule 'blinking' by transient DNA hybridization. Despite blinking kinetics being largely independent of fluorescent dye choice, the dye employed substantially affects measurement quality. Thus far, there has been no systematic overview of dye performance for DNA-PAINT. Here we defined four key parameters characterizing performance: brightness, signal-to-background ratio, DNA-PAINT docking site damage and off-target signal. We then analyzed 18 fluorescent dyes in three spectral regions and examined them both in DNA origami nanostructures, establishing a reference standard, and in a cellular environment, targeting the nuclear pore complex protein Nup96. Finally, having identified several well-performing dyes for each excitation wavelength, we conducted simultaneous three-color DNA-PAINT combined with Exchange-PAINT to image six protein targets in neurons at ~16 nm resolution in less than 2 h. We thus provide guidelines for DNA-PAINT dye selection and evaluation and an overview of performances of commonly used dyes., (© 2024. The Author(s).)
- Published
- 2024
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