ArticleNature methods2024
The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Versatile and Scalable Reflective Micromirrors for Single-Objective Light Sheet Microscopy.Nano letters · 2026Article
- Brightness demixing for simultaneous multi-target imaging in 3D single-molecule localization microscopy.Nature methods · 2026Article
- Versatile and Scalable Reflective Micromirrors for Single-Objective Light Sheet Microscopy.bioRxiv : the preprint server for biology · 2026Article
- Identification of optimal fluorophores for use in theMolecular biology of the cell · 2026Article
- Fluorogenic speed-optimized DNA-PAINT probes enable super-resolution imaging of whole cells.bioRxiv : the preprint server for biology · 2026Article
- Molecular mapping in DNA-PAINT via modified Gaussian Mixture Modeling.Nature communications · 2026Article
- A Simple, Ultrastable, and Cost-Effective Oxygen-Scavenging System for Long-Term DNA-PAINT Imaging.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Optimizing Effective Labeling Efficiency in MINFLUX 3D DNA-PAINT Microscopy by Maximizing Marker Detection Probability.ACS photonics · 2026Article
- Simulating Multicolor Super-Resolution Imaging Using an RGB Camera.Computational and structural biotechnology journal · 2026Article
- Molecular-scale isotropic 3D super-resolution microscopy via interference localization.Nature methods · 2026Article
- Advanced Imaging for Live-Cell Spatiotemporal Monitoring: Technologies and Applications.Research (Washington, D.C.) · 2026Review
- Volumetric localization microscopy with deep learning.Nature communications · 2025Article
- Real-time, high-throughput super-resolution microscopy via panoramic integration.Nature communications · 2025Article
- On-Target Photoassembly of Pyronin Dyes for Super-Resolution Microscopy.Angewandte Chemie (International ed. in English) · 2025Article
- Localization of single molecules with structured illumination and structured detection.Light, science & applications · 2025Article
- Advancing Single-Molecule Biophysics: Next-Generation Organic Fluorophores with Tailored Labeling Strategies.Chemical & biomedical imaging · 2025Review
- Super-resolution imaging in whole cells and tissues via DNA-PAINT on a spinning disk confocal with optical photon reassignment.Nature communications · 2025Article
- Fluorescent labeling strategies for molecular bioimaging.Biophysical reports · 2025Review
- Single-molecule orientation-localization microscopy: Applications and approaches.Quarterly reviews of biophysics · 2024Review
- Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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