Super-resolution microscopy with DNA-PAINT
Open accessAbstract
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy. Using the programmability and specificity of DNA molecules as imaging and labeling probes allows researchers to decouple blinking from dye photophysics, alleviating limitations of current super-resolution techniques, making them compatible with virtually any single-molecule-compatible dye. Recent developments in DNA-PAINT have enabled spectrally unlimited multiplexing, precise molecule counting and ultra-high, molecular-scale (sub-5-nm) spatial resolution, reaching ∼1-nm localization precision. DNA-PAINT can be applied to a multitude of in vitro and cellular applications by linking docking strands to antibodies. Here, we present a protocol for the key aspects of the DNA-PAINT framework for both novice and expert users. This protocol describes the creation of DNA origami test samples, in situ sample preparation, multiplexed data acquisition, data simulation, super-resolution image reconstruction and post-processing such as drift correction, molecule counting (qPAINT) and particle averaging. Moreover, we provide an integrated software package, named Picasso, for the computational steps involved. The protocol is designed to be modular, so that individual components can be chosen and implemented per requirements of a specific application. The procedure can be completed in 1-2 d.
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Docking sites on DNA origami are located using DNA-PAINT, a super-resolution fluorescence imaging method that relies on transient binding of short DNA strands to prepositioned sites on an origami structure.
“Docking sites are located using DNA points accumulation for imaging in nanoscale topography (DNA-PAINT), a form of super resolution fluorescence imaging that relies on transient binding of short DNA strands to prepositioned sites on an origami structure.122”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [122]
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- Authors
- Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F., & Jungmann, R.
- Affiliations
- Center for NanoScience (DE)
- Corresponding author
- Jungmann, Ralf
- Venue
- Nature Protocols
- Published
- 2017-05-18
- Volume
- 12
- Issue
- 6
- Pages
- 1198-1228
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2616524931
- Cited by
- 1,047
- References
- 85
- Citations by year
- 2026: 125 · 2025: 158 · 2024: 136 · 2023: 125 · 2022: 129 · 2021: 120 · 2020: 82 · 2019: 71 · 2018: 87 · 2017: 12
- FWCI
- 40.41
- Type
- journal article
- Language
- en
- Open access
- green
- infoscience.epfl.ch
- Licence
- cc-by-nc-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Keywords
- DNA-PAINT, super-resolution microscopy, DNA origami, blinking, multiplexed imaging, image reconstruction, drift correction, antibody labeling
- MeSH terms
- Cytological Techniques, DNA, Image Processing, Computer-Assisted, Microscopy, Fluorescence, Staining and Labeling, Macromolecular Substances
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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